Starting phenix.real_space_refine on Sat Sep 12 02:14:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p1h_20235/09_2026/6p1h_20235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p1h_20235/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6p1h_20235/09_2026/6p1h_20235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p1h_20235/09_2026/6p1h_20235.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6p1h_20235/09_2026/6p1h_20235.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p1h_20235/09_2026/6p1h_20235.cif" model { file = "/net/cci-nas-00/data/ceres_data/6p1h_20235/09_2026/6p1h_20235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p1h_20235/09_2026/6p1h_20235.cif" } 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-2.2.1-6174/lib/python3.11/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: 2.88, per 1000 atoms: 0.22 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: 1.23 Conformation dependent library (CDL) restraints added in 608.6 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: 1.36 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: 2.32 Time building geometry restraints manager: 1.56 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: 18022 3.92 - 7.84: 93 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: 6963 17.94 - 35.89: 762 35.89 - 53.83: 182 53.83 - 71.77: 37 71.77 - 89.71: 11 Dihedral angle restraints: 7955 sinusoidal: 3423 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 7952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1482 0.054 - 0.108: 460 0.108 - 0.161: 78 0.161 - 0.215: 7 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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= 0.541 Angle : 1.013 30.036 18135 Z= 0.566 Chirality : 0.052 0.269 2029 Planarity : 0.005 0.046 2223 Dihedral : 15.892 89.712 5033 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/Z covalent geometry : bond 0.00949 / 0.54 (13288) covalent geometry : angle 0.89862 / 0.56 (18123) hydrogen bonds : bond 0.17610 / 12.00 ( 464) hydrogen bonds : angle 7.86960 / 5.59 ( 1283) metal coordination : bond 0.12120 / 6.17 ( 4) metal coordination : angle 18.23200 / 8.81 ( 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 : 0.519 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: 0.1218 time to fit residues: 32.1481 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 : 0.522 ------------------------------------------------------------------------------- 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... A 116 GLN A 171 ASN A 175 GLN A 283 ASN A 284 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN B 337 ASN C 28 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073673 restraints weight = 23845.223| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.64 r_work: 0.2904 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13292 Z= 0.160 Angle : 0.751 12.977 18135 Z= 0.379 Chirality : 0.047 0.256 2029 Planarity : 0.005 0.043 2223 Dihedral : 14.198 85.992 1971 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.07 % Favored : 92.60 % Rotamer: Outliers : 1.36 % Allowed : 11.35 % Favored : 87.28 % 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: -2.41 (0.20), residues: 1527 helix: -0.54 (0.22), residues: 513 sheet: -2.71 (0.30), residues: 202 loop : -2.02 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.017 0.002 TYR C 43 PHE 0.013 0.002 PHE A 355 TRP 0.009 0.001 TRP A 203 HIS 0.005 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (13288) covalent geometry : angle 0.72466 / 0.38 (18123) hydrogen bonds : bond 0.04700 / 3.19 ( 464) hydrogen bonds : angle 5.64571 / 4.10 ( 1283) metal coordination : bond 0.01117 / 0.57 ( 4) metal coordination : angle 7.70396 / 3.64 ( 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 189 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8694 (t0) cc_final: 0.8474 (t0) REVERT: A 336 TYR cc_start: 0.9165 (m-80) cc_final: 0.8916 (m-80) REVERT: A 491 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8319 (mmmt) REVERT: A 506 ASP cc_start: 0.8190 (t0) cc_final: 0.7824 (p0) REVERT: A 698 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8928 (tt) REVERT: A 912 ARG cc_start: 0.8610 (ttp80) cc_final: 0.7998 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8656 (tp30) cc_final: 0.8293 (tp30) REVERT: A 1092 GLU cc_start: 0.8751 (tp30) cc_final: 0.8481 (tp30) REVERT: B 211 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7919 (tpp80) REVERT: C 8 PHE cc_start: 0.7654 (t80) cc_final: 0.7335 (t80) REVERT: C 24 ASP cc_start: 0.9030 (m-30) cc_final: 0.8618 (p0) REVERT: C 29 LEU cc_start: 0.9478 (mp) cc_final: 0.9205 (tp) REVERT: C 41 PHE cc_start: 0.9002 (t80) cc_final: 0.8731 (t80) REVERT: C 62 ASP cc_start: 0.8810 (p0) cc_final: 0.8236 (p0) REVERT: C 82 ASP cc_start: 0.6755 (m-30) cc_final: 0.6552 (m-30) outliers start: 19 outliers final: 9 residues processed: 180 average time/residue: 0.1085 time to fit residues: 29.3742 Evaluate side-chains 155 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 681 LEU Chi-restraints excluded: chain A residue 698 LEU 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 B residue 418 CYS Chi-restraints excluded: chain C residue 54 CYS 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: 3.9990 chunk 72 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 832 GLN ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.101920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073002 restraints weight = 24039.378| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.65 r_work: 0.2893 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13292 Z= 0.201 Angle : 0.721 12.005 18135 Z= 0.368 Chirality : 0.047 0.248 2029 Planarity : 0.005 0.044 2223 Dihedral : 14.068 85.326 1971 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.53 % Favored : 92.27 % Rotamer: Outliers : 2.23 % Allowed : 12.93 % Favored : 84.84 % 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: -1.99 (0.21), residues: 1527 helix: -0.03 (0.23), residues: 504 sheet: -2.47 (0.30), residues: 222 loop : -1.83 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.024 0.002 TYR B 53 PHE 0.013 0.001 PHE B 345 TRP 0.008 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (13288) covalent geometry : angle 0.71059 / 0.37 (18123) hydrogen bonds : bond 0.04253 / 2.86 ( 464) hydrogen bonds : angle 5.27799 / 3.86 ( 1283) metal coordination : bond 0.00681 / 0.35 ( 4) metal coordination : angle 4.81655 / 2.17 ( 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 183 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8756 (t0) cc_final: 0.8397 (t0) REVERT: A 336 TYR cc_start: 0.9186 (m-80) cc_final: 0.8932 (m-80) REVERT: A 491 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8373 (mmmt) REVERT: A 506 ASP cc_start: 0.8184 (t0) cc_final: 0.7781 (p0) REVERT: A 698 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8910 (tt) REVERT: A 912 ARG cc_start: 0.8633 (ttp80) cc_final: 0.8010 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8686 (tp30) cc_final: 0.8307 (tp30) REVERT: A 1092 GLU cc_start: 0.8714 (tp30) cc_final: 0.8421 (tp30) REVERT: B 15 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8044 (pp30) REVERT: B 211 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7975 (tpp80) REVERT: C 8 PHE cc_start: 0.7516 (t80) cc_final: 0.7259 (t80) REVERT: C 24 ASP cc_start: 0.9014 (m-30) cc_final: 0.8647 (p0) REVERT: C 29 LEU cc_start: 0.9479 (mp) cc_final: 0.9192 (tp) REVERT: C 41 PHE cc_start: 0.8973 (t80) cc_final: 0.8658 (t80) REVERT: C 62 ASP cc_start: 0.9010 (p0) cc_final: 0.8758 (p0) REVERT: C 81 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.8035 (pt) REVERT: C 82 ASP cc_start: 0.6787 (m-30) cc_final: 0.6584 (m-30) outliers start: 31 outliers final: 19 residues processed: 174 average time/residue: 0.0984 time to fit residues: 26.3875 Evaluate side-chains 166 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 397 VAL 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 B residue 15 GLN Chi-restraints excluded: chain B residue 96 ILE 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 467 THR Chi-restraints excluded: chain C residue 7 TYR 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: 4.9990 chunk 150 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** 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 = 0.3532 r_free = 0.3532 target = 0.102119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.073264 restraints weight = 23956.493| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.64 r_work: 0.2895 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13292 Z= 0.193 Angle : 0.698 10.755 18135 Z= 0.357 Chirality : 0.046 0.247 2029 Planarity : 0.005 0.041 2223 Dihedral : 14.005 84.955 1971 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.20 % Favored : 92.53 % Rotamer: Outliers : 2.59 % Allowed : 14.58 % Favored : 82.83 % 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: 0.07 (0.23), residues: 507 sheet: -2.33 (0.30), residues: 222 loop : -1.66 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.020 0.002 TYR C 43 PHE 0.013 0.001 PHE B 345 TRP 0.011 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (13288) covalent geometry : angle 0.69017 / 0.36 (18123) hydrogen bonds : bond 0.04049 / 2.73 ( 464) hydrogen bonds : angle 5.12557 / 3.76 ( 1283) metal coordination : bond 