Starting phenix.real_space_refine on Sun Aug 9 00:39:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fq0_50642/08_2026/9fq0_50642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fq0_50642/08_2026/9fq0_50642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fq0_50642/08_2026/9fq0_50642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fq0_50642/08_2026/9fq0_50642.map" model { file = "/net/cci-nas-00/data/ceres_data/9fq0_50642/08_2026/9fq0_50642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fq0_50642/08_2026/9fq0_50642.cif" } resolution = 4.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.092 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: 5 Type Number sf(0) Gaussians P 362 5.49 5 S 115 5.16 5 C 18581 2.51 5 N 5859 2.21 5 O 6759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31676 Number of models: 1 Model: "" Number of chains: 17 Chain: "8" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1237 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 22, 'rna3p_pyr': 23} Link IDs: {'rna2p': 13, 'rna3p': 44} Chain: "E" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2498 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 296} Chain: "D" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 937 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain: "1" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 6383 Classifications: {'RNA': 298} Modifications used: {'rna2p_pur': 27, 'rna2p_pyr': 20, 'rna3p_pur': 131, 'rna3p_pyr': 120} Link IDs: {'rna2p': 47, 'rna3p': 250} Chain breaks: 8 Chain: "LY" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1075 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "Lh" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LX" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 950 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 107} Chain: "A" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 1 Chain: "LU" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 825 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "LR" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1281 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "2" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1388 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 6, 'TRANS': 162} Chain: "B" Number of atoms: 6881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6881 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 29, 'TRANS': 804} Chain: "LC" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2908 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 18, 'TRANS': 346} Chain: "LE" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1724 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Chain: "Lr" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.49, per 1000 atoms: 0.20 Number of scatterers: 31676 At special positions: 0 Unit cell: (184.673, 218.917, 251.938, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 115 16.00 P 362 15.00 O 6759 8.00 N 5859 7.00 C 18581 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: 2.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 23 sheets defined 55.3% alpha, 10.5% beta 103 base pairs and 158 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.628A pdb=" N ASP E 110 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 132 through 155 Processing helix chain 'E' and resid 162 through 177 Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 242 through 261 Processing helix chain 'E' and resid 268 through 283 removed outlier: 4.204A pdb=" N LEU E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN E 274 " --> pdb=" O ARG E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 384 Processing helix chain 'D' and resid 51 through 63 Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.537A pdb=" N LYS D 93 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 147 Processing helix chain 'D' and resid 149 through 154 removed outlier: 3.564A pdb=" N ASN D 152 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 removed outlier: 4.015A pdb=" N LYSLY 28 " --> pdb=" O HISLY 24 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 126 removed outlier: 3.878A pdb=" N LYSLY 117 " --> pdb=" O LYSLY 113 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.588A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 37 removed outlier: 3.537A pdb=" N GLNLh 30 " --> pdb=" O VALLh 26 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEULh 31 " --> pdb=" O GLULh 27 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THRLh 37 " --> pdb=" O VALLh 33 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 45 Processing helix chain 'Lh' and resid 45 through 73 removed outlier: 4.282A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 88 through 93 removed outlier: 3.856A pdb=" N ARGLh 93 " --> pdb=" O ARGLh 89 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 96 through 101 Processing helix chain 'Lh' and resid 104 through 114 Processing helix chain 'LX' and resid 72 through 76 Processing helix chain 'LX' and resid 83 through 94 removed outlier: 3.535A pdb=" N METLX 87 " --> pdb=" O THRLX 83 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYSLX 88 " --> pdb=" O GLULX 84 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYSLX 89 " --> pdb=" O SERLX 85 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILELX 90 " --> pdb=" O ALALX 86 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLULX 91 " --> pdb=" O METLX 87 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASPLX 92 " --> pdb=" O LYSLX 88 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASNLX 93 " --> pdb=" O LYSLX 89 " (cutoff:3.500A) Processing helix chain 'LX' and resid 105 through 118 Processing helix chain 'LX' and resid 145 through 154 removed outlier: 3.752A pdb=" N VALLX 149 " --> pdb=" O ASPLX 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.953A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.547A pdb=" N ALA A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 191 through 202 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'LU' and resid 25 through 31 removed outlier: 3.642A pdb=" N ASPLU 31 " --> pdb=" O HISLU 27 " (cutoff:3.500A) Processing helix chain 'LU' and resid 35 through 46 removed outlier: 3.635A pdb=" N GLNLU 44 " --> pdb=" O GLULU 40 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLULU 45 " --> pdb=" O GLNLU 41 " (cutoff:3.500A) Processing helix chain 'LU' and resid 55 through 60 removed outlier: 3.548A pdb=" N GLYLU 59 " --> pdb=" O ASNLU 55 " (cutoff:3.500A) Processing helix chain 'LU' and resid 79 through 94 removed outlier: 3.672A pdb=" N LEULU 83 " --> pdb=" O SERLU 79 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYSLU 84 " --> pdb=" O LYSLU 80 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 16 removed outlier: 3.649A pdb=" N LYSLR 8 " --> pdb=" O LEULR 4 " (cutoff:3.500A) Processing helix chain 'LR' and resid 18 through 20 No H-bonds generated for 'chain 'LR' and resid 18 through 20' Processing helix chain 'LR' and resid 28 through 34 removed outlier: 3.672A pdb=" N ILELR 32 " --> pdb=" O GLULR 28 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 Processing helix chain 'LR' and resid 60 through 71 Processing helix chain 'LR' and resid 77 through 81 removed outlier: 3.562A pdb=" N ARGLR 81 " --> pdb=" O ILELR 78 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 Processing helix chain 'LR' and resid 116 through 129 Processing helix chain 'LR' and resid 134 through 154 removed outlier: 3.959A pdb=" N LEULR 138 " --> pdb=" O ASNLR 134 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYSLR 153 " --> pdb=" O LYSLR 149 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 7 through 16 removed outlier: 3.722A pdb=" N PHELk 11 " --> pdb=" O GLULk 7 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEULk 12 " --> pdb=" O ILELk 8 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEULk 13 " --> pdb=" O LYSLk 9 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 50 through 59 removed outlier: 3.519A pdb=" N GLULk 54 " --> pdb=" O LYSLk 50 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYSLk 55 " --> pdb=" O GLULk 51 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 22 removed outlier: 4.111A pdb=" N LEU 2 19 " --> pdb=" O GLN 2 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU 2 20 " --> pdb=" O HIS 2 16 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 38 Processing helix chain '2' and resid 79 through 82 Processing helix chain '2' and resid 85 through 103 Processing helix chain '2' and resid 115 through 125 Processing helix chain '2' and resid 151 through 170 removed outlier: 3.743A pdb=" N GLU 2 157 " --> pdb=" O GLN 2 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 25 through 39 removed outlier: 3.947A pdb=" N GLN B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 36 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 45 through 58 removed outlier: 4.118A pdb=" N CYS B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 76 Processing helix chain 'B' and resid 79 through 93 removed outlier: 3.609A pdb=" N TRP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 removed outlier: 3.579A pdb=" N LYS B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 Processing helix chain 'B' and resid 129 through 144 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.867A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.766A pdb=" N ALA B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 215 through 220 removed outlier: 5.152A pdb=" N LYS B 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 237 Processing helix chain 'B' and resid 239 through 254 Processing helix chain 'B' and resid 257 through 269 removed outlier: 3.767A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.722A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 4.055A pdb=" N LEU B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 321 removed outlier: 3.876A pdb=" N PHE B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.707A pdb=" N LYS B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 369 through 388 removed outlier: 3.864A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 404 Processing helix chain 'B' and resid 408 through 422 removed outlier: 3.582A pdb=" N LEU B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 438 Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.708A pdb=" N ASN B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.640A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 500 through 521 removed outlier: 3.536A pdb=" N THR B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.762A pdb=" N PHE B 525 " --> pdb=" O ASP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 534 through 547 removed outlier: 3.519A pdb=" N ASP B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 551 through 571 Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 588 through 627 removed outlier: 3.659A pdb=" N ALA B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 629 No H-bonds generated for 'chain 'B' and resid 628 through 629' Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 652 through 667 Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 671 through 685 removed outlier: 4.363A pdb=" N HIS B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 703 removed outlier: 3.890A pdb=" N GLN B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 Processing helix chain 'B' and resid 726 through 741 removed outlier: 3.816A pdb=" N VAL B 732 " --> pdb=" O THR B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 757 Processing helix chain 'B' and resid 760 through 775 Processing helix chain 'B' and resid 778 through 787 removed outlier: 3.548A pdb=" N ALA B 782 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 811 removed outlier: 3.527A pdb=" N GLY B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 831 Processing helix chain 'LC' and resid 25 through 30 Processing helix chain 'LC' and resid 33 through 45 Processing helix chain 'LC' and resid 46 through 49 removed outlier: 3.609A pdb=" N ARGLC 49 " --> pdb=" O LYSLC 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 46 through 49' Processing helix chain 'LC' and resid 116 through 131 removed outlier: 3.572A pdb=" N ILELC 124 " --> pdb=" O LYSLC 120 " (cutoff:3.500A) Processing helix chain 'LC' and resid 133 through 140 Processing helix chain 'LC' and resid 156 through 161 Processing helix chain 'LC' and resid 163 through 174 removed outlier: 3.822A pdb=" N LEULC 171 " --> pdb=" O ALALC 167 " (cutoff:3.500A) Processing helix chain 'LC' and resid 176 through 186 removed outlier: 4.186A pdb=" N ILELC 180 " --> pdb=" O ALALC 176 " (cutoff:3.500A) Processing helix chain 'LC' and resid 192 through 196 removed outlier: 3.607A pdb=" N LYSLC 195 " --> pdb=" O GLYLC 192 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 222 removed outlier: 3.801A pdb=" N PHELC 221 " --> pdb=" O ILELC 217 " (cutoff:3.500A) Processing helix chain 'LC' and resid 236 through 241 Processing helix chain 'LC' and resid 254 through 259 Processing helix chain 'LC' and resid 259 through 265 Processing helix chain 'LC' and resid 288 through 294 Processing helix chain 'LC' and resid 295 through 300 Processing helix chain 'LC' and resid 321 through 329 removed outlier: 3.566A pdb=" N LEULC 328 " --> pdb=" O ILELC 324 " (cutoff:3.500A) Processing helix chain 'LC' and resid 331 through 368 removed outlier: 3.574A pdb=" N LYSLC 353 " --> pdb=" O LEULC 349 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLNLC 362 " --> pdb=" O ALALC 358 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALALC 363 " --> pdb=" O ALALC 359 " (cutoff:3.500A) Processing helix chain 'LE' and resid 58 through 66 removed outlier: 3.584A pdb=" N TYRLE 63 " --> pdb=" O ARGLE 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SERLE 64 " --> pdb=" O SERLE 60 " (cutoff:3.500A) Processing helix chain 'LE' and resid 132 through 136 Processing helix chain 'LE' and resid 178 through 183 Processing helix chain 'LE' and resid 190 through 192 No H-bonds generated for 'chain 'LE' and resid 190 through 192' Processing helix chain 'LE' and resid 213 through 218 Processing helix chain 'LE' and resid 243 through 262 removed outlier: 3.877A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix Processing helix chain 'LE' and resid 266 through 273 Processing helix chain 'LE' and resid 282 through 286 Processing helix chain 'Lr' and resid 3 through 11 removed outlier: 3.671A pdb=" N VALLr 9 " --> pdb=" O LEULr 5 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 31 through 35 removed outlier: 4.151A pdb=" N ARGLr 35 " --> pdb=" O LEULr 32 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 72 through 76 Processing helix chain 'Lr' and resid 85 through 98 removed outlier: 3.649A pdb=" N LEULr 90 " --> pdb=" O ALALr 86 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SERLr 91 " --> pdb=" O ARGLr 87 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 106 through 122 removed outlier: 3.665A pdb=" N ILELr 117 " --> pdb=" O ARGLr 113 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEULr 118 " --> pdb=" O ALALr 114 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARGLr 119 " --> pdb=" O SERLr 115 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SERLr 120 " --> pdb=" O ALALr 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYSLr 122 " --> pdb=" O LEULr 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 180 through 181 Processing sheet with id=AA2, first strand: chain 'E' and resid 180 through 181 Processing sheet with id=AA3, first strand: chain 'E' and resid 200 through 202 removed outlier: 6.493A pdb=" N ALA E 346 