Starting phenix.real_space_refine on Mon Aug 25 23:15:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fq0_50642/08_2025/9fq0_50642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fq0_50642/08_2025/9fq0_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fq0_50642/08_2025/9fq0_50642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fq0_50642/08_2025/9fq0_50642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fq0_50642/08_2025/9fq0_50642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fq0_50642/08_2025/9fq0_50642.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 6.51, per 1000 atoms: 0.21 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: 2.76 Conformation dependent library (CDL) restraints added in 978.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.36 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: 8.23 Time building geometry restraints manager: 3.86 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=" 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=" CA METLR 139 " pdb=" CB METLR 139 " pdb=" CG METLR 139 " ideal model delta sigma weight residual 114.10 127.59 -13.49 2.00e+00 2.50e-01 4.55e+01 angle pdb=" CA LYS B 829 " pdb=" CB LYS B 829 " pdb=" CG LYS B 829 " ideal model delta sigma weight residual 114.10 127.39 -13.29 2.00e+00 2.50e-01 4.41e+01 angle pdb=" C3' C 1 456 " pdb=" O3' C 1 456 " pdb=" P G 1 457 " ideal model delta sigma weight residual 120.20 110.72 9.48 1.50e+00 4.44e-01 4.00e+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: 23.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 31.900 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4669 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= 0.257 Angle : 1.095 26.938 46133 Z= 0.579 Chirality : 0.132 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 aren 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 covalent geometry : bond 0.00534 (32994) covalent geometry : angle 1.09540 (46133) hydrogen bonds : bond 0.21382 ( 1431) hydrogen bonds : angle 7.26970 ( 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 : 1.124 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: 0.8953 (mm) REVERT: E 329 MET cc_start: 0.2878 (mpp) cc_final: 0.2226 (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: 0.3821 (pp) REVERT: Lh 109 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7505 (ptt180) REVERT: A 211 MET cc_start: 0.7037 (mmp) cc_final: 0.6478 (ptp) REVERT: LU 20 LYS cc_start: 0.2915 (OUTLIER) cc_final: 0.1388 (tppt) REVERT: LU 46 ARG cc_start: 0.5939 (ttm110) cc_final: 0.4529 (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: 0.8135 (t0) REVERT: LR 89 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.6139 (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: 0.2518 (mtm) REVERT: LE 151 ILE cc_start: 0.7892 (mt) cc_final: 0.7490 (tp) REVERT: LE 240 TYR cc_start: -0.1465 (OUTLIER) cc_final: -0.2627 (t80) REVERT: Lr 8 MET cc_start: -0.1947 (mmm) cc_final: -0.2238 (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: 0.2451 time to fit residues: 152.7073 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 : 1.098 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: E 198 ASN ** E 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 ASN ** E 279 HIS ** 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 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 73 HIS LX 93 ASN ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** LR 27 ASN 2 15 GLN ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 49 ASN ** 2 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 93 GLN ** 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 383 HIS 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 738 ASN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 21 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 4 HIS Lr 95 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.083708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.072555 restraints weight = 463254.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.072476 restraints weight = 520261.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.072861 restraints weight = 434366.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.072657 restraints weight = 375495.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.072695 restraints weight = 367789.892| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 32994 Z= 0.291 Angle : 0.911 11.320 46133 Z= 0.463 Chirality : 0.047 0.265 5386 Planarity : 0.008 0.100 4541 Dihedral : 21.826 152.743 8982 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 27.