Starting phenix.real_space_refine on Fri Jun 27 07:15:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fq0_50642/06_2025/9fq0_50642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fq0_50642/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fq0_50642/06_2025/9fq0_50642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fq0_50642/06_2025/9fq0_50642.map" model { file = "/net/cci-nas-00/data/ceres_data/9fq0_50642/06_2025/9fq0_50642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fq0_50642/06_2025/9fq0_50642.cif" } resolution = 4.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.72, per 1000 atoms: 0.65 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: 8.81 Conformation dependent library (CDL) restraints added in 3.3 seconds 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 23 sheets defined 55.3% alpha, 10.5% beta 103 base pairs and 158 stacking pairs defined. Time for finding SS restraints: 13.01 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: 15.47 Time building geometry restraints manager: 10.33 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: 30.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.400 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 85.620 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.560 ------------------------------------------------------------------------------- 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 : 31.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (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 TRP 0.056 0.004 TRPLU 99 HIS 0.022 0.002 HISLY 24 PHE 0.045 0.003 PHELU 115 TYR 0.062 0.003 TYR B 451 ARG 0.027 0.001 ARGLC 345 Details of bonding type rmsd hydrogen bonds : bond 0.21382 ( 1431) hydrogen bonds : angle 7.26970 ( 3789) covalent geometry : bond 0.00534 (32994) covalent geometry : angle 1.09540 (46133) *********************** 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 : 3.111 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: 0.5335 time to fit residues: 332.2716 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 : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 130 optimal weight: 0.1980 chunk 253 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 293 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 ASN ** E 279 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 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 65 GLN LX 73 HIS LX 93 ASN ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 27 ASN ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 21 ASN ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN ** LE 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 4 HIS Lr 95 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.087594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.076460 restraints weight = 455723.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.076212 restraints weight = 505042.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.076725 restraints weight = 444516.648| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32994 Z= 0.191 Angle : 0.751 11.214 46133 Z= 0.388 Chirality : 0.043 0.311 5386 Planarity : 0.006 0.053 4541 Dihedral : 21.340 152.688 8982 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 0.31 % Allowed : 4.00 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2927 helix: 0.19 (0.13), residues: 1443 sheet: -0.46 (0.29), residues: 290 loop : -0.15 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 284 HIS 0.011 0.001 HIS E 301 PHE 0.027 0.002 PHE E 300 TYR 0.037 0.002 TYR 2 43 ARG 0.020 0.001 ARGLY 11 Details of bonding type rmsd hydrogen bonds : bond 0.06386 ( 1431) hydrogen bonds : angle 5.44950 ( 3789) covalent geometry : bond 0.00400 (32994) covalent geometry : angle 0.75082 (46133) *********************** 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 329 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 