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 286 through 287 Processing sheet with id=AA5, first strand: chain 'E' and resid 293 through 295 Processing sheet with id=AA6, first strand: chain 'E' and resid 323 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.502A pdb=" N ILE A 121 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 120 " --> pdb=" O ILE D 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR D 131 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA D 125 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR D 133 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL D 123 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR D 135 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS D 137 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 106 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 105 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 107 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 125 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'LY' and resid 31 through 33 removed outlier: 3.620A pdb=" N SERLY 32 " --> pdb=" O METLY 47 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N METLY 47 " --> pdb=" O SERLY 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'LY' and resid 94 through 99 removed outlier: 9.343A pdb=" N VALLY 95 " --> pdb=" O ARGLY 84 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ARGLY 84 " --> pdb=" O VALLY 95 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VALLY 97 " --> pdb=" O ILELY 82 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILELY 82 " --> pdb=" O VALLY 97 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYRLY 81 " --> pdb=" O VALLY 71 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LYSLY 69 " --> pdb=" O GLULY 83 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'LX' and resid 77 through 80 removed outlier: 7.355A pdb=" N ILELX 99 " --> pdb=" O LYSLX 78 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VALLX 97 " --> pdb=" O PROLX 80 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'LU' and resid 62 through 65 removed outlier: 3.717A pdb=" N VALLU 72 " --> pdb=" O PHELU 21 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHELU 21 " --> pdb=" O VALLU 72 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SERLU 74 " --> pdb=" O LEULU 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEULU 19 " --> pdb=" O SERLU 74 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYRLU 110 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N THRLU 22 " --> pdb=" O TYRLU 110 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEULU 112 " --> pdb=" O THRLU 22 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASPLU 24 " --> pdb=" O LEULU 112 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N TYRLU 114 " --> pdb=" O ASPLU 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'LU' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'LR' and resid 22 through 24 Processing sheet with id=AB5, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.481A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '2' and resid 4 through 5 removed outlier: 3.563A pdb=" N ARG 2 4 " --> pdb=" O ILE 2 44 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR 2 43 " --> pdb=" O TYR 2 55 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR 2 55 " --> pdb=" O TYR 2 43 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA 2 45 " --> pdb=" O VAL 2 53 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS 2 59 " --> pdb=" O ILE 2 72 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE 2 72 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY 2 70 " --> pdb=" O SER 2 108 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N HIS 2 110 " --> pdb=" O GLY 2 70 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE 2 72 " --> pdb=" O HIS 2 110 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N ARG 2 112 " --> pdb=" O ILE 2 72 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N SER 2 74 " --> pdb=" O ARG 2 112 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA 2 144 " --> pdb=" O VAL 2 133 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL 2 133 " --> pdb=" O ALA 2 144 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA 2 146 " --> pdb=" O SER 2 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'LC' and resid 17 through 23 removed outlier: 4.928A pdb=" N LYSLC 20 " --> pdb=" O VALLC 10 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALLC 153 " --> pdb=" O SERLC 9 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYSLC 208 " --> pdb=" O ILELC 251 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THRLC 253 " --> pdb=" O CYSLC 208 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILELC 210 " --> pdb=" O THRLC 253 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'LC' and resid 64 through 65 Processing sheet with id=AB9, first strand: chain 'LC' and resid 187 through 189 Processing sheet with id=AC1, first strand: chain 'LE' and resid 49 through 51 removed outlier: 3.674A pdb=" N VALLE 51 " --> pdb=" O ILELE 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'LE' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'LE' and resid 187 through 189 removed outlier: 5.163A pdb=" N LEULE 174 " --> pdb=" O LEULE 165 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THRLE 176 " --> pdb=" O VALLE 163 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THRLE 199 " --> pdb=" O ILELE 149 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILELE 151 " --> pdb=" O THRLE 197 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THRLE 197 " --> pdb=" O ILELE 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Lr' and resid 17 through 20 Processing sheet with id=AC5, first strand: chain 'Lr' and resid 49 through 53 1163 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 270 hydrogen bonds 462 hydrogen bond angles 0 basepair planarities 103 basepair parallelities 158 stacking parallelities Total time for adding SS restraints: 7.80 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6608 1.33 - 1.45: 9192 1.45 - 1.58: 16299 1.58 - 1.70: 709 1.70 - 1.82: 186 Bond restraints: 32994 Sorted by residual: bond pdb=" C5 IHP B 901 " pdb=" O15 IHP B 901 " ideal model delta sigma weight residual 1.389 1.466 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C1 IHP B 901 " pdb=" O11 IHP B 901 " ideal model delta sigma weight residual 1.392 1.465 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C3 IHP B 901 " pdb=" O13 IHP B 901 " ideal model delta sigma weight residual 1.393 1.465 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N HIS D 78 " pdb=" CA HIS D 78 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.16e-02 7.43e+03 1.28e+01 bond pdb=" C6 IHP B 901 " pdb=" O16 IHP B 901 " ideal model delta sigma weight residual 1.394 1.465 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 32989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.39: 45861 5.39 - 10.78: 249 10.78 - 16.16: 18 16.16 - 21.55: 4 21.55 - 26.94: 1 Bond angle restraints: 46133 Sorted by residual: angle pdb=" C1' C 1 485 " pdb=" N1 C 1 485 " pdb=" C2 C 1 485 " ideal model delta sigma weight residual 118.80 128.25 -9.45 1.10e+00 8.26e-01 7.37e+01 angle pdb=" N ARG D 79 " pdb=" CA ARG D 79 " pdb=" C ARG D 79 " ideal model delta sigma weight residual 111.90 101.44 10.46 1.32e+00 5.74e-01 6.28e+01 angle pdb=" CA LEU B 835 " pdb=" CB LEU B 835 " pdb=" CG LEU B 835 " ideal model delta sigma weight residual 116.30 143.24 -26.94 3.50e+00 8.16e-02 5.92e+01 angle pdb=" C3' C 1 456 " pdb=" O3' C 1 456 " pdb=" P G 1 457 " ideal model delta sigma weight residual 119.70 110.72 8.98 1.20e+00 6.94e-01 5.60e+01 angle pdb=" C3' C 1 455 " pdb=" O3' C 1 455 " pdb=" P C 1 456 " ideal model delta sigma weight residual 119.70 110.95 8.75 1.20e+00 6.94e-01 5.32e+01 ... (remaining 