0.00620 / 0.31 ( 4) metal coordination : angle 4.09934 / 1.84 ( 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 186 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8660 (t0) cc_final: 0.8269 (t0) REVERT: A 336 TYR cc_start: 0.9135 (m-80) cc_final: 0.8894 (m-80) REVERT: A 491 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8358 (mmmt) REVERT: A 506 ASP cc_start: 0.8054 (t0) cc_final: 0.7792 (p0) REVERT: A 698 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8841 (tt) REVERT: A 912 ARG cc_start: 0.8516 (ttp80) cc_final: 0.7911 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8567 (tp30) cc_final: 0.8210 (tp30) REVERT: A 1092 GLU cc_start: 0.8624 (tp30) cc_final: 0.8329 (tp30) REVERT: C 8 PHE cc_start: 0.7437 (t80) cc_final: 0.7231 (t80) REVERT: C 24 ASP cc_start: 0.9038 (m-30) cc_final: 0.8610 (p0) REVERT: C 29 LEU cc_start: 0.9461 (mp) cc_final: 0.9165 (tp) REVERT: C 62 ASP cc_start: 0.8987 (p0) cc_final: 0.8745 (p0) REVERT: C 81 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7918 (pt) REVERT: C 82 ASP cc_start: 0.6736 (m-30) cc_final: 0.6522 (m-30) outliers start: 36 outliers final: 23 residues processed: 173 average time/residue: 0.0929 time to fit residues: 25.4340 Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 397 VAL 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 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 446 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR 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: 0.6980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 754 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072386 restraints weight = 23987.539| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.70 r_work: 0.2885 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13292 Z= 0.215 Angle : 0.693 10.307 18135 Z= 0.357 Chirality : 0.047 0.244 2029 Planarity : 0.005 0.042 2223 Dihedral : 13.969 84.611 1971 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 2.95 % Allowed : 14.73 % Favored : 82.33 % 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: -1.68 (0.21), residues: 1527 helix: 0.10 (0.23), residues: 516 sheet: -2.32 (0.30), residues: 228 loop : -1.54 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 211 TYR 0.015 0.002 TYR C 43 PHE 0.028 0.002 PHE C 84 TRP 0.010 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (13288) covalent geometry : angle 0.68526 / 0.36 (18123) hydrogen bonds : bond 0.04041 / 2.73 ( 464) hydrogen bonds : angle 5.04805 / 3.70 ( 1283) metal coordination : bond 0.00679 / 0.34 ( 4) metal coordination : angle 4.02672 / 1.76 ( 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 193 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8757 (t0) cc_final: 0.8398 (t0) REVERT: A 336 TYR cc_start: 0.9149 (m-80) cc_final: 0.8886 (m-80) REVERT: A 491 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8352 (mmmt) REVERT: A 506 ASP cc_start: 0.8013 (t0) cc_final: 0.7736 (p0) REVERT: A 540 MET cc_start: 0.9126 (tpt) cc_final: 0.8647 (tpt) REVERT: A 698 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8815 (tt) REVERT: A 912 ARG cc_start: 0.8530 (ttp80) cc_final: 0.7885 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8590 (tp30) cc_final: 0.8181 (tp30) REVERT: A 1092 GLU cc_start: 0.8626 (tp30) cc_final: 0.8366 (tp30) REVERT: C 29 LEU cc_start: 0.9436 (mp) cc_final: 0.9124 (tp) REVERT: C 62 ASP cc_start: 0.8876 (p0) cc_final: 0.8530 (p0) outliers start: 41 outliers final: 29 residues processed: 180 average time/residue: 0.0923 time to fit residues: 26.0794 Evaluate side-chains 176 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 261 ASP 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 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 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 299 MET 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 451 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 1 optimal weight: 0.0070 chunk 11 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 C 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.103545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.074826 restraints weight = 23780.343| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.64 r_work: 0.2938 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13292 Z= 0.143 Angle : 0.654 10.145 18135 Z= 0.337 Chirality : 0.045 0.243 2029 Planarity : 0.004 0.040 2223 Dihedral : 13.871 83.963 1971 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.94 % Favored : 92.80 % Rotamer: Outliers : 2.80 % Allowed : 15.59 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.52 (0.21), residues: 1527 helix: 0.18 (0.23), residues: 517 sheet: -2.07 (0.30), residues: 233 loop : -1.46 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 211 TYR 0.026 0.001 TYR C 43 PHE 0.031 0.001 PHE C 8 TRP 0.011 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13288) covalent geometry : angle 0.64598 / 0.34 (18123) hydrogen bonds : bond 0.03622 / 2.44 ( 464) hydrogen bonds : angle 4.93729 / 3.63 ( 1283) metal coordination : bond 0.00505 / 0.25 ( 4) metal coordination : angle 4.06022 / 1.91 ( 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 192 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8849 (t0) cc_final: 0.8451 (t0) REVERT: A 336 TYR cc_start: 0.9187 (m-80) cc_final: 0.8917 (m-80) REVERT: A 491 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8327 (mmmt) REVERT: A 506 ASP cc_start: 0.8126 (t0) cc_final: 0.7740 (p0) REVERT: A 540 MET cc_start: 0.9187 (tpt) cc_final: 0.8745 (tpt) REVERT: A 912 ARG cc_start: 0.8620 (ttp80) cc_final: 0.7957 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8641 (tp30) cc_final: 0.8274 (tp30) REVERT: A 1092 GLU cc_start: 0.8703 (tp30) cc_final: 0.8425 (tp30) REVERT: B 403 MET cc_start: 0.8719 (mmm) cc_final: 0.8423 (mmm) REVERT: C 29 LEU cc_start: 0.9412 (mp) cc_final: 0.9107 (tp) REVERT: C 62 ASP cc_start: 0.8866 (p0) cc_final: 0.8585 (p0) outliers start: 39 outliers final: 26 residues processed: 178 average time/residue: 0.0959 time to fit residues: 26.9003 Evaluate side-chains 172 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 397 VAL 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 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 451 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 36 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.104561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076199 restraints weight = 23770.623| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.60 r_work: 0.2948 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13292 Z= 0.143 Angle : 0.660 9.990 18135 Z= 0.340 Chirality : 0.046 0.236 2029 Planarity : 0.004 0.040 2223 Dihedral : 13.811 83.791 1971 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.94 % Favored : 92.80 % Rotamer: Outliers : 2.37 % Allowed : 15.88 % Favored : 81.75 % 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: -1.41 (0.21), residues: 1527 helix: 0.31 (0.23), residues: 516 sheet: -2.07 (0.30), residues: 241 loop : -1.38 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.021 0.001 TYR A 410 PHE 0.029 0.001 PHE B 8 TRP 0.010 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13288) covalent geometry : angle 0.65229 / 0.34 (18123) hydrogen bonds : bond 0.03584 / 2.43 ( 464) hydrogen bonds : angle 4.89636 / 3.59 ( 1283) metal coordination : bond 0.00498 / 0.25 ( 4) metal coordination : angle 4.04320 / 1.99 ( 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 182 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8861 (t0) cc_final: 0.8452 (t0) REVERT: A 336 TYR cc_start: 0.9184 (m-80) cc_final: 0.8945 (m-80) REVERT: A 491 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8298 (mmmt) REVERT: A 506 ASP cc_start: 0.8113 (t0) cc_final: 0.7725 (p0) REVERT: A 912 ARG cc_start: 0.8619 (ttp80) cc_final: 0.7959 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8646 (tp30) cc_final: 0.8243 (tp30) REVERT: A 1092 GLU cc_start: 0.8694 (tp30) cc_final: 0.8401 (tp30) REVERT: B 403 MET cc_start: 0.8680 (mmm) cc_final: 0.8384 (mmm) REVERT: C 29 LEU cc_start: 0.9384 (mp) cc_final: 0.9116 (tp) REVERT: C 31 ILE cc_start: 0.8048 (tp) cc_final: 0.7729 (tt) REVERT: C 62 ASP cc_start: 0.8919 (p0) cc_final: 0.8593 (p0) REVERT: C 89 ASN cc_start: 0.7934 (p0) cc_final: 0.7660 (p0) REVERT: C 91 MET cc_start: 0.8143 (pmm) cc_final: 0.6794 (ppp) outliers start: 33 outliers final: 27 residues processed: 172 average time/residue: 0.0970 time to fit residues: 26.4806 Evaluate side-chains 172 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 261 ASP Chi-restraints excluded: chain A residue 359 VAL 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 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 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 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 109 ILE 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: 9.