321 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.9207 (mpp) cc_final: 0.8999 (tpp) REVERT: D 77 VAL cc_start: 0.8960 (m) cc_final: 0.8659 (t) REVERT: D 92 LEU cc_start: 0.6440 (mt) cc_final: 0.5420 (pp) REVERT: D 103 ILE cc_start: 0.8782 (mm) cc_final: 0.8485 (mm) REVERT: LY 74 TYR cc_start: 0.6875 (t80) cc_final: 0.5662 (t80) REVERT: Lh 14 LYS cc_start: 0.9512 (pptt) cc_final: 0.8919 (mmtt) REVERT: Lh 43 LYS cc_start: 0.9617 (mppt) cc_final: 0.9322 (ptmm) REVERT: Lh 109 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7303 (ptt180) REVERT: LX 90 ILE cc_start: 0.8285 (mm) cc_final: 0.7906 (mp) REVERT: LX 93 ASN cc_start: 0.6133 (OUTLIER) cc_final: 0.5890 (m-40) REVERT: LX 99 ILE cc_start: 0.9008 (pt) cc_final: 0.8790 (tt) REVERT: A 80 MET cc_start: 0.6752 (mmp) cc_final: 0.5646 (mmt) REVERT: A 110 ASP cc_start: 0.7800 (m-30) cc_final: 0.7322 (m-30) REVERT: LR 76 MET cc_start: 0.5392 (ttt) cc_final: 0.4496 (ttt) REVERT: LR 93 VAL cc_start: 0.8123 (t) cc_final: 0.7351 (t) REVERT: LR 142 ILE cc_start: 0.9249 (tt) cc_final: 0.9012 (tp) REVERT: 2 28 MET cc_start: 0.3220 (tpt) cc_final: 0.2513 (tpt) REVERT: 2 89 LYS cc_start: 0.8883 (mttt) cc_final: 0.8633 (ptmm) REVERT: B 51 MET cc_start: 0.6525 (tpt) cc_final: 0.6259 (ttt) REVERT: B 91 ARG cc_start: 0.8886 (tpm170) cc_final: 0.8269 (tpt90) REVERT: B 712 MET cc_start: 0.0162 (ptp) cc_final: -0.0319 (ptp) REVERT: LC 286 ASN cc_start: 0.8575 (t0) cc_final: 0.8222 (p0) REVERT: LC 297 GLU cc_start: 0.9223 (mp0) cc_final: 0.8734 (tt0) REVERT: LE 151 ILE cc_start: 0.8378 (mt) cc_final: 0.8016 (tp) outliers start: 8 outliers final: 2 residues processed: 328 average time/residue: 0.5351 time to fit residues: 262.7525 Evaluate side-chains 224 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 221 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 210 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 279 HIS E 283 ASN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 94 ASN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN ** 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 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 190 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.081235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.064056 restraints weight = 369811.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.064843 restraints weight = 309626.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.065354 restraints weight = 274985.982| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32994 Z= 0.147 Angle : 0.653 11.443 46133 Z= 0.334 Chirality : 0.040 0.182 5386 Planarity : 0.005 0.054 4541 Dihedral : 21.330 152.068 8982 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.25 % Favored : 96.62 % Rotamer: Outliers : 0.08 % Allowed : 4.58 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2927 helix: 0.29 (0.13), residues: 1446 sheet: -0.22 (0.31), residues: 239 loop : -0.15 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 284 HIS 0.008 0.001 HIS B 709 PHE 0.047 0.002 PHE B 699 TYR 0.027 0.002 TYR B 21 ARG 0.007 0.001 ARGLY 50 Details of bonding type rmsd hydrogen bonds : bond 0.05213 ( 1431) hydrogen bonds : angle 5.00337 ( 3789) covalent geometry : bond 0.00308 (32994) covalent geometry : angle 0.65292 (46133) *********************** 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 298 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 3.175 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: LY 42 TYR cc_start: 0.8999 (m-10) cc_final: 0.8773 (m-10) REVERT: LY 74 TYR cc_start: 0.7747 (t80) cc_final: 0.7451 (t80) REVERT: LY 97 VAL cc_start: 0.8122 (t) cc_final: 0.7857 (t) REVERT: Lh 14 LYS cc_start: 0.9197 (pptt) cc_final: 0.8690 (mmtt) REVERT: Lh 43 LYS cc_start: 0.9320 (mppt) cc_final: 0.8730 (tmtt) REVERT: LX 152 LYS cc_start: 0.7389 (tppt) cc_final: 0.7108 (tppt) REVERT: LR 76 MET cc_start: 0.5633 (ttt) cc_final: 0.5244 (ttt) REVERT: 2 28 MET cc_start: 0.5792 (tpt) cc_final: 0.4949 (tpp) REVERT: 2 147 MET cc_start: 0.7739 (mmm) cc_final: 0.7292 (mmm) REVERT: B 13 LEU cc_start: 0.8128 (tt) cc_final: 0.7873 (tt) REVERT: B 51 MET cc_start: 0.6036 (tpt) cc_final: 0.5650 (ttt) REVERT: B 482 MET cc_start: 0.5155 (tpt) cc_final: 0.4818 (tpp) REVERT: B 712 MET cc_start: -0.0782 (ptp) cc_final: -0.1011 (ptt) REVERT: B 714 ARG cc_start: 0.8380 (mpt180) cc_final: 0.7975 (mpt180) REVERT: LC 252 TRP cc_start: 0.9212 (m-90) cc_final: 0.8967 (m-90) REVERT: LE 151 ILE cc_start: 0.8250 (mt) cc_final: 0.8000 (tp) outliers start: 2 outliers final: 1 residues processed: 298 average time/residue: 0.5298 time to fit residues: 238.6716 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 : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 80 optimal weight: 20.0000 chunk 260 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 211 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 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 178 ASN E 188 ASN E 203 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN LY 14 ASN ** LY 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 107 HIS ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 118 HIS ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 15 GLN ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** 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 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 215 ASN LC 245 HIS ** Lr 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 31 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 = 0.3881 r_free = 0.3881 target = 0.079560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.067507 restraints weight = 469545.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.067631 restraints weight = 470527.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.068054 restraints weight = 419300.959| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 32994 Z= 0.325 Angle : 0.995 13.860 46133 Z= 0.505 Chirality : 0.049 0.316 5386 Planarity : 0.008 0.122 4541 Dihedral : 22.313 152.218 8982 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 34.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.18 % Rotamer: Outliers : 0.35 % Allowed : 5.92 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 2927 helix: -0.44 (0.13), residues: 1431 sheet: -0.51 (0.33), residues: 205 loop : -0.67 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP B 284 HIS 0.013 0.002 HIS E 301 PHE 0.027 0.003 PHE E 300 TYR 0.033 0.004 TYRLU 90 ARG 0.069 0.002 ARGLC 258 Details of bonding type rmsd hydrogen bonds : bond 0.10476 ( 1431) hydrogen bonds : angle 5.68620 ( 3789) covalent geometry : bond 0.00668 (32994) covalent geometry : angle 0.99462 (46133) *********************** 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 304 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 295 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 268 ARG cc_start: 0.9605 (tmm-80) cc_final: 0.9394 (tmm-80) REVERT: E 329 MET cc_start: 0.4863 (mmm) cc_final: 0.4621 (mmm) REVERT: D 103 ILE cc_start: 0.8742 (mm) cc_final: 0.8452 (mm) REVERT: D 131 THR cc_start: 0.2788 (p) cc_final: 0.1898 (m) REVERT: LY 74 TYR cc_start: 0.7690 (t80) cc_final: 0.6676 (t80) REVERT: LY 81 TYR cc_start: 0.8199 (m-80) cc_final: 0.7855 (m-80) REVERT: Lh 14 LYS cc_start: 0.9614 (pptt) cc_final: 0.9181 (mmtt) REVERT: LX 73 HIS cc_start: 0.8244 (p-80) cc_final: 0.8041 (p90) REVERT: LX 116 LEU cc_start: 0.6174 (mm) cc_final: 0.5583 (mm) REVERT: LX 152 LYS cc_start: 0.8100 (tppt) cc_final: 0.7878 (tppt) REVERT: A 75 LYS cc_start: 0.7262 (tptt) cc_final: 0.7029 (tptp) REVERT: A 80 MET cc_start: 0.8201 (mmp) cc_final: 0.7185 (mmp) REVERT: A 110 ASP cc_start: 0.8044 (m-30) cc_final: 0.7727 (m-30) REVERT: LR 31 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8506 (tp30) REVERT: LR 70 