46128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 19229 31.42 - 62.84: 1338 62.84 - 94.25: 347 94.25 - 125.67: 27 125.67 - 157.09: 4 Dihedral angle restraints: 20945 sinusoidal: 12247 harmonic: 8698 Sorted by residual: dihedral pdb=" O4' U 1 233 " pdb=" C1' U 1 233 " pdb=" N1 U 1 233 " pdb=" C2 U 1 233 " ideal model delta sinusoidal sigma weight residual 200.00 42.91 157.09 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" CA LEU D 147 " pdb=" C LEU D 147 " pdb=" N PRO D 148 " pdb=" CA PRO D 148 " ideal model delta harmonic sigma weight residual 0.00 -42.67 42.67 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" O4' U 1 209 " pdb=" C1' U 1 209 " pdb=" N1 U 1 209 " pdb=" C2 U 1 209 " ideal model delta sinusoidal sigma weight residual 200.00 73.85 126.15 1 1.50e+01 4.44e-03 6.78e+01 ... (remaining 20942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 5383 1.020 - 2.041: 0 2.041 - 3.061: 0 3.061 - 4.081: 0 4.081 - 5.102: 3 Chirality restraints: 5386 Sorted by residual: chirality pdb=" C2 IHP B 901 " pdb=" C1 IHP B 901 " pdb=" C3 IHP B 901 " pdb=" O12 IHP B 901 " both_signs ideal model delta sigma weight residual False -2.52 2.58 -5.10 2.00e-01 2.50e+01 6.51e+02 chirality pdb=" C5 IHP B 901 " pdb=" C4 IHP B 901 " pdb=" C6 IHP B 901 " pdb=" O15 IHP B 901 " both_signs ideal model delta sigma weight residual False -2.42 2.65 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C1 IHP B 901 " pdb=" C2 IHP B 901 " pdb=" C6 IHP B 901 " pdb=" O11 IHP B 901 " both_signs ideal model delta sigma weight residual False 2.32 -2.61 4.92 2.00e-01 2.50e+01 6.06e+02 ... (remaining 5383 not shown) Planarity restraints: 4541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 77 " -0.044 2.00e-02 2.50e+03 8.50e-02 7.23e+01 pdb=" C VAL D 77 " 0.147 2.00e-02 2.50e+03 pdb=" O VAL D 77 " -0.054 2.00e-02 2.50e+03 pdb=" N HIS D 78 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 833 " 0.030 2.00e-02 2.50e+03 5.86e-02 3.43e+01 pdb=" C TYR B 833 " -0.101 2.00e-02 2.50e+03 pdb=" O TYR B 833 " 0.037 2.00e-02 2.50e+03 pdb=" N ALA B 834 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLULh 16 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLULh 16 " 0.065 2.00e-02 2.50e+03 pdb=" O GLULh 16 " -0.024 2.00e-02 2.50e+03 pdb=" N LEULh 17 " -0.022 2.00e-02 2.50e+03 ... (remaining 4538 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 599 2.60 - 3.17: 28867 3.17 - 3.75: 58773 3.75 - 4.32: 76250 4.32 - 4.90: 111254 Nonbonded interactions: 275743 Sorted by model distance: nonbonded pdb=" O2' C 1 202 " pdb=" OD1 ASP B 632 " model vdw 2.021 3.040 nonbonded pdb=" OP2 A 12527 " pdb=" NH2 ARGLR 38 " model vdw 2.055 3.120 nonbonded pdb=" OG SER D 126 " pdb=" OG1 THR D 131 " model vdw 2.063 3.040 nonbonded pdb=" OP2 U 1 200 " pdb=" NH1 ARGLY 39 " model vdw 2.066 3.120 nonbonded pdb=" O4 U 1 512 " pdb=" O6 G 1 647 " model vdw 2.072 2.432 ... (remaining 275738 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 group one per residue 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: 27.760 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: 0.050 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 33.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.090 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:1.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 32994 Z= 0.309 Angle : 1.136 26.938 46133 Z= 0.687 Chirality : 0.135 5.102 5386 Planarity : 0.006 0.085 4541 Dihedral : 20.504 157.089 15305 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 31.05 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.51 % Favored : 94.88 % Rotamer: Outliers : 2.23 % Allowed : 25.88 % Favored : 71.88 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 2927 helix: 0.34 (0.14), residues: 1357 sheet: -0.49 (0.31), residues: 268 loop : -0.22 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARGLC 345 TYR 0.062 0.003 TYR B 451 PHE 0.045 0.003 PHELU 115 TRP 0.056 0.004 TRPLU 99 HIS 0.022 0.002 HISLY 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.31 (32994) covalent geometry : angle 1.13639 / 0.69 (46133) hydrogen bonds : bond 0.21382 / 22.20 ( 1431) hydrogen bonds : angle 7.26970 / 7.92 ( 3789) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 370 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 130 LEU cc_start: 0.9300 (mm) cc_final: 0.8954 (mm) REVERT: E 329 MET cc_start: 0.2878 (mpp) cc_final: 0.2221 (mmm) REVERT: E 383 MET cc_start: 0.8481 (mtt) cc_final: 0.8063 (ppp) REVERT: D 92 LEU cc_start: 0.4295 (mt) cc_final: 0.3820 (pp) REVERT: Lh 109 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7506 (ptt180) REVERT: A 211 MET cc_start: 0.7037 (mmp) cc_final: 0.6477 (ptp) REVERT: LU 20 LYS cc_start: 0.2915 (OUTLIER) cc_final: 0.1383 (tppt) REVERT: LU 46 ARG cc_start: 0.5939 (ttm110) cc_final: 0.4524 (mtt180) REVERT: LR 25 ASP cc_start: 0.6816 (m-30) cc_final: 0.6497 (m-30) REVERT: LR 66 ASN cc_start: 0.8351 (m110) cc_final: 0.8128 (t0) REVERT: LR 89 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.6151 (mmm) REVERT: B 127 MET cc_start: 0.3394 (pmm) cc_final: 0.3161 (pmm) REVERT: B 273 MET cc_start: 0.4266 (tmm) cc_final: 0.3636 (ppp) REVERT: LC 211 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7151 (p90) REVERT: LC 263 LEU cc_start: 0.9413 (mt) cc_final: 0.9189 (mt) REVERT: LC 319 LEU cc_start: 0.5328 (mt) cc_final: 0.5085 (mm) REVERT: LC 325 MET cc_start: 0.7521 (ptp) cc_final: 0.6559 (ptt) REVERT: LC 335 MET cc_start: 0.4531 (ptp) cc_final: 0.2517 (mtm) REVERT: LE 151 ILE cc_start: 0.7892 (mt) cc_final: 0.7490 (tp) REVERT: LE 240 TYR cc_start: -0.1464 (OUTLIER) cc_final: -0.2627 (t80) REVERT: Lr 8 MET cc_start: -0.1946 (mmm) cc_final: -0.2237 (ptt) REVERT: Lr 32 LEU cc_start: 0.4856 (mt) cc_final: 0.4145 (tp) outliers start: 58 outliers final: 25 residues processed: 414 average time/residue: 0.2340 time to fit residues: 146.4303 Evaluate side-chains 262 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 ASN ** E 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN LY 14 ASN ** LY 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN Lh 65 GLN Lh 108 GLN LX 73 HIS LX 93 ASN ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN LU 94 ASN LR 27 ASN 2 15 GLN ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 161 HIS B 35 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN B 738 ASN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 21 ASN LC 299 GLN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 4 HIS Lr 95 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.085914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.074180 restraints weight = 458815.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.073694 restraints weight = 494991.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.073990 restraints weight = 462742.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.073958 restraints weight = 426365.