Starting phenix.real_space_refine on Wed Mar 4 10:57:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p1h_20235/03_2026/6p1h_20235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p1h_20235/03_2026/6p1h_20235.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 { model { file = "/net/cci-nas-00/data/ceres_data/6p1h_20235/03_2026/6p1h_20235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p1h_20235/03_2026/6p1h_20235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p1h_20235/03_2026/6p1h_20235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p1h_20235/03_2026/6p1h_20235.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 1.053 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 Fe 4 7.16 5 P 30 5.49 5 S 67 5.16 5 C 8171 2.51 5 N 2180 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13006 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7691 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 920} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3755 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 27, 'TRANS': 441} Chain breaks: 2 Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 921 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 233 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 40 Unusual residues: {' CA': 4, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7452 SG CYS A1069 62.579 62.764 63.623 1.00 91.25 S ATOM 7489 SG CYS A1074 64.626 65.090 58.264 1.00 84.90 S ATOM 7355 SG CYS A1056 58.493 66.521 60.923 1.00 96.71 S ATOM 7381 SG CYS A1059 60.216 60.875 58.005 1.00 95.96 S Time building chain proxies: 2.99, per 1000 atoms: 0.23 Number of scatterers: 13006 At special positions: 0 Unit cell: (143.623, 129.945, 100.023, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 5 19.99 S 67 16.00 P 30 15.00 O 2549 8.00 N 2180 7.00 C 8171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 675.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1101 " pdb="FE1 SF4 A1101 " - pdb=" SG CYS A1069 " pdb="FE2 SF4 A1101 " - pdb=" SG CYS A1074 " pdb="FE4 SF4 A1101 " - pdb=" SG CYS A1059 " pdb="FE3 SF4 A1101 " - pdb=" SG CYS A1056 " Number of angles added : 12 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 17 sheets defined 35.3% alpha, 15.2% beta 12 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.512A pdb=" N ASN A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 172 through 187 Processing helix chain 'A' and resid 222 through 234 removed outlier: 4.129A pdb=" N LYS A 226 " --> pdb=" O HIS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 378 through 394 Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 497 through 504 removed outlier: 4.281A pdb=" N ASP A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.859A pdb=" N LEU A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 552' Processing helix chain 'A' and resid 556 through 572 Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 661 through 682 removed outlier: 4.086A pdb=" N ILE A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP A 680 " --> pdb=" O ARG A 676 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.540A pdb=" N ASP A 691 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.740A pdb=" N GLN A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.147A pdb=" N TYR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 746 removed outlier: 3.775A pdb=" N THR A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 791 removed outlier: 3.591A pdb=" N GLU A 784 " --> pdb=" O ASP A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 859 removed outlier: 3.601A pdb=" N SER A 847 " --> pdb=" O CYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 879 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 901 through 915 Processing helix chain 'A' and resid 941 through 949 removed outlier: 3.531A pdb=" N GLU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 961 removed outlier: 3.793A pdb=" N TYR A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 975 Proline residue: A 972 - end of helix Processing helix chain 'A' and resid 975 through 984 removed outlier: 3.721A pdb=" N ALA A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1037 Processing helix chain 'A' and resid 1041 through 1061 removed outlier: 4.405A pdb=" N GLU A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN A1057 " --> pdb=" O TRP A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1095 removed outlier: 3.516A pdb=" N GLU A1089 " --> pdb=" O LYS A1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 54 through 73 removed outlier: 4.526A pdb=" N GLU B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 228 through 241 Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.700A pdb=" N ILE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 321 through 327 removed outlier: 4.283A pdb=" N SER B 326 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 368 removed outlier: 3.583A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'C' and resid 21 through 30 removed outlier: 3.861A pdb=" N LEU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE C 26 " --> pdb=" O PHE C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 46 removed outlier: 4.909A pdb=" N LYS C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.505A pdb=" N VAL A 137 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 151 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL A 293 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A 150 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 295 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN A 152 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 163 removed outlier: 3.786A pdb=" N SER A 193 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL A 574 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN A 200 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.642A pdb=" N SER A 319 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 344 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP A 321 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A 342 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A 323 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 348 removed outlier: 3.563A pdb=" N VAL A 397 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 320 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 436 through 441 Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.906A pdb=" N ARG A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR A 816 " --> pdb=" O GLN A 832 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN A 832 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 818 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 830 " --> pdb=" O GLY A 818 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE A 820 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR A 822 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LYS A 826 " --> pdb=" O THR A 822 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 604 through 609 removed outlier: 3.707A pdb=" N LYS A 803 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP A 608 " --> pdb=" O PHE A 801 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE A 801 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 628 removed outlier: 4.045A pdb=" N TYR A 652 " --> pdb=" O CYS A 628 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 757 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 889 through 892 Processing sheet with id=AB3, first strand: chain 'B' and resid 102 through 111 removed outlier: 4.670A pdb=" N ILE B 146 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 155 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY B 153 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 176 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE B 190 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY B 174 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 173 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 106 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 102 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.274A pdb=" N ARG B 256 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 343 through 347 removed outlier: 3.525A pdb=" N TYR B 347 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 440 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 445 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 56 removed outlier: 4.851A pdb=" N VAL C 55 " --> pdb=" O TYR C 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.676A pdb=" N ASP C 82 " --> pdb=" O CYS C 59 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 5412 1.40 - 1.62: 7765 1.62 - 1.84: 99 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 13288 Sorted by residual: bond pdb=" C3' DCP A1102 " pdb=" C4' DCP A1102 " ideal model delta sigma weight residual 1.527 1.335 0.192 1.10e-02 8.26e+03 3.05e+02 bond pdb=" C4' DCP A1102 " pdb=" O4' DCP A1102 " ideal model delta sigma weight residual 1.444 1.603 -0.159 1.00e-02 1.00e+04 2.52e+02 bond pdb=" C4 DCP A1102 " pdb=" N4 DCP A1102 " ideal model delta sigma weight residual 1.334 1.466 -0.132 1.20e-02 6.94e+03 1.21e+02 bond pdb=" C1' DCP A1102 " pdb=" O4' DCP A1102 " ideal model delta sigma weight residual 1.418 1.291 0.127 1.20e-02 6.94e+03 1.12e+02 bond pdb=" C5 DCP A1102 " pdb=" C6 DCP A1102 " ideal model delta sigma weight