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.03 % Favored : 95.80 % Rotamer: Outliers : 0.42 % Allowed : 5.65 % Favored : 93.92 % 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 aren not related in a simple way. whole: -0.54 (0.15), residues: 2927 helix: -0.18 (0.13), residues: 1439 sheet: -0.40 (0.33), residues: 223 loop : -0.37 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG B 714 TYR 0.043 0.003 TYRLE 116 PHE 0.024 0.003 PHELr 16 TRP 0.050 0.003 TRP B 284 HIS 0.010 0.002 HIS E 301 Details of bonding type rmsd covalent geometry : bond 0.00584 (32994) covalent geometry : angle 0.91080 (46133) hydrogen bonds : bond 0.08366 ( 1431) hydrogen bonds : angle 5.63996 ( 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 326 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 315 time to evaluate : 1.133 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: E 268 ARG cc_start: 0.9453 (mtp-110) cc_final: 0.9206 (mmm-85) REVERT: E 317 VAL cc_start: 0.9157 (p) cc_final: 0.8325 (p) REVERT: D 77 VAL cc_start: 0.8922 (m) cc_final: 0.8569 (t) REVERT: D 92 LEU cc_start: 0.7138 (mt) cc_final: 0.6396 (pp) REVERT: LY 30 MET cc_start: 0.4789 (ptt) cc_final: 0.4572 (ptt) REVERT: LY 74 TYR cc_start: 0.7564 (t80) cc_final: 0.7242 (t80) REVERT: LY 81 TYR cc_start: 0.7777 (m-10) cc_final: 0.7575 (m-80) REVERT: LY 100 HIS cc_start: 0.7764 (t70) cc_final: 0.7370 (m90) REVERT: Lh 14 LYS cc_start: 0.9600 (pptt) cc_final: 0.9050 (mmtt) REVERT: Lh 43 LYS cc_start: 0.9649 (mppt) cc_final: 0.9327 (pptt) REVERT: LX 90 ILE cc_start: 0.8388 (mm) cc_final: 0.8127 (mp) REVERT: LX 99 ILE cc_start: 0.9152 (pt) cc_final: 0.8868 (tt) REVERT: A 80 MET cc_start: 0.7733 (mmp) cc_final: 0.6822 (mmm) REVERT: A 110 ASP cc_start: 0.7717 (m-30) cc_final: 0.7367 (m-30) REVERT: LR 76 MET cc_start: 0.5756 (ttt) cc_final: 0.5049 (ttt) REVERT: LR 93 VAL cc_start: 0.8529 (t) cc_final: 0.7771 (t) REVERT: LR 142 ILE cc_start: 0.9417 (tt) cc_final: 0.9208 (tp) REVERT: 2 28 MET cc_start: 0.4203 (tpt) cc_final: 0.3845 (tpt) REVERT: B 21 TYR cc_start: 0.7571 (t80) cc_final: 0.7295 (t80) REVERT: B 51 MET cc_start: 0.6765 (tpt) cc_final: 0.6230 (ttt) REVERT: B 705 HIS cc_start: 0.8322 (t-90) cc_final: 0.8113 (t70) REVERT: LC 231 ASN cc_start: 0.9041 (t0) cc_final: 0.8689 (t0) REVERT: LC 252 TRP cc_start: 0.9262 (m-90) cc_final: 0.8970 (m-90) REVERT: LC 258 ARG cc_start: 0.9559 (mtm-85) cc_final: 0.9337 (mtt-85) REVERT: LE 151 ILE cc_start: 0.8713 (mt) cc_final: 0.8413 (tp) outliers start: 11 outliers final: 0 residues processed: 326 average time/residue: 0.2584 time to fit residues: 126.3902 Evaluate side-chains 232 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 8.9990 chunk 166 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 178 ASN E 188 ASN E 203 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 GLN ** 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** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 14 ASN ** LY 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 107 HIS ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 116 GLN ** LR 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 118 HIS 2 25 ASN ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN ** 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 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 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN Lr 6 GLN ** Lr 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.078965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.068312 restraints weight = 475740.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.067561 restraints weight = 520051.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.068099 restraints weight = 448352.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067971 restraints weight = 386584.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067964 restraints weight = 380723.146| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 32994 Z= 0.316 Angle : 0.969 13.589 46133 Z= 0.497 Chirality : 0.049 0.350 5386 Planarity : 0.008 0.187 4541 Dihedral : 22.636 157.832 8982 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 32.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.58 % Favored : 95.25 % Rotamer: Outliers : 0.38 % Allowed : 7.77 % Favored : 91.85 % 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 aren not related in a simple way. whole: -1.00 (0.15), residues: 2927 helix: -0.45 (0.13), residues: 1431 sheet: -0.96 (0.32), residues: 210 loop : -0.69 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARGLC 71 TYR 0.037 0.003 TYRLC 331 PHE 0.080 0.004 PHE B 699 TRP 0.030 0.004 TRPLR 95 HIS 0.013 0.003 HIS E 111 Details of bonding type rmsd covalent geometry : bond 0.00639 (32994) covalent geometry : angle 0.96905 (46133) hydrogen bonds : bond 0.09597 ( 1431) hydrogen bonds : angle 5.80167 ( 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 323 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 313 time to evaluate : 1.180 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: D 92 LEU cc_start: 0.8482 (mt) cc_final: 0.8198 (pp) REVERT: LY 30 MET cc_start: 0.6784 (ptt) cc_final: 0.6557 (ptt) REVERT: LY 74 TYR cc_start: 0.7661 (t80) cc_final: 0.6840 (t80) REVERT: Lh 14 LYS cc_start: 0.9649 (pptt) cc_final: 0.9181 (mmtt) REVERT: A 80 MET cc_start: 0.8732 (mmp) cc_final: 0.8321 (mmm) REVERT: A 110 ASP cc_start: 0.7794 (m-30) cc_final: 0.7185 (m-30) REVERT: A 112 TYR cc_start: 0.9090 (m-80) cc_final: 0.8794 (m-80) REVERT: LR 31 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8528 (tp30) REVERT: LR 76 MET cc_start: 0.5482 (ttt) cc_final: 0.3629 (tpt) REVERT: 2 28 MET cc_start: 0.5861 (tpt) cc_final: 0.5224 (tpp) REVERT: 2 60 MET cc_start: 0.9248 (mmp) cc_final: 0.8966 (mmm) REVERT: 2 93 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6490 (pt0) REVERT: B 21 TYR cc_start: 0.7910 (t80) cc_final: 0.7461 (t80) REVERT: B 51 MET cc_start: 0.7114 (tpt) cc_final: 0.6894 (tpt) REVERT: B 116 ILE cc_start: -0.3728 (OUTLIER) cc_final: -0.4228 (mt) REVERT: B 528 