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 0.0000 chunk 105 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 862 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073290 restraints weight = 23797.289| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.63 r_work: 0.2909 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13292 Z= 0.235 Angle : 0.695 9.853 18135 Z= 0.357 Chirality : 0.047 0.249 2029 Planarity : 0.004 0.041 2223 Dihedral : 13.860 83.904 1971 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.53 % Favored : 92.21 % Rotamer: Outliers : 2.59 % Allowed : 16.09 % Favored : 81.32 % 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: -1.42 (0.21), residues: 1527 helix: 0.30 (0.23), residues: 517 sheet: -2.15 (0.30), residues: 248 loop : -1.34 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.015 0.002 TYR A 220 PHE 0.026 0.002 PHE C 84 TRP 0.009 0.001 TRP B 417 HIS 0.007 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (13288) covalent geometry : angle 0.68821 / 0.36 (18123) hydrogen bonds : bond 0.03906 / 2.65 ( 464) hydrogen bonds : angle 4.93578 / 3.61 ( 1283) metal coordination : bond 0.00694 / 0.35 ( 4) metal coordination : angle 3.94123 / 1.83 ( 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 180 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8873 (t0) cc_final: 0.8467 (t0) REVERT: A 336 TYR cc_start: 0.9196 (m-80) cc_final: 0.8942 (m-80) REVERT: A 491 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8437 (mmmt) REVERT: A 506 ASP cc_start: 0.8162 (t0) cc_final: 0.7789 (p0) REVERT: A 912 ARG cc_start: 0.8621 (ttp80) cc_final: 0.7943 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8668 (tp30) cc_final: 0.8266 (tp30) REVERT: A 1092 GLU cc_start: 0.8708 (tp30) cc_final: 0.8415 (tp30) REVERT: B 253 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8207 (pp) REVERT: B 476 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7875 (mm-30) REVERT: C 29 LEU cc_start: 0.9408 (mp) cc_final: 0.9151 (tp) REVERT: C 31 ILE cc_start: 0.8182 (tp) cc_final: 0.7857 (tt) REVERT: C 62 ASP cc_start: 0.8910 (p0) cc_final: 0.8570 (p0) REVERT: C 89 ASN cc_start: 0.8071 (p0) cc_final: 0.7856 (p0) REVERT: C 91 MET cc_start: 0.8141 (pmm) cc_final: 0.6875 (ppp) outliers start: 36 outliers final: 29 residues processed: 171 average time/residue: 0.0955 time to fit residues: 25.8287 Evaluate side-chains 173 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 261 ASP Chi-restraints excluded: chain A residue 348 ILE 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 862 ASN Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 946 LEU 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 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 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 94 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075338 restraints weight = 23720.277| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.65 r_work: 0.2949 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13292 Z= 0.132 Angle : 0.656 9.865 18135 Z= 0.338 Chirality : 0.045 0.252 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.802 83.443 1971 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.75 % Favored : 93.06 % Rotamer: Outliers : 2.37 % Allowed : 16.24 % Favored : 81.39 % 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: -1.29 (0.21), residues: 1527 helix: 0.39 (0.23), residues: 517 sheet: -2.05 (0.30), residues: 250 loop : -1.26 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 211 TYR 0.014 0.001 TYR C 43 PHE 0.032 0.001 PHE C 84 TRP 0.011 0.001 TRP B 417 HIS 0.007 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (13288) covalent geometry : angle 0.64770 / 0.34 (18123) hydrogen bonds : bond 0.03534 / 2.39 ( 464) hydrogen bonds : angle 4.89124 / 3.57 ( 1283) metal coordination : bond 0.00481 / 0.24 ( 4) metal coordination : angle 4.01871 / 1.98 ( 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 182 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8870 (t0) cc_final: 0.8504 (t0) REVERT: A 336 TYR cc_start: 0.9192 (m-80) cc_final: 0.8947 (m-80) REVERT: A 491 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8327 (mmmt) REVERT: A 506 ASP cc_start: 0.8117 (t0) cc_final: 0.7720 (p0) REVERT: A 912 ARG cc_start: 0.8630 (ttp80) cc_final: 0.7945 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8667 (tp30) cc_final: 0.8305 (tp30) REVERT: A 1092 GLU cc_start: 0.8716 (tp30) cc_final: 0.8420 (tp30) REVERT: B 253 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8156 (pp) REVERT: B 476 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7856 (mm-30) REVERT: C 29 LEU cc_start: 0.9380 (mp) cc_final: 0.9142 (tp) REVERT: C 31 ILE cc_start: 0.8199 (tp) cc_final: 0.7887 (tt) REVERT: C 62 ASP cc_start: 0.8926 (p0) cc_final: 0.8587 (p0) REVERT: C 88 PHE cc_start: 0.8875 (m-10) cc_final: 0.8545 (m-80) REVERT: C 91 MET cc_start: 0.8104 (pmm) cc_final: 0.6889 (ppp) outliers start: 33 outliers final: 28 residues processed: 173 average time/residue: 0.0949 time to fit residues: 26.2084 Evaluate side-chains 171 