residual 1.345 1.495 -0.150 1.80e-02 3.09e+03 6.99e+01 ... (remaining 13283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 18024 3.92 - 7.84: 91 7.84 - 11.76: 5 11.76 - 15.69: 1 15.69 - 19.61: 2 Bond angle restraints: 18123 Sorted by residual: angle pdb=" PB DCP A1102 " pdb=" O3B DCP A1102 " pdb=" PG DCP A1102 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PA DCP A1102 " pdb=" O3A DCP A1102 " pdb=" PB DCP A1102 " ideal model delta sigma weight residual 136.83 119.63 17.20 1.00e+00 1.00e+00 2.96e+02 angle pdb=" C2' DCP A1102 " pdb=" C1' DCP A1102 " pdb=" N1 DCP A1102 " ideal model delta sigma weight residual 113.92 106.37 7.55 1.28e+00 6.12e-01 3.49e+01 angle pdb=" O2G DCP A1102 " pdb=" PG DCP A1102 " pdb=" O3B DCP A1102 " ideal model delta sigma weight residual 104.48 110.31 -5.83 1.14e+00 7.76e-01 2.64e+01 angle pdb=" O3A DCP A1102 " pdb=" PB DCP A1102 " pdb=" O3B DCP A1102 " ideal model delta sigma weight residual 101.57 109.28 -7.71 1.54e+00 4.24e-01 2.52e+01 ... (remaining 18118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6972 17.94 - 35.89: 774 35.89 - 53.83: 182 53.83 - 71.77: 40 71.77 - 89.71: 11 Dihedral angle restraints: 7979 sinusoidal: 3447 harmonic: 4532 Sorted by residual: dihedral pdb=" CA VAL B 87 " pdb=" C VAL B 87 " pdb=" N LEU B 88 " pdb=" CA LEU B 88 " ideal model delta harmonic sigma weight residual 180.00 -122.71 -57.29 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA PRO B 22 " pdb=" C PRO B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 dihedral pdb=" CA GLN B 85 " pdb=" C GLN B 85 " pdb=" N LEU B 86 " pdb=" CA LEU B 86 " ideal model delta harmonic sigma weight residual -180.00 -139.58 -40.42 0 5.00e+00 4.00e-02 6.53e+01 ... (remaining 7976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1497 0.054 - 0.108: 457 0.108 - 0.161: 68 0.161 - 0.215: 5 0.215 - 0.269: 2 Chirality restraints: 2029 Sorted by residual: chirality pdb=" C3' DCP A1102 " pdb=" C2' DCP A1102 " pdb=" C4' DCP A1102 " pdb=" O3' DCP A1102 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE C 109 " pdb=" CA ILE C 109 " pdb=" CG1 ILE C 109 " pdb=" CG2 ILE C 109 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE C 74 " pdb=" CA ILE C 74 " pdb=" CG1 ILE C 74 " pdb=" CG2 ILE C 74 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2026 not shown) Planarity restraints: 2223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 405 " -0.015 2.00e-02 2.50e+03 1.28e-02 4.08e+00 pdb=" CG TRP B 405 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 405 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 405 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 405 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 405 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 405 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 405 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 405 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 405 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 663 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 664 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 806 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 807 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " 0.026 5.00e-02 4.00e+02 ... (remaining 2220 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 157 2.53 - 3.12: 10667 3.12 - 3.72: 19561 3.72 - 4.31: 29252 4.31 - 4.90: 48283 Nonbonded interactions: 107920 Sorted by model distance: nonbonded pdb=" OD2 ASP A 321 " pdb="CA CA A1106 " model vdw 1.939 2.510 nonbonded pdb=" OE1 GLN A 832 " pdb=" OG SER A 837 " model vdw 2.023 3.040 nonbonded pdb=" OD2 ASP B 297 " pdb=" OH TYR B 347 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASP B 307 " model vdw 2.176 3.040 nonbonded pdb=" O ASP A 337 " pdb=" OH TYR A 410 " model vdw 2.181 3.040 ... (remaining 107915 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: 2.770 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.010 0.192 13292 Z= 0.485 Angle : 1.004 30.036 18135 Z= 0.535 Chirality : 0.051 0.269 2029 Planarity : 0.005 0.046 2223 Dihedral : 15.972 89.712 5057 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.17 % Favored : 90.18 % Rotamer: Outliers : 0.07 % Allowed : 8.69 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.18), residues: 1527 helix: -1.69 (0.19), residues: 504 sheet: -2.96 (0.29), residues: 217 loop : -2.53 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 815 TYR 0.020 0.002 TYR A 805 PHE 0.021 0.002 PHE A 806 TRP 0.035 0.002 TRP B 405 HIS 0.005 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00945 (13288) covalent geometry : angle 0.88774 (18123) hydrogen bonds : bond 