TYR cc_start: 0.7545 (t80) cc_final: 0.7218 (t80) REVERT: B 586 ASN cc_start: 0.9373 (p0) cc_final: 0.9153 (m110) REVERT: B 712 MET cc_start: 0.1147 (ptp) cc_final: 0.0840 (ptp) REVERT: LC 101 MET cc_start: 0.3268 (tpt) cc_final: 0.2943 (tpt) REVERT: LE 68 MET cc_start: 0.9635 (mpp) cc_final: 0.9419 (mpp) outliers start: 10 outliers final: 1 residues processed: 322 average time/residue: 0.2478 time to fit residues: 122.1685 Evaluate side-chains 240 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 237 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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: 20.0000 chunk 64 optimal weight: 10.0000 chunk 202 optimal weight: 30.0000 chunk 209 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 160 optimal weight: 40.0000 chunk 283 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN E 229 HIS ** 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 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 130 ASN ** LY 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 208 ASN ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN ** 2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 161 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 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 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 212 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.077544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.065804 restraints weight = 473562.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.065434 restraints weight = 473042.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.065693 restraints weight = 436412.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.065635 restraints weight = 392462.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.065690 restraints weight = 373384.844| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.8939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 32994 Z= 0.290 Angle : 0.875 14.087 46133 Z= 0.447 Chirality : 0.047 0.274 5386 Planarity : 0.007 0.124 4541 Dihedral : 22.840 152.102 8982 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 32.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 0.19 % Allowed : 5.08 % Favored : 94.73 % 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 aren not related in a simple way. whole: -1.27 (0.15), residues: 2927 helix: -0.53 (0.12), residues: 1442 sheet: -1.16 (0.31), residues: 225 loop : -1.00 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 16 TYR 0.042 0.003 TYR B 833 PHE 0.023 0.003 PHELU 21 TRP 0.070 0.004 TRP B 284 HIS 0.012 0.002 HIS E 301 Details of bonding type rmsd covalent geometry : bond 0.00572 (32994) covalent geometry : angle 0.87535 (46133) hydrogen bonds : bond 0.08263 ( 1431) hydrogen bonds : angle 5.75290 ( 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 302 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 297 time to evaluate : 0.776 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: D 92 LEU cc_start: 0.8713 (mt) cc_final: 0.8270 (tp) REVERT: LY 74 TYR cc_start: 0.7555 (t80) cc_final: 0.6665 (t80) REVERT: LY 81 TYR cc_start: 0.8273 (m-80) cc_final: 0.8017 (m-80) REVERT: Lh 14 LYS cc_start: 0.9682 (pptt) cc_final: 0.9239 (mmtt) REVERT: A 75 LYS cc_start: 0.7892 (tptt) cc_final: 0.7618 (tptp) REVERT: A 80 MET cc_start: 0.8457 (mmp) cc_final: 0.7719 (mmm) REVERT: A 110 ASP cc_start: 0.7922 (m-30) cc_final: 0.7460 (m-30) REVERT: A 112 TYR cc_start: 0.9053 (m-80) cc_final: 0.8828 (m-80) REVERT: A 121 ILE cc_start: 0.8772 (pt) cc_final: 0.8437 (pt) REVERT: LR 25 ASP cc_start: 0.8646 (m-30) cc_final: 0.8396 (m-30) REVERT: LR 31 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8443 (tp30) REVERT: LR 76 MET cc_start: 0.6481 (ttt) cc_final: 0.5371 (tpt) REVERT: LR 151 ARG cc_start: 0.9450 (mmp80) cc_final: 0.9230 (tpm170) REVERT: 2 28 MET cc_start: 0.7035 (tpt) cc_final: 0.6227 (tpp) REVERT: 2 93 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6399 (pp30) REVERT: B 21 TYR cc_start: 0.7872 (t80) cc_final: 0.7523 (t80) REVERT: B 51 MET cc_start: 0.7363 (tpt) cc_final: 0.7072 (tpt) REVERT: B 714 ARG cc_start: 0.8491 (mpt180) cc_final: 0.8051 (mpt180) REVERT: LC 252 TRP cc_start: 0.9387 (m-90) cc_final: 0.9102 (m-90) REVERT: LC 262 GLU cc_start: 0.9475 (pp20) cc_final: 0.9238 (pm20) REVERT: LC 273 LEU cc_start: 0.8349 (mt) cc_final: 0.8141 (mt) REVERT: LC 325 MET cc_start: 0.9100 (ptp) cc_final: 0.8607 (ptm) REVERT: LC 335 MET cc_start: 0.5309 (mtp) cc_final: 0.5035 (mtp) outliers start: 5 outliers final: 0 residues processed: 302 average time/residue: 0.2026 time to fit residues: 93.2925 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 : 0.789 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 275 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 286 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN LY 56 GLN ** LY 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 65 GLN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 HIS ** 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 480 ASN ** 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 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.077549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.066268 restraints weight = 474532.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.065701 restraints weight = 475377.