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.074023 restraints weight = 414416.869| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 32994 Z= 0.270 Angle : 0.882 19.340 46133 Z= 0.468 Chirality : 0.050 0.314 5386 Planarity : 0.007 0.086 4541 Dihedral : 21.483 152.320 8982 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.76 % Favored : 96.07 % Rotamer: Outliers : 0.50 % Allowed : 5.69 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2927 helix: -0.19 (0.13), residues: 1425 sheet: -0.42 (0.32), residues: 239 loop : -0.31 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARGLh 32 TYR 0.025 0.003 TYRLE 116 PHE 0.023 0.003 PHE A 143 TRP 0.045 0.003 TRP B 284 HIS 0.007 0.002 HISLC 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 (32994) covalent geometry : angle 0.88207 / 0.47 (46133) hydrogen bonds : bond 0.08179 / 8.33 ( 1431) hydrogen bonds : angle 5.76848 / 6.14 ( 3789) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 308 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 329 MET cc_start: 0.2642 (mmp) cc_final: 0.2346 (mmm) REVERT: D 77 VAL cc_start: 0.8838 (m) cc_final: 0.8604 (t) REVERT: D 92 LEU cc_start: 0.7170 (mt) cc_final: 0.6496 (pp) REVERT: LY 81 TYR cc_start: 0.7515 (m-10) cc_final: 0.7295 (m-10) REVERT: Lh 14 LYS cc_start: 0.9539 (pptt) cc_final: 0.9003 (mmtt) REVERT: Lh 109 ARG cc_start: 0.7607 (ttt90) cc_final: 0.7364 (ptt180) REVERT: LX 90 ILE cc_start: 0.8296 (mm) cc_final: 0.7932 (mp) REVERT: LX 93 ASN cc_start: 0.6323 (OUTLIER) cc_final: 0.5904 (m-40) REVERT: LX 99 ILE cc_start: 0.9060 (pt) cc_final: 0.8838 (tt) REVERT: LX 116 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6384 (mm) REVERT: A 80 MET cc_start: 0.7783 (mmp) cc_final: 0.6910 (mmm) REVERT: A 110 ASP cc_start: 0.7929 (m-30) cc_final: 0.7464 (m-30) REVERT: LR 76 MET cc_start: 0.5813 (ttt) cc_final: 0.5035 (ttt) REVERT: LR 142 ILE cc_start: 0.9313 (tt) cc_final: 0.9096 (tp) REVERT: 2 28 MET cc_start: 0.3711 (tpt) cc_final: 0.2820 (tmm) REVERT: 2 147 MET cc_start: 0.5587 (mmm) cc_final: 0.5155 (mmm) REVERT: B 21 TYR cc_start: 0.7528 (t80) cc_final: 0.7159 (t80) REVERT: B 51 MET cc_start: 0.6540 (tpt) cc_final: 0.5975 (ttt) REVERT: B 91 ARG cc_start: 0.8880 (tpt170) cc_final: 0.8343 (tpm170) REVERT: B 712 MET cc_start: 0.0390 (ptp) cc_final: -0.0022 (ptt) REVERT: B 714 ARG cc_start: 0.8185 (mpt180) cc_final: 0.7426 (mpt180) REVERT: B 737 MET cc_start: 0.3443 (ppp) cc_final: 0.3220 (ppp) REVERT: LC 231 ASN cc_start: 0.8958 (t0) cc_final: 0.8554 (t0) REVERT: LC 252 TRP cc_start: 0.9114 (m-90) cc_final: 0.8900 (m-90) REVERT: LC 325 MET cc_start: 0.8447 (ptp) cc_final: 0.8001 (ppp) REVERT: LE 68 MET cc_start: 0.9561 (mpp) cc_final: 0.9318 (mpp) REVERT: LE 151 ILE cc_start: 0.8368 (mt) cc_final: 0.8059 (tp) REVERT: LE 267 LEU cc_start: 0.9250 (tp) cc_final: 0.9049 (mt) outliers start: 13 outliers final: 0 residues processed: 320 average time/residue: 0.2263 time to fit residues: 109.9996 Evaluate side-chains 218 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 171 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 313 optimal weight: 0.0020 chunk 152 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 65 optimal weight: 40.0000 chunk 3 optimal weight: 30.0000 chunk 268 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 245 optimal weight: 8.9990 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 198 ASN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 107 HIS A 136 GLN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 223 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.083981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.072321 restraints weight = 470369.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.071919 restraints weight = 491025.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.072245 restraints weight = 426882.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.072325 restraints weight = 377163.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.072336 restraints weight = 360294.912| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 32994 Z= 0.229 Angle : 0.777 13.680 46133 Z= 0.413 Chirality : 0.044 0.351 5386 Planarity : 0.007 0.179 4541 Dihedral : 21.654 156.287 8982 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 0.19 % Allowed : 5.85 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 2927 helix: 0.05 (0.13), residues: 1424 sheet: -0.66 (0.33), residues: 220 loop : -0.35 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARGLE 56 TYR 0.032 0.003 TYRLE 57 PHE 0.049 0.003 PHE B 699 TRP 0.031 0.003 TRPLR 95 HIS 0.015 0.002 HIS B 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 (32994) covalent geometry : angle 0.77673 / 0.41 (46133) hydrogen bonds : bond 0.07527 / 7.62 ( 1431) hydrogen bonds : angle 5.41609 / 5.83 ( 3789) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 294 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 305 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8081 (t0) REVERT: D 92 LEU cc_start: 0.7277 (mt) cc_final: 0.6953 (pp) REVERT: LY 30 MET cc_start: 0.5003 (ptt) cc_final: 0.4505 (ptt) REVERT: LY 42 TYR cc_start: 0.9311 (m-80) cc_final: 0.9093 (m-80) REVERT: Lh 14 LYS cc_start: 0.9483 (pptt) cc_final: 0.8975 (mmtt) REVERT: LX 99 ILE cc_start: 0.8866 (pt) cc_final: 0.8532 (tt) REVERT: A 80 MET cc_start: 0.8342 (mmp) cc_final: 0.7769 (mmm) REVERT: A 185 MET cc_start: 0.9202 (mpp) cc_final: 0.8996 (mpp) REVERT: LU 98 ASP cc_start: 0.9102 (p0) cc_final: 0.8894 (p0) REVERT: LR 31 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8077 (tp30) REVERT: LR 76 MET cc_start: 0.5479 (ttt) cc_final: 0.5138 (ttt) REVERT: 2 60 MET cc_start: 0.9300 (mmp) cc_final: 0.9084 (mmm) REVERT: B 13 LEU cc_start: 0.9132 (tt) cc_final: 0.8915 (tt) REVERT: B 21 TYR cc_start: 0.7405 (t80) cc_final: 0.7122 (t80) REVERT: B 51 MET cc_start: 0.6846 (tpt) cc_final: 0.6359 (ttt) REVERT: B 586 ASN cc_start: 0.9418 (p0) cc_final: 0.9151 (m110) REVERT: LC 189 MET cc_start: 0.8715 (mmp) cc_final: 0.8502 (mmp) REVERT: LC 231 ASN cc_start: 0.9048 (t0) cc_final: 0.8803 (t0) outliers start: 5 outliers final: 1 residues processed: 298 average time/residue: 0.2233 time to fit residues: 102.9934 Evaluate side-chains 217 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 2 optimal weight: 50.0000 chunk 64 optimal weight: 30.0000 chunk 202 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 283 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 50.0000 chunk 153 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 94 ASN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 94 ASN ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 212 ASN LC 236 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.083655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.071608 restraints weight = 464186.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.071566 restraints weight = 467407.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.072026 restraints weight = 402320.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.072079 restraints weight = 346353.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.072163 restraints weight = 332574.723| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32994 Z= 0.167 Angle : 0.659 11.298 46133 Z= 0.355 Chirality : 0.042 0.207 5386 Planarity : 0.005 0.059 4541 Dihedral : 21.676 155.291 8982 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 0.12 % Allowed : 4.12 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 2927 helix: 0.11 (0.13), residues: 1438 sheet: -0.74 (0.31), residues: 232 loop : -0.37 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGLY 17 TYR 0.058 0.002 TYR B 833 PHE 0.031 0.002 PHE B 32 TRP 0.046 0.003 TRP B 284 HIS 0.014 0.001 HISLY 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (32994) covalent geometry : angle 0.65947 / 0.36 (46133) hydrogen bonds : bond 0.06442 / 6.42 ( 1431) hydrogen bonds : angle 5.21173 / 5.60 ( 3789) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 287 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 VAL cc_start: 0.6226 (p) cc_final: 0.6004 (p) REVERT: LY 30 MET cc_start: 0.5042 (ptt) cc_final: 0.4834 (ptt) REVERT: LY 81 TYR cc_start: 0.7965 (m-80) cc_final: 0.7694 (m-80) REVERT: LY 100 HIS cc_start: 0.8000 (t-170) cc_final: 0.6851 (m90) REVERT: Lh 14 LYS cc_start: 0.9496 (pptt) cc_final: 0.9019 (mmtt) REVERT: Lh 43 LYS cc_start: 0.9644 (mppt) cc_final: 0.9356 (pptt) REVERT: LX 79 PHE cc_start: 0.9714 (p90) cc_final: 0.9459 (p90) REVERT: LX 99 ILE cc_start: 0.8756 (pt) cc_final: 0.8344 (tt) REVERT: A 75 LYS cc_start: 0.6531 (tptt) cc_final: 0.6273 (tptt) REVERT: A 80 MET cc_start: 0.8134 (mmp) cc_final: 0.7658 (mmm) REVERT: LU 23 LEU cc_start: 0.8598 (tt) cc_final: 