0.17610 ( 464) hydrogen bonds : angle 7.86960 ( 1283) metal coordination : bond 0.12120 ( 4) metal coordination : angle 18.23200 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8392 (mmmt) REVERT: A 1089 GLU cc_start: 0.8294 (tp30) cc_final: 0.7963 (tp30) REVERT: A 1092 GLU cc_start: 0.8551 (tp30) cc_final: 0.8289 (tp30) REVERT: B 5 LEU cc_start: 0.7141 (mm) cc_final: 0.6228 (mm) REVERT: B 211 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7695 (tpp80) REVERT: C 8 PHE cc_start: 0.7380 (t80) cc_final: 0.7110 (t80) REVERT: C 41 PHE cc_start: 0.8960 (t80) cc_final: 0.8717 (t80) REVERT: C 62 ASP cc_start: 0.8614 (p0) cc_final: 0.8397 (p0) REVERT: C 89 ASN cc_start: 0.6604 (t0) cc_final: 0.5118 (t0) REVERT: C 91 MET cc_start: 0.7870 (mpp) cc_final: 0.7001 (tmm) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1290 time to fit residues: 33.6207 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 171 ASN A 175 GLN A 283 ASN A 284 ASN A 358 ASN ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 434 GLN A 485 HIS A 949 ASN A1073 ASN A1088 GLN A1093 GLN B 15 GLN B 38 ASN B 124 ASN B 272 ASN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 312 GLN B 332 ASN B 337 ASN C 28 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075033 restraints weight = 23764.382| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.65 r_work: 0.2938 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13292 Z= 0.147 Angle : 0.688 10.990 18135 Z= 0.352 Chirality : 0.046 0.274 2029 Planarity : 0.005 0.044 2223 Dihedral : 14.226 89.859 1995 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.81 % Favored : 92.86 % Rotamer: Outliers : 1.36 % Allowed : 10.92 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.20), residues: 1527 helix: -0.34 (0.22), residues: 515 sheet: -2.71 (0.30), residues: 220 loop : -1.95 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.015 0.002 TYR A 496 PHE 0.014 0.001 PHE C 88 TRP 0.009 0.001 TRP A1053 HIS 0.005 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00332 (13288) covalent geometry : angle 0.67853 (18123) hydrogen bonds : bond 0.03984 ( 464) hydrogen bonds : angle 5.36168 ( 1283) metal coordination : bond 0.00860 ( 4) metal coordination : angle 4.38923 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8748 (t0) cc_final: 0.8539 (t0) REVERT: A 336 TYR cc_start: 0.9126 (m-80) cc_final: 0.8912 (m-80) REVERT: A 491 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8336 (mmmt) REVERT: A 506 ASP cc_start: 0.8152 (t0) cc_final: 0.7808 (p0) REVERT: A 698 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8883 (tt) REVERT: A 912 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8007 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8648 (tp30) cc_final: 0.8417 (tp30) REVERT: A 1092 GLU cc_start: 0.8761 (tp30) cc_final: 0.8450 (tp30) REVERT: C 8 PHE cc_start: 0.7500 (t80) cc_final: 0.7262 (t80) REVERT: C 29 LEU cc_start: 0.9462 (mp) cc_final: 0.9118 (tp) REVERT: C 41 PHE cc_start: 0.8983 (t80) cc_final: 0.8706 (t80) REVERT: C 52 TYR cc_start: 0.5695 (p90) cc_final: 0.4765 (p90) REVERT: C 62 ASP cc_start: 0.8853 (p0) cc_final: 0.8261 (p0) REVERT: C 89 ASN cc_start: 0.6875 (t0) cc_final: 0.6499 (p0) outliers start: 19 outliers final: 10 residues processed: 186 average time/residue: 0.1050 time to fit residues: 29.3233 Evaluate side-chains 155 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 59 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.103499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075015 restraints weight = 23872.391| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.72 r_work: 0.2934 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13292 Z= 0.150 Angle : 0.656 11.906 18135 Z= 0.334 Chirality : 0.045 0.251 2029 Planarity : 0.005 0.040 2223 Dihedral : 13.961 89.593 1995 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.14 % Favored : 92.67 % Rotamer: Outliers : 1.94 % Allowed : 12.72 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.21), residues: 1527 helix: 0.11 (0.23), residues: 519 sheet: -2.31 (0.29), residues: 241 loop : -1.69 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.024 0.001 TYR C 43 PHE 0.010 0.001 PHE A 426 TRP 0.007 0.001 TRP A1053 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00345 (13288) covalent geometry : angle 0.64777 (18123) hydrogen bonds : bond 0.03591 ( 464) hydrogen bonds : angle 5.01158 ( 1283) metal coordination : bond 0.00528 ( 4) metal coordination : angle 4.03396 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8755 (t0) cc_final: 0.8457 (t0) REVERT: A 336 TYR cc_start: 0.9114 (m-80) cc_final: 0.8905 (m-80) REVERT: A 491 