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.066246 restraints weight = 411006.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.066141 restraints weight = 366702.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.066211 restraints weight = 362570.028| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.9488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32994 Z= 0.197 Angle : 0.752 17.931 46133 Z= 0.384 Chirality : 0.043 0.184 5386 Planarity : 0.006 0.083 4541 Dihedral : 22.691 153.863 8982 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 0.12 % Allowed : 4.35 % Favored : 95.54 % 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 aren not related in a simple way. whole: -1.10 (0.15), residues: 2927 helix: -0.29 (0.13), residues: 1426 sheet: -1.17 (0.32), residues: 213 loop : -1.02 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 268 TYR 0.034 0.002 TYR B 833 PHE 0.030 0.002 PHE B 699 TRP 0.032 0.003 TRP B 284 HIS 0.008 0.001 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00406 (32994) covalent geometry : angle 0.75247 (46133) hydrogen bonds : bond 0.06935 ( 1431) hydrogen bonds : angle 5.49028 ( 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 307 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 304 time to evaluate : 0.826 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: 0.3176 (mmt) cc_final: 0.2772 (mmm) REVERT: D 92 LEU cc_start: 0.8727 (mt) cc_final: 0.8394 (pp) REVERT: LY 74 TYR cc_start: 0.7404 (t80) cc_final: 0.6886 (t80) REVERT: Lh 14 LYS cc_start: 0.9722 (pptt) cc_final: 0.9304 (mmtt) REVERT: Lh 28 LEU cc_start: 0.9734 (tt) cc_final: 0.9493 (pp) REVERT: A 75 LYS cc_start: 0.8018 (tptt) cc_final: 0.7754 (tptp) REVERT: A 80 MET cc_start: 0.8797 (mmp) cc_final: 0.8178 (mmm) REVERT: A 110 ASP cc_start: 0.7974 (m-30) cc_final: 0.7470 (m-30) REVERT: A 112 TYR cc_start: 0.9096 (m-80) cc_final: 0.8818 (m-80) REVERT: A 121 ILE cc_start: 0.8975 (pt) cc_final: 0.8503 (pt) REVERT: A 185 MET cc_start: 0.9151 (mpp) cc_final: 0.8918 (mpp) REVERT: LR 25 ASP cc_start: 0.8723 (m-30) cc_final: 0.8453 (m-30) REVERT: LR 70 ARG cc_start: 0.8325 (tmm160) cc_final: 0.7872 (mmm-85) REVERT: LR 76 MET cc_start: 0.5703 (ttt) cc_final: 0.4904 (tpt) REVERT: 2 28 MET cc_start: 0.6969 (tpt) cc_final: 0.5938 (tpp) REVERT: 2 29 LYS cc_start: 0.9560 (tptp) cc_final: 0.9235 (tppt) REVERT: 2 30 TYR cc_start: 0.9672 (m-80) cc_final: 0.9469 (m-80) REVERT: 2 93 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.6069 (pp30) REVERT: B 9 LYS cc_start: 0.8072 (tptt) cc_final: 0.7763 (tppt) REVERT: B 21 TYR cc_start: 0.7961 (t80) cc_final: 0.7479 (t80) REVERT: B 51 MET cc_start: 0.7449 (tpt) cc_final: 0.7114 (tpt) REVERT: B 254 ASN cc_start: 0.7287 (t0) cc_final: 0.7083 (t0) REVERT: B 714 ARG cc_start: 0.8675 (mpt180) cc_final: 0.8390 (mpt180) REVERT: LC 262 GLU cc_start: 0.9519 (pp20) cc_final: 0.9277 (pm20) REVERT: LC 325 MET cc_start: 0.9196 (ptp) cc_final: 0.8716 (ptm) REVERT: LC 335 MET cc_start: 0.4899 (mtp) cc_final: 0.4621 (mtp) REVERT: LE 205 ASN cc_start: 0.9015 (p0) cc_final: 0.8779 (p0) outliers start: 3 outliers final: 2 residues processed: 306 average time/residue: 0.1916 time to fit residues: 90.1217 Evaluate side-chains 227 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 224 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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: 8.9990 chunk 110 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 211 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 305 ASN E 308 HIS ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 124 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 14 ASN ** LY 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 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** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS B 105 ASN ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** 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 675 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** ** LE 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.077729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.066192 restraints weight = 471196.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.065912 restraints weight = 487276.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.066004 restraints weight = 449573.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.066036 restraints weight = 381431.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.066096 restraints weight = 358358.773| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.9904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32994 Z= 0.182 Angle : 0.731 13.386 46133 Z= 0.374 Chirality : 0.042 0.264 5386 Planarity : 0.006 0.080 4541 Dihedral : 22.612 152.886 8982 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.64 % Rotamer: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.77 % 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 aren not related in a simple way. whole: -0.97 (0.15), residues: 2927 helix: -0.14 (0.13), residues: 1425 sheet: -1.15 (0.33), residues: 206 loop : -1.01 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGLR 100 TYR 0.047 0.002 TYR B 86 PHE 0.022 0.002 PHE B 32 TRP 0.065 0.003 TRP B 284 HIS 0.008 0.001 