0.8371 (tt) REVERT: LU 27 HIS cc_start: 0.9614 (m90) cc_final: 0.9403 (m90) REVERT: 2 93 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.6373 (pt0) REVERT: 2 147 MET cc_start: 0.7569 (mmp) cc_final: 0.7189 (mmm) REVERT: B 21 TYR cc_start: 0.7505 (t80) cc_final: 0.7121 (t80) REVERT: B 51 MET cc_start: 0.6648 (tpt) cc_final: 0.6112 (ttt) REVERT: B 254 ASN cc_start: 0.7466 (t0) cc_final: 0.7091 (t0) REVERT: B 586 ASN cc_start: 0.9454 (p0) cc_final: 0.9202 (m110) REVERT: B 712 MET cc_start: -0.0164 (ptp) cc_final: -0.0470 (ptt) REVERT: B 714 ARG cc_start: 0.8331 (mpt180) cc_final: 0.7808 (mpt180) REVERT: LC 150 LEU cc_start: 0.9333 (tt) cc_final: 0.9025 (tt) REVERT: LC 189 MET cc_start: 0.8770 (mmp) cc_final: 0.8551 (mmp) REVERT: LC 231 ASN cc_start: 0.9054 (t0) cc_final: 0.8808 (t0) REVERT: LC 252 TRP cc_start: 0.9311 (m-90) cc_final: 0.8947 (m-90) REVERT: LE 151 ILE cc_start: 0.8804 (mt) cc_final: 0.8517 (tp) REVERT: LE 167 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8503 (tp-100) outliers start: 3 outliers final: 0 residues processed: 290 average time/residue: 0.2259 time to fit residues: 102.3489 Evaluate side-chains 218 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 121 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 260 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 242 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 279 HIS E 283 ASN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LY 14 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 27 GLN ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 236 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.084187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.072424 restraints weight = 467022.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.072272 restraints weight = 467674.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.072526 restraints weight = 416095.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.072673 restraints weight = 351393.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.072723 restraints weight = 332676.578| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32994 Z= 0.140 Angle : 0.632 13.495 46133 Z= 0.337 Chirality : 0.041 0.312 5386 Planarity : 0.005 0.128 4541 Dihedral : 21.574 154.352 8982 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 2927 helix: 0.19 (0.13), residues: 1426 sheet: -0.64 (0.31), residues: 242 loop : -0.35 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 86 TYR 0.044 0.002 TYR B 833 PHE 0.026 0.002 PHELU 115 TRP 0.034 0.002 TRP B 284 HIS 0.010 0.001 HISLY 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (32994) covalent geometry : angle 0.63247 / 0.34 (46133) hydrogen bonds : bond 0.05582 / 5.48 ( 1431) hydrogen bonds : angle 5.02236 / 5.45 ( 3789) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 271 GLU cc_start: 0.8068 (pt0) cc_final: 0.7413 (pt0) REVERT: D 112 GLN cc_start: 0.8793 (pp30) cc_final: 0.8588 (pp30) REVERT: LY 30 MET cc_start: 0.4974 (ptt) cc_final: 0.4749 (ptt) REVERT: LY 74 TYR cc_start: 0.7472 (t80) cc_final: 0.6540 (t80) REVERT: LY 81 TYR cc_start: 0.7969 (m-80) cc_final: 0.7765 (m-80) REVERT: LY 100 HIS cc_start: 0.7643 (t-170) cc_final: 0.6889 (m170) REVERT: Lh 14 LYS cc_start: 0.9471 (pptt) cc_final: 0.8944 (mmtt) REVERT: Lh 43 LYS cc_start: 0.9625 (mppt) cc_final: 0.9334 (ptmm) REVERT: LX 79 PHE cc_start: 0.9691 (p90) cc_final: 0.9465 (p90) REVERT: A 75 LYS cc_start: 0.6637 (tptt) cc_final: 0.6373 (tptt) REVERT: A 80 MET cc_start: 0.8212 (mmp) cc_final: 0.7615 (mmm) REVERT: A 110 ASP cc_start: 0.7519 (m-30) cc_final: 0.7144 (m-30) REVERT: A 112 TYR cc_start: 0.8964 (m-80) cc_final: 0.8757 (m-80) REVERT: A 185 MET cc_start: 0.9044 (mpp) cc_final: 0.8800 (mpp) REVERT: LR 25 ASP cc_start: 0.7257 (m-30) cc_final: 0.6975 (m-30) REVERT: LR 76 MET cc_start: 0.4530 (ttt) cc_final: 0.1920 (tpt) REVERT: B 21 TYR cc_start: 0.7487 (t80) cc_final: 0.7069 (t80) REVERT: B 51 MET cc_start: 0.6748 (tpt) cc_final: 0.6239 (ttt) REVERT: B 91 ARG cc_start: 0.8899 (tpm170) cc_final: 0.8232 (tpt170) REVERT: B 119 ASP cc_start: 0.9501 (t70) cc_final: 0.9204 (t0) REVERT: B 273 MET cc_start: 0.4693 (ppp) cc_final: 0.4340 (ppp) REVERT: B 586 ASN cc_start: 0.9483 (p0) cc_final: 0.9256 (m110) REVERT: B 714 ARG cc_start: 0.8208 (mpt180) cc_final: 0.7779 (mpt180) REVERT: LC 189 MET cc_start: 0.8902 (mmp) cc_final: 0.8673 (mmp) REVERT: LC 231 ASN cc_start: 0.9018 (t0) cc_final: 0.8800 (t0) REVERT: LC 252 TRP cc_start: 0.9291 (m-90) cc_final: 0.8904 (m-90) REVERT: LE 151 ILE cc_start: 0.8827 (mt) cc_final: 0.8460 (tp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2346 time to fit residues: 102.8983 Evaluate side-chains 221 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 193 optimal weight: 50.0000 chunk 110 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 228 optimal weight: 30.0000 chunk 50 optimal weight: 40.0000 chunk 131 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 194 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 ASN E 203 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** LY 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 215 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.081529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.069916 restraints weight = 464365.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.069578 restraints weight = 483892.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.069896 restraints weight = 450963.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.069924 restraints weight = 418587.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.069920 restraints weight = 405768.534| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 32994 Z= 0.222 Angle : 0.766 18.112 46133 Z= 0.406 Chirality : 0.045 0.197 5386 Planarity : 0.006 0.111 4541 Dihedral : 21.799 152.050 8982 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.51 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2927 helix: -0.00 (0.13), residues: 1425 sheet: -0.67 (0.32), residues: 218 loop : -0.55 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARGLC 258 TYR 0.039 0.003 TYR B 833 PHE 0.049 0.003 PHE B 699 TRP 0.052 0.003 TRPLC 177 HIS 0.012 0.002 HISLY 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (32994) covalent geometry : angle 0.76619 / 0.41 (46133) hydrogen bonds : bond 0.08104 / 8.32 ( 1431) hydrogen bonds : angle 5.33345 / 5.79 ( 3789) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 329 MET cc_start: 0.4485 (mmm) cc_final: 0.3840 (mmm) REVERT: D 131 THR cc_start: 0.5069 (p) cc_final: 0.4399 (m) REVERT: LY 30 MET cc_start: 0.6067 (ptt) cc_final: 0.5855 (ptt) REVERT: LY 81 TYR cc_start: 0.8112 (m-80) cc_final: 0.7890 (m-80) REVERT: LY 100 HIS cc_start: 0.8095 (t-170) cc_final: 0.7408 (m-70) REVERT: Lh 14 LYS cc_start: 0.9597 (pptt) cc_final: 0.9181 (mmtt) REVERT: Lh 65 GLN cc_start: 0.9579 (mp10) cc_final: 0.9353 (mp-120) REVERT: LX 73 HIS cc_start: 0.8223 (p-80) cc_final: 0.8014 (p-80) REVERT: A 75 LYS cc_start: 0.6919 (tptt) cc_final: 0.6692 (tptt) REVERT: A 80 MET cc_start: 0.8418 (mmp) cc_final: 0.7456 (mmp) REVERT: A 110 ASP cc_start: 0.7628 (m-30) cc_final: 0.7212 (m-30) REVERT: A 112 TYR cc_start: 0.9052 (m-80) cc_final: 0.8729 (m-80) REVERT: A 185 MET cc_start: 0.9035 (mpp) cc_final: 0.8821 (mpp) REVERT: LR 25 ASP cc_start: 0.8000 (m-30) cc_final: 0.7781 (m-30) REVERT: LR 76 MET cc_start: 0.5076 (ttt) cc_final: 0.3361 (tpt) REVERT: B 21 TYR cc_start: 0.7673 (t80) cc_final: 0.7267 (t80) REVERT: B 51 MET cc_start: 0.6847 (tpt) cc_final: 0.6370 (ttt) REVERT: B 586 ASN cc_start: 0.9438 (p0) cc_final: 0.9205 (m110) REVERT: B 712 MET cc_start: 0.0551 (ptp) cc_final: 0.0323 (ptt) REVERT: B 714 ARG cc_start: 0.8313 (mpt180) cc_final: 0.7903 (mpt180) REVERT: LC 95 MET cc_start: 0.2807 (mmp) cc_final: 0.2603 (tpt) REVERT: LC 101 MET cc_start: 0.3023 (tpt) cc_final: 0.2672 (tpt) REVERT: LC 221 PHE cc_start: 0.9187 (m-10) cc_final: 0.8812 (m-80) REVERT: LC 231 ASN cc_start: 0.8901 (t0) cc_final: 0.8654 (t0) REVERT: LC 325 MET cc_start: 0.9175 (ptp) cc_final: 0.8728 (ptt) REVERT: LE 151 ILE cc_start: 0.9080 (mt) cc_final: 0.8850 (tp) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2355 time to fit residues: 105.0027 Evaluate side-chains 218 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 200 optimal weight: 0.0870 chunk 8 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 50.0000 chunk 37 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 chunk 120 optimal weight: 7.