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8269 (mmmt) REVERT: A 506 ASP cc_start: 0.8013 (t0) cc_final: 0.7677 (p0) REVERT: A 912 ARG cc_start: 0.8509 (ttp80) cc_final: 0.7870 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8581 (tp30) cc_final: 0.8355 (tp30) REVERT: B 431 LYS cc_start: 0.9089 (pttp) cc_final: 0.8821 (pttm) REVERT: C 29 LEU cc_start: 0.9349 (mp) cc_final: 0.9042 (tp) REVERT: C 62 ASP cc_start: 0.8916 (p0) cc_final: 0.8628 (p0) REVERT: C 89 ASN cc_start: 0.7294 (t0) cc_final: 0.6409 (t0) REVERT: C 90 PRO cc_start: 0.7298 (Cg_exo) cc_final: 0.6982 (Cg_endo) REVERT: C 91 MET cc_start: 0.8217 (pmm) cc_final: 0.7824 (pmm) outliers start: 27 outliers final: 20 residues processed: 173 average time/residue: 0.0965 time to fit residues: 25.9066 Evaluate side-chains 169 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 81 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 85 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074414 restraints weight = 23977.244| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.64 r_work: 0.2927 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13292 Z= 0.186 Angle : 0.658 10.839 18135 Z= 0.336 Chirality : 0.045 0.235 2029 Planarity : 0.004 0.041 2223 Dihedral : 13.874 89.572 1995 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.40 % Favored : 92.47 % Rotamer: Outliers : 2.44 % Allowed : 13.72 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.21), residues: 1527 helix: 0.26 (0.23), residues: 519 sheet: -2.16 (0.29), residues: 240 loop : -1.47 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.014 0.001 TYR A 410 PHE 0.015 0.001 PHE C 84 TRP 0.009 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00436 (13288) covalent geometry : angle 0.65026 (18123) hydrogen bonds : bond 0.03668 ( 464) hydrogen bonds : angle 4.91079 ( 1283) metal coordination : bond 0.00580 ( 4) metal coordination : angle 4.04368 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8878 (t0) cc_final: 0.8517 (t0) REVERT: A 336 TYR cc_start: 0.9194 (m-80) cc_final: 0.8931 (m-80) REVERT: A 491 LYS cc_start: 0.8681 (mmmm) cc_final: 0.8334 (mmmt) REVERT: A 506 ASP cc_start: 0.8162 (t0) cc_final: 0.7765 (p0) REVERT: A 698 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8883 (tt) REVERT: A 912 ARG cc_start: 0.8628 (ttp80) cc_final: 0.7957 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8651 (tp30) cc_final: 0.8258 (tp30) REVERT: A 1092 GLU cc_start: 0.8603 (tp30) cc_final: 0.8368 (tp30) REVERT: B 476 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7952 (mm-30) REVERT: C 29 LEU cc_start: 0.9355 (mp) cc_final: 0.9017 (tp) REVERT: C 31 ILE cc_start: 0.8384 (tp) cc_final: 0.8106 (tt) REVERT: C 62 ASP cc_start: 0.8942 (p0) cc_final: 0.8614 (p0) REVERT: C 89 ASN cc_start: 0.7328 (t0) cc_final: 0.6347 (t0) REVERT: C 91 MET cc_start: 0.8244 (pmm) cc_final: 0.7583 (pmm) REVERT: C 110 LYS cc_start: 0.7838 (tmtt) cc_final: 0.7597 (tmtt) outliers start: 34 outliers final: 24 residues processed: 177 average time/residue: 0.0987 time to fit residues: 27.2978 Evaluate side-chains 169 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 81 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 73 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075354 restraints weight = 23951.386| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.66 r_work: 0.2939 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13292 Z= 0.157 Angle : 0.640 10.677 18135 Z= 0.326 Chirality : 0.045 0.236 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.731 89.811 1995 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.88 % Favored : 92.93 % Rotamer: Outliers : 2.66 % Allowed : 14.15 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.21), residues: 1527 helix: 0.36 (0.23), residues: 521 sheet: -2.05 (0.30), residues: 240 loop : -1.35 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.016 0.001 TYR C 43 PHE 0.016 0.001 PHE C 84 TRP 0.009 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00362 (13288) covalent geometry : angle 0.63205 (18123) hydrogen bonds : bond 0.03411 ( 464) hydrogen bonds : angle 4.82149 ( 1283) metal coordination : bond 0.00453 ( 4) metal coordination : angle 4.00293 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8864 (t0) cc_final: 0.8507 (t0) REVERT: A 336 TYR cc_start: 0.9196 (m-80) cc_final: 0.8923 (m-80) REVERT: A 491 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8319 (mmmt) REVERT: A 506 ASP cc_start: 0.8124 (t0) cc_final: 0.7734 (p0) REVERT: A 912 ARG cc_start: 0.8627 (ttp80) cc_final: 0.7937 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8647 (tp30) cc_final: 0.8249 (tp30) REVERT: A 1092 GLU cc_start: 0.8640 (tp30) cc_final: 0.8361 (tp30) REVERT: B 476 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7899 (mm-30) REVERT: C 24 ASP cc_start: 0.9048 (m-30) cc_final: 0.8803 (m-30) REVERT: C 29 LEU cc_start: 0.9353 (mp) cc_final: 0.9005 (tp) REVERT: C 31 ILE cc_start: 0.8436 (tp) cc_final: 0.8169 (tt) REVERT: C 43 TYR cc_start: 0.8340 (t80) cc_final: 0.8115 (t80) REVERT: C 62 ASP cc_start: 0.8908 (p0) cc_final: 0.8540 (p0) REVERT: C 89 ASN cc_start: 0.7305 (t0) cc_final: 0.6076 (t0) REVERT: C 91 MET cc_start: 0.8282 (pmm) cc_final: 0.7683 (pmm) outliers start: 37 outliers final: 28 residues processed: 181 average time/residue: 0.0965 time to fit residues: 27.3914 Evaluate side-chains 174 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 109 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.076077 restraints weight = 23558.976| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.72 r_work: 0.2946 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13292 Z= 0.139 Angle : 0.627 10.234 18135 Z= 0.319 Chirality : 0.044 0.244 2029 Planarity : 0.004 0.044 2223 Dihedral : 13.608 89.473 1995 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.35 % Favored : 93.52 % Rotamer: Outliers : 2.51 % Allowed : 14.94 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.22), residues: 1527 helix: 0.53 (0.23), residues: 520 sheet: -1.96 (0.30), residues: 242 loop : -1.27 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.016 0.001 TYR C 98 PHE 0.017 0.001 PHE C 41 TRP 0.009 0.001 TRP B 417 HIS 0.005 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00319 (13288) covalent geometry : angle 0.61913 (18123) hydrogen bonds : bond 0.03249 ( 464) hydrogen bonds : angle 4.74162 ( 1283) metal coordination : bond 0.00422 ( 4) metal coordination : angle 3.90848 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8773 (t0) cc_final: 0.8445 (t0) REVERT: A 336 TYR cc_start: 0.9149 (m-80) cc_final: 0.8892 (m-80) REVERT: A 491 LYS cc_start: 0.8578 (mmmm) cc_final: 0.8229 (mmmt) REVERT: A 540 MET cc_start: 0.9069 (tpt) cc_final: 0.8734 (tpt) REVERT: A 850 MET cc_start: 0.9133 (mmm) cc_final: 0.8916 (mmt) REVERT: A 912 ARG cc_start: 0.8514 (ttp80) cc_final: 0.7789 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8595 (tp30) cc_final: 0.8348 (tp30) REVERT: A 1092 GLU cc_start: 0.8658 (tp30) cc_final: 0.8348 (tp30) REVERT: B 469 MET cc_start: 0.8899 (ttm) cc_final: 0.8546 (ttt) REVERT: C 24 ASP cc_start: 0.9023 (m-30) cc_final: 0.8752 (m-30) REVERT: C 29 LEU cc_start: 0.9314 (mp) cc_final: 0.9017 (tp) REVERT: C 31 ILE cc_start: 0.8480 (tp) cc_final: 0.8231 (tt) REVERT: C 43 TYR cc_start: 0.8366 (t80) cc_final: 0.8117 (t80) REVERT: C 62 ASP cc_start: 0.8863 (p0) cc_final: 0.8443 (p0) REVERT: C 89 ASN cc_start: 0.7173 (t0) cc_final: 0.6839 (t0) outliers start: 35 outliers final: 28 residues processed: 183 average time/residue: 0.0931 time to fit residues: 26.9379 Evaluate side-chains 177 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 109 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 36 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 0.0010 chunk 112 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078158 restraints weight = 23639.617| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.64 r_work: 0.2980 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13292 Z= 0.124 Angle : 0.626 9.968 18135 Z= 0.316 Chirality : 0.044 0.235 2029 Planarity : 0.004 0.048 2223 Dihedral : 13.495 89.078 1995 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.29 % Favored : 93.58 % Rotamer: Outliers : 2.73 % Allowed : 15.66 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.22), residues: 1527 helix: 0.73 (0.24), residues: 520 sheet: -1.93 (0.31), residues: 248 loop : -1.17 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.015 0.001 TYR A 496 PHE 0.012 0.001 PHE C 22 TRP 0.008 0.001 TRP B 417 HIS 0.008 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00279 (13288) covalent geometry : angle 0.61757 (18123) hydrogen bonds : bond 0.03131 ( 464) hydrogen bonds : angle 4.67190 ( 1283) metal coordination : bond 0.00399 ( 4) metal coordination : angle 3.91644 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8730 (t0) cc_final: 0.8386 (t0) REVERT: A 336 TYR cc_start: 0.9149 (m-80) cc_final: 0.8890 (m-80) REVERT: A 382 MET cc_start: 0.9162 (ttp) cc_final: 0.8956 (ttm) REVERT: A 491 LYS cc_start: 0.8539 (mmmm) cc_final: 0.8179 (mmmt) REVERT: A 540 MET cc_start: 0.9045 (tpt) cc_final: 0.8810 (tpt) REVERT: A 912 ARG cc_start: 0.8535 (ttp80) cc_final: 0.7810 (mtm-85) REVERT: A 1047 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 1089 GLU