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00376 (32994) covalent geometry : angle 0.73061 (46133) hydrogen bonds : bond 0.06590 ( 1431) hydrogen bonds : angle 5.44926 ( 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 303 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 300 time to evaluate : 1.084 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: E 329 MET cc_start: 0.4149 (mmt) cc_final: 0.3613 (mmm) REVERT: D 92 LEU cc_start: 0.8784 (mt) cc_final: 0.8266 (tp) REVERT: D 131 THR cc_start: 0.3398 (m) cc_final: 0.2938 (m) REVERT: Lh 14 LYS cc_start: 0.9719 (pptt) cc_final: 0.9299 (mmtt) REVERT: Lh 73 TYR cc_start: 0.9425 (m-80) cc_final: 0.9149 (m-10) REVERT: A 75 LYS cc_start: 0.8076 (tptt) cc_final: 0.7817 (tptp) REVERT: A 80 MET cc_start: 0.8562 (mmp) cc_final: 0.7800 (mmm) REVERT: A 110 ASP cc_start: 0.7923 (m-30) cc_final: 0.7510 (m-30) REVERT: A 121 ILE cc_start: 0.8998 (pt) cc_final: 0.8543 (pt) REVERT: LR 30 ASN cc_start: 0.8172 (p0) cc_final: 0.7869 (p0) REVERT: LR 70 ARG cc_start: 0.8282 (tmm160) cc_final: 0.7596 (mmm-85) REVERT: LR 76 MET cc_start: 0.5916 (ttt) cc_final: 0.4994 (tpt) REVERT: 2 28 MET cc_start: 0.7398 (tpt) cc_final: 0.6074 (tpp) REVERT: 2 29 LYS cc_start: 0.9567 (tptp) cc_final: 0.9087 (mmmt) REVERT: 2 60 MET cc_start: 0.9305 (mmp) cc_final: 0.8940 (mmm) REVERT: 2 93 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5720 (pp30) REVERT: B 9 LYS cc_start: 0.8130 (tptt) cc_final: 0.7836 (tppt) REVERT: B 21 TYR cc_start: 0.7914 (t80) cc_final: 0.7405 (t80) REVERT: B 51 MET cc_start: 0.7505 (tpt) cc_final: 0.7109 (tpt) REVERT: B 68 LEU cc_start: 0.9572 (tp) cc_final: 0.9367 (tp) REVERT: B 431 MET cc_start: 0.7286 (mmp) cc_final: 0.7035 (mmp) REVERT: B 528 TYR cc_start: 0.7629 (t80) cc_final: 0.7414 (t80) REVERT: B 714 ARG cc_start: 0.8727 (mpt180) cc_final: 0.8396 (mmt-90) REVERT: LC 138 MET cc_start: 0.9450 (tmm) cc_final: 0.9164 (tmm) REVERT: LC 152 LEU cc_start: 0.8971 (mt) cc_final: 0.8598 (mt) REVERT: LC 252 TRP cc_start: 0.9301 (m-90) cc_final: 0.9088 (m-90) REVERT: LC 262 GLU cc_start: 0.9536 (pp20) cc_final: 0.9297 (pm20) REVERT: LC 325 MET cc_start: 0.9126 (ptp) cc_final: 0.8612 (ptm) REVERT: LC 335 MET cc_start: 0.4906 (mtp) cc_final: 0.4644 (mtp) REVERT: LE 205 ASN cc_start: 0.9052 (p0) cc_final: 0.8805 (p0) outliers start: 3 outliers final: 1 residues processed: 303 average time/residue: 0.2259 time to fit residues: 105.0748 Evaluate side-chains 219 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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: 7.9990 chunk 8 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 218 ASN ** 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 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 62 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 27 GLN 2 93 GLN 2 161 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** 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 580 HIS ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 61 GLN LC 236 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 256 GLN ** 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 = 0.3811 r_free = 0.3811 target = 0.075929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064359 restraints weight = 477616.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.064102 restraints weight = 465795.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.064372 restraints weight = 421471.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.064361 restraints weight = 367248.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.064457 restraints weight = 364574.606| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 1.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 32994 Z= 0.240 Angle : 0.813 10.935 46133 Z= 0.416 Chirality : 0.044 0.281 5386 Planarity : 0.006 0.077 4541 Dihedral : 22.786 151.854 8982 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 32.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.25 % Favored : 93.65 % Rotamer: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.27 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: -1.18 (0.15), residues: 2927 helix: -0.26 (0.13), residues: 1431 sheet: -1.50 (0.33), residues: 215 loop : -1.15 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARGLC 71 TYR 0.040 0.003 TYRLX 74 PHE 0.024 0.003 PHE E 386 TRP 0.043 0.003 TRP B 284 HIS 0.012 0.002 HIS 2 120 Details of bonding type rmsd covalent geometry : bond 0.00498 (32994) covalent geometry : angle 0.81317 (46133) hydrogen bonds : bond 0.08019 ( 1431) hydrogen bonds : angle 5.60074 ( 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 290 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 288 time to evaluate : 1.127 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: E 329 MET cc_start: 0.4944 (mmt) cc_final: 0.4357 (mmm) REVERT: D 92 LEU cc_start: 0.8820 (mt) cc_final: 0.8341 (tp) REVERT: LY 74 TYR cc_start: 0.7331 (t80) cc_final: 0.6510 (t80) REVERT: Lh 73 TYR cc_start: 0.9432 (m-80) cc_final: 0.9232 (m-10) REVERT: A 75 LYS cc_start: 0.8206 (tptt) cc_final: 0.7951 (tptp) REVERT: A 80 MET cc_start: 0.8885 (mmp) cc_final: 0.8111 (mmp) REVERT: A 110 ASP cc_start: 0.8028 (m-30) cc_final: 0.7614 (m-30) REVERT: A 121 ILE cc_start: 0.8953 (pt) cc_final: 0.8735 (pt) REVERT: LR 25 ASP cc_start: 0.8903 (m-30) cc_final: 0.8648 (m-30) REVERT: LR 31 GLU cc_start: 0.8841 (tp30) cc_final: 0.8436 (tp30) REVERT: LR 70 ARG cc_start: 0.8426 (tmm160) cc_final: 0.7971 (mmm-85) REVERT: LR 76 MET cc_start: 0.5938 (ttt) cc_final: 0.5612 (tpt) REVERT: LR 137 ILE cc_start: 0.9552 (mp) cc_final: 0.8744 (mp) REVERT: 2 28 MET cc_start: 0.7571 (tpt) cc_final: 0.6583 (tpp) REVERT: 2 29 LYS cc_start: 0.9628 (tptp) cc_final: 0.9315 (mmmt) REVERT: 2 60 MET cc_start: 0.9362 (mmp) cc_final: 0.8913 (mmm) REVERT: B 9 LYS cc_start: 0.8502 (tptt) cc_final: 0.8244 (tppt) REVERT: B 21 TYR cc_start: 0.8255 (t80) cc_final: 0.7746 (t80) REVERT: B 51 MET cc_start: 0.7665 (tpt) cc_final: 0.7221 (tpt) REVERT: B 431 MET cc_start: 0.7437 (mmp) cc_final: 0.7149 (mmp) REVERT: B 712 MET cc_start: 0.1432 (ptp) cc_final: 0.0988 (ptp) REVERT: LC 138 MET cc_start: 0.9613 (tmm) cc_final: 0.9405 (tmm) REVERT: LC 258 ARG cc_start: 0.9598 (mtm-85) cc_final: 0.9363 (mtt-85) REVERT: LC 310 HIS cc_start: 0.8004 (m-70) cc_final: 0.7745 (m-70) REVERT: LC 325 MET cc_start: 0.9032 (ptp) cc_final: 0.8473 (ptp) REVERT: LC 335 MET cc_start: 0.5577 (mtp) cc_final: 0.5326 (mtp) REVERT: Lr 96 MET cc_start: 0.7344 (mpp) cc_final: 0.7142 (mpp) outliers start: 2 outliers final: 1 residues processed: 290 average time/residue: 0.2411 time to fit residues: 106.7325 Evaluate side-chains 208 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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: 0.8980 chunk 254 optimal weight: 8.9990 chunk 215 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 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** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 40 GLN ** LR 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 2 ASN ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 161 HIS B 142 GLN ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** 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 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 236 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 205 ASN LE 245 GLN LE 256 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.076256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.064427 restraints weight = 473970.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064342 restraints weight = 455197.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.064660 restraints weight = 402783.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.064677 restraints weight = 336857.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064685 restraints weight = 326886.420| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 1.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32994 Z= 0.194 Angle : 0.745 10.788 46133 Z= 0.382 Chirality : 0.043 0.289 5386 Planarity : 0.006 0.067 4541 Dihedral : 22.689 153.315 8982 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.81 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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 aren not related in a simple way. whole: -1.15 (0.15), residues: 2927 helix: -0.19 (0.13), residues: 1431 sheet: -1.38 (0.32), residues: 226 loop : -1.19 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGLC 71 TYR 0.027 0.002 TYRLE 116 PHE 0.022 0.002 PHE D 118 TRP 0.039 0.003 TRPLC 108 HIS 0.010 0.001 HISLC 142 Details of bonding type rmsd covalent geometry : bond 0.00404 (32994) covalent geometry : angle 0.74487 (46133) hydrogen bonds : bond 0.06672 ( 1431) hydrogen bonds : angle 5.54350 ( 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 298 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.157 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: E 329 MET cc_start: 0.4745 (mmt) cc_final: 0.4170 (mmm) REVERT: D 92 LEU cc_start: 0.8836 (mt) cc_final: 0.8388 (tp) REVERT: LY 74 TYR cc_start: 0.7343 (t80) cc_final: 0.6466 (t80) REVERT: LY 81 TYR cc_start: 0.8536 (m-80) cc_final: 0.8277 (m-80) REVERT: Lh 73 TYR cc_start: 0.9439 (m-80) cc_final: 0.9203 (m-10) REVERT: Lh 109 ARG cc_start: 0.8394 (ttt90) cc_final: 0.8173 (mpt180) REVERT: A 75 LYS cc_start: 0.8269 (tptt) cc_final: 0.8041 (tptp) REVERT: A 80 MET cc_start: 0.8439 (mmp) cc_final: 0.7759 (mmp) REVERT: A 110 ASP cc_start: 0.7922 (m-30) cc_final: 0.7541 (m-30) REVERT: A 112 TYR cc_start: 0.8993 (m-80) cc_final: 0.8770 (m-80) REVERT: A 121 ILE cc_start: 0.8950 (pt) cc_final: 0.8471 (pt) REVERT: LR 25 ASP cc_start: 0.8830 (m-30) cc_final: 0.8584 (m-30) REVERT: LR 28 GLU cc_start: 0.8205 (tp30) cc_final: 0.7897 (tm-30) REVERT: LR 31 GLU cc_start: 0.8848 (tp30) cc_final: 0.8554 (tp30) REVERT: LR 70 ARG cc_start: 0.8331 (tmm160) cc_final: 0.7923 (mmm-85) REVERT: LR 137 ILE cc_start: 0.9168 (mp) cc_final: 0.8872 (mp) REVERT: 2 28 MET cc_start: 0.7971 (tpt) cc_final: 0.6775 (tpp) REVERT: 2 29 LYS cc_start: 0.9684 (tptp) cc_final: 0.9258 (mmmt) REVERT: 2 60 MET cc_start: 0.9275 (mmp) cc_final: 0.8862 (mmm) REVERT: B 9 LYS cc_start: 0.8542 (tptt) cc_final: 0.8247 (tmtt) REVERT: B 21 TYR cc_start: 0.8276 (t80) cc_final: 0.7851 (t80) REVERT: B 51 MET cc_start: 0.7712 (tpt) cc_final: 0.7301 (tpt) REVERT: B 431 MET cc_start: 0.7314 (mmp) cc_final: 0.7057 (mmp) REVERT: B 712 MET cc_start: 0.1602 (ptp) cc_final: 0.1190 (ptp) REVERT: LC 138 MET cc_start: 0.9654 (tmm) cc_final: 0.9298 (tmm) REVERT: LC 310 HIS cc_start: 0.7865 (m-70) cc_final: 0.7589 (m-70) REVERT: LC 