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 203 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 118 HIS ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN ** 2 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN B 435 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.081173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.070276 restraints weight = 465197.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.069898 restraints weight = 476640.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.070313 restraints weight = 402587.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.070192 restraints weight = 349959.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.070229 restraints weight = 347995.775| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 32994 Z= 0.187 Angle : 0.696 16.418 46133 Z= 0.371 Chirality : 0.043 0.261 5386 Planarity : 0.006 0.063 4541 Dihedral : 21.997 153.172 8982 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2927 helix: 0.02 (0.13), residues: 1427 sheet: -0.83 (0.33), residues: 225 loop : -0.55 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG B 622 TYR 0.030 0.002 TYRLX 74 PHE 0.035 0.002 PHE B 699 TRP 0.075 0.003 TRP B 284 HIS 0.011 0.001 HISLE 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (32994) covalent geometry : angle 0.69550 / 0.37 (46133) hydrogen bonds : bond 0.06557 / 6.54 ( 1431) hydrogen bonds : angle 5.22481 / 5.71 ( 3789) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 156 MET cc_start: 0.3976 (ttm) cc_final: 0.3609 (tmm) REVERT: LY 100 HIS cc_start: 0.7921 (t-170) cc_final: 0.7363 (m90) REVERT: Lh 14 LYS cc_start: 0.9610 (pptt) cc_final: 0.9158 (mmtt) REVERT: LX 116 LEU cc_start: 0.5420 (mm) cc_final: 0.4876 (mm) REVERT: A 75 LYS cc_start: 0.6908 (tptt) cc_final: 0.6640 (tptt) REVERT: A 80 MET cc_start: 0.8045 (mmp) cc_final: 0.7668 (mmm) REVERT: A 110 ASP cc_start: 0.7701 (m-30) cc_final: 0.7234 (m-30) REVERT: A 112 TYR cc_start: 0.9080 (m-80) cc_final: 0.8722 (m-80) REVERT: LR 25 ASP cc_start: 0.7975 (m-30) cc_final: 0.7728 (m-30) REVERT: LR 76 MET cc_start: 0.4614 (ttt) cc_final: 0.3253 (tpt) REVERT: 2 28 MET cc_start: 0.4455 (tpt) cc_final: 0.4253 (tpp) REVERT: 2 167 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8878 (mmtm) REVERT: B 21 TYR cc_start: 0.7874 (t80) cc_final: 0.7476 (t80) REVERT: B 51 MET cc_start: 0.7068 (tpt) cc_final: 0.6627 (ttt) REVERT: B 435 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6703 (tp40) REVERT: B 712 MET cc_start: 0.1231 (ptp) cc_final: 0.0827 (ptt) REVERT: B 714 ARG cc_start: 0.8326 (mpt180) cc_final: 0.7851 (mpt180) REVERT: LC 95 MET cc_start: 0.1760 (mmp) cc_final: 0.1408 (tpt) REVERT: LC 101 MET cc_start: 0.1821 (tpt) cc_final: 0.1437 (tpt) REVERT: LC 189 MET cc_start: 0.9084 (mmp) cc_final: 0.8756 (mmp) REVERT: LC 221 PHE cc_start: 0.9348 (m-10) cc_final: 0.9022 (m-80) REVERT: LC 325 MET cc_start: 0.9231 (ptp) cc_final: 0.8704 (ptt) REVERT: LE 151 ILE cc_start: 0.9180 (mt) cc_final: 0.8941 (tp) REVERT: Lr 96 MET cc_start: 0.5544 (mpp) cc_final: 0.5113 (mpp) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.2340 time to fit residues: 103.5714 Evaluate side-chains 222 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 288 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 309 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 110 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 183 optimal weight: 0.0170 chunk 66 optimal weight: 30.0000 overall best weight: 1.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 125 ASN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 190 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.075776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.058311 restraints weight = 379098.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.059594 restraints weight = 319464.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.059642 restraints weight = 262818.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.059842 restraints weight = 245851.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.059955 restraints weight = 238935.251| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.7075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 32994 Z= 0.137 Angle : 0.656 14.299 46133 Z= 0.349 Chirality : 0.041 0.223 5386 Planarity : 0.005 0.122 4541 Dihedral : 21.843 152.010 8982 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 2927 helix: 0.20 (0.13), residues: 1434 sheet: -0.67 (0.33), residues: 227 loop : -0.58 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 622 TYR 0.041 0.002 TYR 2 145 PHE 0.038 0.002 PHE B 699 TRP 0.055 0.003 TRP B 284 HIS 0.008 0.001 HIS 2 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (32994) covalent geometry : angle 0.65638 / 0.35 (46133) hydrogen bonds : bond 0.05665 / 5.59 ( 1431) hydrogen bonds : angle 5.08223 / 5.57 ( 3789) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 156 MET cc_start: 0.6202 (ttm) cc_final: 0.5488 (tmm) REVERT: LY 81 TYR cc_start: 0.8416 (m-80) cc_final: 0.8208 (m-80) REVERT: Lh 14 LYS cc_start: 0.9425 (pptt) cc_final: 0.9080 (mmtt) REVERT: Lh 43 LYS cc_start: 0.9439 (mppt) cc_final: 0.9204 (ptmt) REVERT: A 110 ASP cc_start: 0.7729 (m-30) cc_final: 0.7387 (m-30) REVERT: LR 25 ASP cc_start: 0.7105 (m-30) cc_final: 0.6887 (m-30) REVERT: LR 76 MET cc_start: 0.4735 (ttt) cc_final: 0.3924 (tpt) REVERT: LR 94 THR cc_start: 0.8336 (m) cc_final: 0.7949 (m) REVERT: 2 28 MET cc_start: 0.7903 (tpt) cc_final: 0.6897 (tpp) REVERT: B 21 TYR cc_start: 0.6783 (t80) cc_final: 0.6573 (t80) REVERT: B 51 MET cc_start: 0.6141 (tpt) cc_final: 0.5662 (ttt) REVERT: B 712 MET cc_start: 0.0872 (ptp) cc_final: 0.0461 (ptt) REVERT: B 714 ARG cc_start: 0.8307 (mpt180) cc_final: 0.8050 (mpt180) REVERT: LC 95 MET cc_start: 0.1672 (mmp) cc_final: 0.1322 (tpt) REVERT: LC 101 MET cc_start: 0.2161 (tpt) cc_final: 0.1866 (tpt) REVERT: LC 325 MET cc_start: 0.9156 (ptp) cc_final: 0.8722 (ptp) REVERT: Lr 96 MET cc_start: 0.6087 (mpp) cc_final: 0.5728 (mpp) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.2353 time to fit residues: 105.8210 Evaluate side-chains 226 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 298 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 296 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 105 ASN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 40 GLN ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 25 ASN 2 93 GLN 2 161 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.080946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.070004 restraints weight = 464624.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.069558 restraints weight = 464392.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.070079 restraints weight = 416325.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.069910 restraints weight = 364549.