cc_start: 0.8604 (tp30) cc_final: 0.8358 (tp30) REVERT: A 1092 GLU cc_start: 0.8722 (tp30) cc_final: 0.8403 (tp30) REVERT: B 431 LYS cc_start: 0.9016 (pttp) cc_final: 0.8741 (pttm) REVERT: B 476 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7749 (mm-30) REVERT: C 8 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6946 (p90) REVERT: C 24 ASP cc_start: 0.9002 (m-30) cc_final: 0.8728 (m-30) REVERT: C 31 ILE cc_start: 0.8452 (tp) cc_final: 0.8217 (tt) REVERT: C 43 TYR cc_start: 0.8367 (t80) cc_final: 0.8154 (t80) REVERT: C 62 ASP cc_start: 0.8902 (p0) cc_final: 0.8489 (p0) REVERT: C 89 ASN cc_start: 0.7297 (t0) cc_final: 0.7048 (t0) outliers start: 38 outliers final: 25 residues processed: 188 average time/residue: 0.0995 time to fit residues: 29.0486 Evaluate side-chains 179 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 8 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 93 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 754 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074093 restraints weight = 23806.908| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.64 r_work: 0.2923 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 13292 Z= 0.226 Angle : 0.686 11.240 18135 Z= 0.347 Chirality : 0.046 0.266 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.692 88.896 1995 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 2.66 % Allowed : 16.02 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.22), residues: 1527 helix: 0.64 (0.23), residues: 522 sheet: -2.07 (0.29), residues: 257 loop : -1.21 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.018 0.002 TYR A 410 PHE 0.022 0.002 PHE B 388 TRP 0.010 0.001 TRP B 417 HIS 0.010 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00537 (13288) covalent geometry : angle 0.67886 (18123) hydrogen bonds : bond 0.03739 ( 464) hydrogen bonds : angle 4.83312 ( 1283) metal coordination : bond 0.00643 ( 4) metal coordination : angle 4.01864 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8854 (t0) cc_final: 0.8526 (t0) REVERT: A 336 TYR cc_start: 0.9219 (m-80) cc_final: 0.8911 (m-80) REVERT: A 491 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8470 (mmmt) REVERT: A 506 ASP cc_start: 0.8112 (t0) cc_final: 0.7664 (p0) REVERT: A 1089 GLU cc_start: 0.8683 (tp30) cc_final: 0.8446 (tp30) REVERT: A 1092 GLU cc_start: 0.8729 (tp30) cc_final: 0.8413 (tp30) REVERT: B 102 CYS cc_start: 0.7560 (p) cc_final: 0.7196 (t) REVERT: B 272 ASN cc_start: 0.8579 (m-40) cc_final: 0.8226 (p0) REVERT: B 476 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 8 PHE cc_start: 0.7465 (p90) cc_final: 0.6947 (p90) REVERT: C 24 ASP cc_start: 0.9053 (m-30) cc_final: 0.8771 (m-30) REVERT: C 31 ILE cc_start: 0.8531 (tp) cc_final: 0.8298 (tt) REVERT: C 62 ASP cc_start: 0.8961 (p0) cc_final: 0.8523 (p0) REVERT: C 89 ASN cc_start: 0.7441 (t0) cc_final: 0.6383 (t0) REVERT: C 91 MET cc_start: 0.8117 (pmm) cc_final: 0.7475 (pmm) outliers start: 37 outliers final: 31 residues processed: 174 average time/residue: 0.0871 time to fit residues: 24.1082 Evaluate side-chains 176 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 109 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 620 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074152 restraints weight = 24112.586| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.61 r_work: 0.2911 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13292 Z= 0.240 Angle : 0.700 9.683 18135 Z= 0.353 Chirality : 0.047 0.306 2029 Planarity : 0.004 0.041 2223 Dihedral : 13.773 89.903 1995 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.40 % Rotamer: Outliers : 2.59 % Allowed : 16.52 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.22), residues: 1527 helix: 0.55 (0.23), residues: 522 sheet: -2.12 (0.29), residues: 260 loop : -1.23 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.015 0.002 TYR A 410 PHE 0.022 0.002 PHE C 84 TRP 0.010 0.001 TRP B 417 HIS 0.008 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00569 (13288) covalent geometry : angle 0.69173 (18123) hydrogen bonds : bond 0.03804 ( 464) hydrogen bonds : angle 4.88539 ( 1283) metal coordination : bond 0.00668 ( 4) metal coordination : angle 4.22164 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8870 (t0) cc_final: 0.8528 (t0) REVERT: A 336 TYR cc_start: 0.9206 (m-80) cc_final: 0.8862 (m-80) REVERT: A 491 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8487 (mmmt) REVERT: A 506 ASP cc_start: 0.8140 (t0) cc_final: 0.7698 (p0) REVERT: A 698 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8858 (tt) REVERT: A 912 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7674 