325 MET cc_start: 0.9072 (ptp) cc_final: 0.8599 (ptp) REVERT: LC 335 MET cc_start: 0.5575 (mtp) cc_final: 0.5339 (mtp) REVERT: Lr 125 MET cc_start: -0.0274 (mmm) cc_final: -0.0481 (mmm) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2405 time to fit residues: 109.8766 Evaluate side-chains 210 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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: 7.9990 chunk 197 optimal weight: 0.1980 chunk 264 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 296 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 94 ASN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** 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 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.076808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.064523 restraints weight = 473570.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.064490 restraints weight = 455797.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.064977 restraints weight = 408734.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.064916 restraints weight = 347912.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.064964 restraints weight = 358121.640| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 1.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32994 Z= 0.163 Angle : 0.726 11.716 46133 Z= 0.374 Chirality : 0.043 0.235 5386 Planarity : 0.005 0.059 4541 Dihedral : 22.501 155.362 8982 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.71 % Favored : 94.16 % Rotamer: Outliers : 0.08 % Allowed : 1.00 % Favored : 98.92 % 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 aren not related in a simple way. whole: -1.04 (0.15), residues: 2927 helix: -0.12 (0.13), residues: 1426 sheet: -1.34 (0.32), residues: 228 loop : -1.11 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLR 98 TYR 0.025 0.002 TYR B 86 PHE 0.014 0.002 PHELU 21 TRP 0.036 0.003 TRP B 284 HIS 0.010 0.001 HISLR 141 Details of bonding type rmsd covalent geometry : bond 0.00340 (32994) covalent geometry : angle 0.72556 (46133) hydrogen bonds : bond 0.05960 ( 1431) hydrogen bonds : angle 5.49206 ( 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 302 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 time to evaluate : 0.755 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: E 306 VAL cc_start: 0.9127 (t) cc_final: 0.8833 (p) REVERT: E 329 MET cc_start: 0.4725 (mmt) cc_final: 0.4082 (mmm) REVERT: LY 74 TYR cc_start: 0.7400 (t80) cc_final: 0.6441 (t80) REVERT: LY 80 ILE cc_start: 0.8837 (pt) cc_final: 0.8538 (tp) REVERT: LY 81 TYR cc_start: 0.8486 (m-80) cc_final: 0.8218 (m-80) REVERT: Lh 14 LYS cc_start: 0.9767 (pptt) cc_final: 0.9300 (mmtt) REVERT: Lh 20 GLN cc_start: 0.9840 (mp10) cc_final: 0.9592 (mp10) REVERT: Lh 73 TYR cc_start: 0.9469 (m-80) cc_final: 0.9226 (m-10) REVERT: Lh 109 ARG cc_start: 0.8397 (ttt90) cc_final: 0.8177 (mpt180) REVERT: A 75 LYS cc_start: 0.8575 (tptt) cc_final: 0.8298 (tptp) REVERT: A 80 MET cc_start: 0.7243 (mmp) cc_final: 0.6905 (mmp) REVERT: A 110 ASP cc_start: 0.7964 (m-30) cc_final: 0.7621 (m-30) REVERT: A 112 TYR cc_start: 0.8866 (m-80) cc_final: 0.8645 (m-80) REVERT: A 121 ILE cc_start: 0.8662 (pt) cc_final: 0.8122 (pt) REVERT: LR 25 ASP cc_start: 0.8451 (m-30) cc_final: 0.8188 (m-30) REVERT: LR 31 GLU cc_start: 0.8761 (tp30) cc_final: 0.8294 (tp30) REVERT: LR 70 ARG cc_start: 0.8336 (tmm160) cc_final: 0.7955 (mmm-85) REVERT: LR 94 THR cc_start: 0.8008 (m) cc_final: 0.7767 (m) REVERT: LR 96 MET cc_start: 0.3042 (tpp) cc_final: 0.2825 (mmm) REVERT: LR 99 MET cc_start: -0.4863 (ptm) cc_final: -0.5327 (ttt) REVERT: LR 102 LEU cc_start: 0.9411 (mm) cc_final: 0.9119 (pp) REVERT: LR 137 ILE cc_start: 0.9113 (mp) cc_final: 0.8828 (mp) REVERT: 2 28 MET cc_start: 0.8248 (tpt) cc_final: 0.7081 (tpp) REVERT: 2 93 GLN cc_start: 0.6269 (OUTLIER) cc_final: 0.6014 (pp30) REVERT: B 9 LYS cc_start: 0.8579 (tptt) cc_final: 0.8308 (tmtt) REVERT: B 21 TYR cc_start: 0.8327 (t80) cc_final: 0.7903 (t80) REVERT: B 51 MET cc_start: 0.7635 (tpt) cc_final: 0.7101 (mtp) REVERT: B 431 MET cc_start: 0.7043 (mmp) cc_final: 0.6794 (mmp) REVERT: B 712 MET cc_start: 0.1626 (ptp) cc_final: 0.1195 (ptp) REVERT: LC 138 MET cc_start: 0.9651 (tmm) cc_final: 0.9344 (tmm) REVERT: LC 310 HIS cc_start: 0.7529 (m-70) cc_final: 0.7280 (m-70) REVERT: LC 325 MET cc_start: 0.8967 (ptp) cc_final: 0.8512 (ptp) REVERT: LC 335 MET cc_start: 0.5559 (mtp) cc_final: 0.5324 (mtp) REVERT: Lr 125 MET cc_start: 0.0271 (mmm) cc_final: -0.0072 (mmm) outliers start: 2 outliers final: 0 residues processed: 302 average time/residue: 0.1981 time to fit residues: 92.6188 Evaluate side-chains 220 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 2.9990 chunk 268 optimal weight: 8.9990 chunk 104 optimal weight: 0.0370 chunk 213 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 overall best weight: 1.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN LY 61 HIS ** LY 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** 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 136 GLN LR 40 GLN 2 161 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** B 480 ASN ** 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 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 757 ASN ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 36 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 = 0.3847 r_free = 0.3847 target = 0.077554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.065892 restraints weight = 467969.