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 261 ASP Chi-restraints excluded: chain A residue 348 ILE 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 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 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 7 TYR Chi-restraints excluded: chain C residue 20 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075536 restraints weight = 23610.980| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.72 r_work: 0.2945 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 13292 Z= 0.137 Angle : 0.660 13.072 18135 Z= 0.338 Chirality : 0.045 0.248 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.714 83.113 1971 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.94 % Favored : 92.86 % Rotamer: Outliers : 2.30 % Allowed : 16.52 % Favored : 81.18 % 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: -1.20 (0.22), residues: 1527 helix: 0.44 (0.23), residues: 522 sheet: -1.93 (0.30), residues: 259 loop : -1.21 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 861 TYR 0.016 0.001 TYR C 43 PHE 0.039 0.001 PHE C 8 TRP 0.010 0.001 TRP B 417 HIS 0.009 0.001 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (13288) covalent geometry : angle 0.65234 / 0.34 (18123) hydrogen bonds : bond 0.03484 / 2.36 ( 464) hydrogen bonds : angle 4.84852 / 3.54 ( 1283) metal coordination : bond 0.00441 / 0.22 ( 4) metal coordination : angle 4.00146 / 2.04 ( 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 187 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8759 (t0) cc_final: 0.8416 (t0) REVERT: A 336 TYR cc_start: 0.9152 (m-80) cc_final: 0.8929 (m-80) REVERT: A 491 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8242 (mmmt) REVERT: A 506 ASP cc_start: 0.7943 (t0) cc_final: 0.7641 (p0) REVERT: A 850 MET cc_start: 0.9169 (mmm) cc_final: 0.8954 (mmt) REVERT: A 912 ARG cc_start: 0.8497 (ttp80) cc_final: 0.7797 (mtm-85) REVERT: A 1037 LYS cc_start: 0.9010 (tppt) cc_final: 0.8761 (mmmt) REVERT: A 1047 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 1089 GLU cc_start: 0.8610 (tp30) cc_final: 0.8205 (tp30) REVERT: A 1092 GLU cc_start: 0.8655 (tp30) cc_final: 0.8355 (tp30) REVERT: B 253 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8094 (pp) REVERT: B 476 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7711 (mm-30) REVERT: C 29 LEU cc_start: 0.9353 (mp) cc_final: 0.9123 (tp) REVERT: C 31 ILE cc_start: 0.8310 (tp) cc_final: 0.7970 (tt) REVERT: C 62 ASP cc_start: 0.8914 (p0) cc_final: 0.8594 (p0) REVERT: C 63 GLN cc_start: 0.7977 (mp10) cc_final: 0.7742 (pm20) REVERT: C 88 PHE cc_start: 0.8815 (m-10) cc_final: 0.8530 (m-80) REVERT: C 91 MET cc_start: 0.8033 (pmm) cc_final: 0.6841 (ppp) outliers start: 32 outliers final: 29 residues processed: 180 average time/residue: 0.1030 time to fit residues: 28.9114 Evaluate side-chains 183 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 261 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 359 VAL 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 253 LEU 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 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 58 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 30 optimal weight: 0.0470 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 0.0170 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 116 optimal weight: 0.0870 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3596 r_free = 0.3596 target = 0.105758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077174 restraints weight = 23438.554| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.73 r_work: 0.2978 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13292 Z= 0.121 Angle : 0.644 12.313 18135 Z= 0.330 Chirality : 0.045 0.275 2029 Planarity : 0.004 0.041 2223 Dihedral : 13.625 83.075 1971 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.55 % Favored : 93.25 % Rotamer: Outliers : 2.01 % Allowed : 16.67 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.13 (0.22), residues: 1527 helix: 0.53 (0.23), residues: 523 sheet: -1.93 (0.31), residues: 248 loop : -1.19 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 211 TYR 0.025 0.001 TYR C 52 PHE 0.021 0.001 PHE C 84 TRP 0.010 0.001 TRP A1053 HIS 0.009 0.001 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13288) covalent geometry : angle 0.63585 / 0.33 (18123) hydrogen bonds : bond 0.03348 / 2.26 ( 464) hydrogen bonds : angle 4.77874 / 3.49 ( 1283) metal coordination : bond 0.00435 / 0.22 ( 4) metal coordination : angle 4.06686 / 2.16 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3392.35 seconds wall clock time: 59 minutes 1.55 seconds (3541.55 seconds total)