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8708 (tp30) cc_final: 0.8358 (tp30) REVERT: A 1092 GLU cc_start: 0.8724 (tp30) cc_final: 0.8421 (tp30) REVERT: B 102 CYS cc_start: 0.7587 (p) cc_final: 0.7237 (t) REVERT: B 241 MET cc_start: 0.8575 (mmt) cc_final: 0.8074 (mmm) REVERT: B 476 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7783 (mm-30) REVERT: C 24 ASP cc_start: 0.9070 (m-30) cc_final: 0.8774 (m-30) REVERT: C 31 ILE cc_start: 0.8567 (tp) cc_final: 0.8322 (tt) REVERT: C 62 ASP cc_start: 0.8907 (p0) cc_final: 0.8387 (p0) REVERT: C 89 ASN cc_start: 0.7479 (t0) cc_final: 0.6411 (t0) REVERT: C 91 MET cc_start: 0.8114 (pmm) cc_final: 0.7567 (pmm) outliers start: 36 outliers final: 31 residues processed: 172 average time/residue: 0.0897 time to fit residues: 24.3174 Evaluate side-chains 174 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 109 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 56 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 124 optimal weight: 0.0980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077431 restraints weight = 23667.877| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.64 r_work: 0.2977 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13292 Z= 0.125 Angle : 0.648 11.534 18135 Z= 0.323 Chirality : 0.044 0.270 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.512 89.392 1995 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 2.16 % Allowed : 16.88 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.22), residues: 1527 helix: 0.74 (0.24), residues: 521 sheet: -1.90 (0.30), residues: 250 loop : -1.14 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 211 TYR 0.018 0.001 TYR A 496 PHE 0.028 0.001 PHE B 388 TRP 0.009 0.001 TRP A1053 HIS 0.009 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00283 (13288) covalent geometry : angle 0.63928 (18123) hydrogen bonds : bond 0.03155 ( 464) hydrogen bonds : angle 4.71506 ( 1283) metal coordination : bond 0.00366 ( 4) metal coordination : angle 4.10862 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8721 (t0) cc_final: 0.8412 (t0) REVERT: A 336 TYR cc_start: 0.9129 (m-80) cc_final: 0.8834 (m-80) REVERT: A 491 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8212 (mmmt) REVERT: A 506 ASP cc_start: 0.7944 (t0) cc_final: 0.7467 (p0) REVERT: A 850 MET cc_start: 0.9121 (mmm) cc_final: 0.8908 (mmt) REVERT: A 912 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7587 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8611 (tp30) cc_final: 0.8271 (tp30) REVERT: A 1092 GLU cc_start: 0.8692 (tp30) cc_final: 0.8369 (tp30) REVERT: A 1096 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8504 (mmtp) REVERT: B 272 ASN cc_start: 0.8611 (m-40) cc_final: 0.8269 (p0) REVERT: B 469 MET cc_start: 0.8882 (ttm) cc_final: 0.8563 (ttt) REVERT: B 476 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7753 (mm-30) REVERT: C 24 ASP cc_start: 0.9049 (m-30) cc_final: 0.8758 (m-30) REVERT: C 31 ILE cc_start: 0.8527 (tp) cc_final: 0.8285 (tt) REVERT: C 62 ASP cc_start: 0.8896 (p0) cc_final: 0.8465 (p0) REVERT: C 88 PHE cc_start: 0.8505 (m-80) cc_final: 0.8146 (m-80) REVERT: C 89 ASN cc_start: 0.7452 (t0) cc_final: 0.6745 (t0) REVERT: C 91 MET cc_start: 0.7975 (pmm) cc_final: 0.6812 (ppp) outliers start: 30 outliers final: 25 residues processed: 168 average time/residue: 0.0878 time to fit residues: 23.5951 Evaluate side-chains 168 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 109 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.106548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077096 restraints weight = 23700.915| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.68 r_work: 0.2967 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 13292 Z= 0.138 Angle : 0.649 11.501 18135 Z= 0.324 Chirality : 0.044 0.247 2029 Planarity : 0.004 0.040 2223 Dihedral : 13.509 89.784 1995 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 1.72 % Allowed : 17.39 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.22), residues: 1527 helix: 0.73 (0.24), residues: 521 sheet: -1.93 (0.30), residues: 256 loop : -1.09 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 211 TYR 0.014 0.001 TYR A 410 PHE 0.024 0.001 PHE C 84 TRP 0.009 0.001 TRP B 417 HIS 0.009 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00322 (13288) covalent geometry : angle 0.64078 (18123) hydrogen bonds : bond 0.03229 ( 464) hydrogen bonds : angle 4.71040 ( 1283) metal coordination : bond 0.00439 ( 4) metal coordination : angle 4.07360 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3068.68 seconds wall clock time: 53 minutes 25.00 seconds (3205.00 seconds total)