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.069947 restraints weight = 366729.013| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.7453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32994 Z= 0.164 Angle : 0.674 13.027 46133 Z= 0.360 Chirality : 0.041 0.201 5386 Planarity : 0.005 0.064 4541 Dihedral : 21.869 152.017 8982 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.51 % Favored : 95.35 % Rotamer: Outliers : 0.08 % Allowed : 1.04 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 2927 helix: 0.13 (0.13), residues: 1430 sheet: -0.72 (0.32), residues: 243 loop : -0.57 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 91 TYR 0.050 0.002 TYRLX 74 PHE 0.031 0.002 PHE E 382 TRP 0.051 0.002 TRP B 284 HIS 0.009 0.001 HISLE 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (32994) covalent geometry : angle 0.67416 / 0.36 (46133) hydrogen bonds : bond 0.06254 / 6.22 ( 1431) hydrogen bonds : angle 5.15450 / 5.74 ( 3789) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 156 MET cc_start: 0.3907 (ttm) cc_final: 0.3636 (tmm) REVERT: E 383 MET cc_start: 0.9252 (mpp) cc_final: 0.9033 (ptp) REVERT: LY 81 TYR cc_start: 0.8185 (m-80) cc_final: 0.7924 (m-80) REVERT: Lh 14 LYS cc_start: 0.9649 (pptt) cc_final: 0.9189 (mmtt) REVERT: LX 73 HIS cc_start: 0.8504 (p90) cc_final: 0.8163 (p90) REVERT: LX 79 PHE cc_start: 0.9742 (p90) cc_final: 0.9518 (p90) REVERT: LX 116 LEU cc_start: 0.5406 (mm) cc_final: 0.5145 (mm) REVERT: A 75 LYS cc_start: 0.7074 (tptt) cc_final: 0.6811 (tptp) REVERT: A 80 MET cc_start: 0.7902 (mmp) cc_final: 0.7403 (mmm) REVERT: A 110 ASP cc_start: 0.7831 (m-30) cc_final: 0.7275 (m-30) REVERT: A 112 TYR cc_start: 0.9159 (m-80) cc_final: 0.8759 (m-80) REVERT: LR 25 ASP cc_start: 0.7950 (m-30) cc_final: 0.7656 (m-30) REVERT: LR 76 MET cc_start: 0.5072 (ttt) cc_final: 0.3870 (tpt) REVERT: LR 94 THR cc_start: 0.8473 (m) cc_final: 0.8109 (m) REVERT: 2 60 MET cc_start: 0.8980 (mmm) cc_final: 0.8777 (mmm) REVERT: B 21 TYR cc_start: 0.7876 (t80) cc_final: 0.7464 (t80) REVERT: B 51 MET cc_start: 0.7233 (tpt) cc_final: 0.6791 (ttt) REVERT: B 586 ASN cc_start: 0.9428 (p0) cc_final: 0.9225 (m110) REVERT: B 712 MET cc_start: 0.1009 (ptp) cc_final: 0.0661 (ptt) REVERT: B 714 ARG cc_start: 0.8227 (mpt180) cc_final: 0.7738 (mpt180) REVERT: LC 95 MET cc_start: 0.1302 (mmp) cc_final: 0.0998 (tpt) REVERT: LC 101 MET cc_start: 0.2377 (tpt) cc_final: 0.1977 (tpt) REVERT: LC 189 MET cc_start: 0.9028 (mmp) cc_final: 0.8698 (mmp) REVERT: LC 221 PHE cc_start: 0.9511 (m-10) cc_final: 0.9155 (m-80) REVERT: LC 252 TRP cc_start: 0.9340 (m-90) cc_final: 0.8967 (m-90) REVERT: LC 325 MET cc_start: 0.9288 (ptp) cc_final: 0.8661 (ptp) REVERT: Lr 96 MET cc_start: 0.6227 (mpp) cc_final: 0.5792 (mpp) outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 0.2243 time to fit residues: 100.0677 Evaluate side-chains 224 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 103 optimal weight: 5.9990 chunk 268 optimal weight: 40.0000 chunk 104 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 51 optimal weight: 50.0000 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 ASN ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS B 80 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 205 ASN ** Lr 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.078999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.068081 restraints weight = 469923.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.067313 restraints weight = 469195.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.067646 restraints weight = 419968.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.067627 restraints weight = 373000.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.067671 restraints weight = 366904.342| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32994 Z= 0.208 Angle : 0.763 20.972 46133 Z= 0.409 Chirality : 0.044 0.270 5386 Planarity : 0.006 0.104 4541 Dihedral : 22.139 151.304 8982 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 28.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 2927 helix: -0.07 (0.13), residues: 1414 sheet: -0.87 (0.33), residues: 220 loop : -0.81 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 622 TYR 0.043 0.003 TYRLX 74 PHE 0.030 0.002 PHE E 382 TRP 0.048 0.003 TRP B 284 HIS 0.015 0.002 HIS B 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (32994) covalent geometry : angle 0.76316 / 0.41 (46133) hydrogen bonds : bond 0.07756 / 7.85 ( 1431) hydrogen bonds : angle 5.43996 / 5.99 ( 3789) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 156 MET cc_start: 0.4222 (ttm) cc_final: 0.3921 (tmm) REVERT: LY 81 TYR cc_start: 0.8150 (m-80) cc_final: 0.7949 (m-80) REVERT: Lh 14 LYS cc_start: 0.9664 (pptt) cc_final: 0.9192 (mmtt) REVERT: LX 73 HIS cc_start: 0.8684 (p90) cc_final: 0.8388 (p90) REVERT: LX 123 LYS cc_start: 0.7977 (ptmt) cc_final: 0.7594 (pptt) REVERT: A 78 LYS cc_start: 0.8547 (mttt) cc_final: 0.8223 (pttt) REVERT: A 80 MET cc_start: 0.8510 (mmp) cc_final: 0.7654 (mmm) REVERT: A 110 ASP cc_start: 0.7889 (m-30) cc_final: 0.7462 (m-30) REVERT: A 112 TYR cc_start: 0.9115 (m-80) cc_final: 0.8848 (m-80) REVERT: A 121 ILE cc_start: 0.8875 (pt) cc_final: 0.8663 (pt) REVERT: LR 25 ASP cc_start: 0.8255 (m-30) cc_final: 0.8038 (m-30) REVERT: LR 30 ASN cc_start: 0.7832 (p0) cc_final: 0.7261 (p0) REVERT: LR 31 GLU cc_start: 0.9330 (mp0) cc_final: 0.8747 (tp30) REVERT: LR 76 MET cc_start: 0.5751 (ttt) cc_final: 0.4931 (tpt) REVERT: LR 94 THR cc_start: 0.8747 (m) cc_final: 0.8479 (m) REVERT: 2 28 MET cc_start: 0.6106 (tpt) cc_final: 0.5729 (tpp) REVERT: B 21 TYR cc_start: 0.7808 (t80) cc_final: 0.7364 (t80) REVERT: B 51 MET cc_start: 0.7479 (tpt) cc_final: 0.7026 (ttt) REVERT: B 712 MET cc_start: 0.1461 (ptp) cc_final: 0.1154 (ptt) REVERT: B 714 ARG cc_start: 0.8346 (mpt180) cc_final: 0.7908 (mpt180) REVERT: LC 95 MET cc_start: 0.0415 (mmp) cc_final: -0.0241 (tpt) REVERT: LC 221 PHE cc_start: 0.9606 (m-10) cc_final: 0.9322 (m-80) REVERT: LC 325 MET cc_start: 0.9206 (ptp) cc_final: 0.8551 (ptp) REVERT: LE 288 PHE cc_start: 0.7955 (m-80) cc_final: 0.7601 (m-80) REVERT: Lr 96 MET cc_start: 0.6061 (mpp) cc_final: 0.5780 (mpp) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2357 time to fit residues: 102.1149 Evaluate side-chains 212 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 193 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 271 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 170 optimal weight: 0.0270 chunk 38 optimal weight: 0.6980 chunk 262 optimal weight: 9.9990 overall best weight: 2.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 HIS ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 14 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.079672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.068194 restraints weight = 468728.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.067669 restraints weight = 473934.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067970 restraints weight = 437014.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.067983 restraints weight = 376518.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.068072 restraints weight = 369815.894| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.8541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32994 Z= 0.156 Angle : 0.691 12.449 46133 Z= 0.369 Chirality : 0.042 0.207 5386 Planarity : 0.005 0.063 4541 Dihedral : 22.071 152.300 8982 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 2927 helix: 0.02 (0.13), residues: 1420 sheet: -1.17 (0.31), residues: 246 loop : -0.78 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 91 TYR 0.042 0.002 TYRLX 74 PHE 0.031 0.002 PHE E 382 TRP 0.047 0.003 TRP B 284 HIS 0.008 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (32994) covalent geometry : angle 0.69069 / 0.37 (46133) hydrogen bonds : bond 0.06295 / 6.25 ( 1431) hydrogen bonds : angle 5.30600 / 5.83 ( 3789) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6778.76 seconds wall clock time: 118 minutes 32.67 seconds (7112.67 seconds total)