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.065370 restraints weight = 468868.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.065373 restraints weight = 444699.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.065410 restraints weight = 405522.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.065485 restraints weight = 384527.659| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 1.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32994 Z= 0.144 Angle : 0.689 12.813 46133 Z= 0.354 Chirality : 0.041 0.198 5386 Planarity : 0.006 0.158 4541 Dihedral : 22.260 158.021 8982 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 aren not related in a simple way. whole: -0.90 (0.15), residues: 2927 helix: -0.06 (0.13), residues: 1426 sheet: -1.13 (0.33), residues: 233 loop : -1.00 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGLC 71 TYR 0.026 0.002 TYR B 833 PHE 0.029 0.002 PHE D 118 TRP 0.037 0.002 TRP B 284 HIS 0.009 0.001 HISLC 282 Details of bonding type rmsd covalent geometry : bond 0.00302 (32994) covalent geometry : angle 0.68886 (46133) hydrogen bonds : bond 0.05322 ( 1431) hydrogen bonds : angle 5.30471 ( 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 303 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.901 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: 0.4495 (mmt) cc_final: 0.3983 (mmm) REVERT: LY 80 ILE cc_start: 0.8837 (pt) cc_final: 0.8508 (tp) REVERT: LY 81 TYR cc_start: 0.8422 (m-80) cc_final: 0.8107 (m-80) REVERT: LY 100 HIS cc_start: 0.8637 (t70) cc_final: 0.8236 (m90) REVERT: Lh 14 LYS cc_start: 0.9747 (pptt) cc_final: 0.9249 (mmtt) REVERT: Lh 73 TYR cc_start: 0.9501 (m-80) cc_final: 0.9300 (m-10) REVERT: Lh 109 ARG cc_start: 0.8399 (ttt90) cc_final: 0.8169 (mpt180) REVERT: A 80 MET cc_start: 0.8773 (mmp) cc_final: 0.8089 (mmp) REVERT: A 110 ASP cc_start: 0.8057 (m-30) cc_final: 0.7658 (m-30) REVERT: A 121 ILE cc_start: 0.8936 (pt) cc_final: 0.8603 (pt) REVERT: LR 25 ASP cc_start: 0.8184 (m-30) cc_final: 0.7947 (m-30) REVERT: LR 31 GLU cc_start: 0.8767 (tp30) cc_final: 0.8397 (tp30) REVERT: LR 70 ARG cc_start: 0.8453 (tmm160) cc_final: 0.8189 (mmm-85) REVERT: LR 94 THR cc_start: 0.8021 (m) cc_final: 0.7695 (m) REVERT: LR 137 ILE cc_start: 0.8895 (mp) cc_final: 0.8644 (mp) REVERT: 2 28 MET cc_start: 0.7406 (tpt) cc_final: 0.6688 (tpt) REVERT: 2 29 LYS cc_start: 0.9632 (tptp) cc_final: 0.9170 (tppt) REVERT: B 9 LYS cc_start: 0.8607 (tptt) cc_final: 0.8334 (tmtt) REVERT: B 712 MET cc_start: 0.1756 (ptp) cc_final: 0.0911 (ptp) REVERT: LC 138 MET cc_start: 0.9680 (tmm) cc_final: 0.9058 (ptm) REVERT: LC 252 TRP cc_start: 0.9431 (m-90) cc_final: 0.9163 (m-90) REVERT: LC 310 HIS cc_start: 0.8000 (m-70) cc_final: 0.7730 (m-70) REVERT: LC 325 MET cc_start: 0.8915 (ptp) cc_final: 0.8498 (ptp) REVERT: LC 335 MET cc_start: 0.5436 (mtp) cc_final: 0.5157 (mtp) REVERT: Lr 96 MET cc_start: 0.8329 (mpp) cc_final: 0.7856 (mpp) REVERT: Lr 125 MET cc_start: 0.0938 (mmm) cc_final: 0.0571 (mmm) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2370 time to fit residues: 110.4783 Evaluate side-chains 225 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 6.9990 chunk 250 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 304 optimal weight: 5.9990 chunk 263 optimal weight: 0.3980 chunk 82 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 262 optimal weight: 0.3980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 161 HIS ** B 480 ASN ** 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 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 236 ASN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.076407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.064554 restraints weight = 475692.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.064332 restraints weight = 450089.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.064848 restraints weight = 407417.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064676 restraints weight = 356806.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.064726 restraints weight = 349091.184| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 1.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32994 Z= 0.175 Angle : 0.720 12.112 46133 Z= 0.370 Chirality : 0.042 0.247 5386 Planarity : 0.006 0.134 4541 Dihedral : 22.351 157.128 8982 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.02 % 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 : 0.00 % 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 aren not related in a simple way. whole: -1.06 (0.15), residues: 2927 helix: -0.12 (0.13), residues: 1437 sheet: -1.46 (0.30), residues: 246 loop : -1.11 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 19 TYR 0.024 0.002 TYR B 833 PHE 0.037 0.002 PHE 2 32 TRP 0.036 0.003 TRPLC 108 HIS 0.007 0.001 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00366 (32994) covalent geometry : angle 0.72040 (46133) hydrogen bonds : bond 0.06299 ( 1431) hydrogen bonds : angle 5.44329 ( 3789) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6630.89 seconds wall clock time: 116 minutes 13.81 seconds (6973.81 seconds total)