ARG cc_start: 0.8358 (tmm160) cc_final: 0.7560 (mmm-85) REVERT: LR 76 MET cc_start: 0.5731 (ttt) cc_final: 0.3462 (tpt) REVERT: B 51 MET cc_start: 0.7086 (tpt) cc_final: 0.6803 (ttt) REVERT: B 91 ARG cc_start: 0.8828 (tpt90) cc_final: 0.8487 (tpt90) REVERT: B 127 MET cc_start: 0.6964 (ptp) cc_final: 0.6719 (ptt) REVERT: B 435 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: B 452 MET cc_start: 0.9477 (ptp) cc_final: 0.8946 (ttp) REVERT: B 712 MET cc_start: 0.0719 (ptp) cc_final: 0.0230 (ptp) REVERT: B 714 ARG cc_start: 0.8305 (mpt180) cc_final: 0.7942 (mpt180) REVERT: LC 95 MET cc_start: 0.2394 (mmp) cc_final: 0.2190 (tpt) REVERT: LC 101 MET cc_start: 0.2589 (tpt) cc_final: 0.2183 (tpt) REVERT: LC 221 PHE cc_start: 0.9239 (m-10) cc_final: 0.8848 (m-80) REVERT: LC 231 ASN cc_start: 0.9062 (t0) cc_final: 0.8777 (t0) REVERT: LC 325 MET cc_start: 0.9137 (ptp) cc_final: 0.8697 (ptt) outliers start: 9 outliers final: 1 residues processed: 302 average time/residue: 0.5317 time to fit residues: 243.6812 Evaluate side-chains 223 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 252 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS ** E 218 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 359 HIS ** D 61 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 40 GLN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 HIS ** 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 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 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 136 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.075876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.058743 restraints weight = 386011.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.059685 restraints weight = 307731.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.060251 restraints weight = 264759.461| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32994 Z= 0.147 Angle : 0.674 12.655 46133 Z= 0.343 Chirality : 0.041 0.229 5386 Planarity : 0.005 0.054 4541 Dihedral : 21.971 154.095 8982 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.42 % Favored : 96.48 % Rotamer: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2927 helix: -0.02 (0.13), residues: 1438 sheet: -0.77 (0.30), residues: 258 loop : -0.47 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 284 HIS 0.007 0.001 HIS B 709 PHE 0.022 0.002 PHE B 443 TYR 0.042 0.002 TYR B 833 ARG 0.010 0.001 ARGLR 108 Details of bonding type rmsd hydrogen bonds : bond 0.05384 ( 1431) hydrogen bonds : angle 5.10131 ( 3789) covalent geometry : bond 0.00305 (32994) covalent geometry : angle 0.67371 (46133) *********************** 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 300 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 2.995 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: E 329 MET cc_start: 0.5398 (mmm) cc_final: 0.5071 (mmm) REVERT: Lh 14 LYS cc_start: 0.9468 (pptt) cc_final: 0.9126 (mmtt) REVERT: Lh 22 ASP cc_start: 0.9159 (p0) cc_final: 0.8679 (p0) REVERT: A 75 LYS cc_start: 0.8032 (tptt) cc_final: 0.7750 (tptp) REVERT: LR 70 ARG cc_start: 0.8089 (tmm160) cc_final: 0.7391 (mmm-85) REVERT: LR 76 MET cc_start: 0.4681 (ttt) cc_final: 0.2626 (tpt) REVERT: LR 153 LYS cc_start: 0.8215 (tmmt) cc_final: 0.7885 (ptpp) REVERT: 2 28 MET cc_start: 0.7735 (tpt) cc_final: 0.6949 (tpp) REVERT: 2 147 MET cc_start: 0.8847 (mmp) cc_final: 0.8644 (mmm) REVERT: B 51 MET cc_start: 0.6763 (tpt) cc_final: 0.6466 (ttt) REVERT: B 91 ARG cc_start: 0.8253 (tpt90) cc_final: 0.7969 (tpt90) REVERT: B 482 MET cc_start: 0.6208 (tpt) cc_final: 0.5995 (tpt) REVERT: B 712 MET cc_start: 0.0232 (ptp) cc_final: -0.0107 (ptt) REVERT: B 714 ARG cc_start: 0.8382 (mpt180) cc_final: 0.8073 (mpt180) REVERT: LC 95 MET cc_start: 0.2222 (mmp) cc_final: 0.1927 (tpt) REVERT: LC 101 MET cc_start: 0.2615 (tpt) cc_final: 0.2371 (tpt) REVERT: LC 221 PHE cc_start: 0.9283 (m-10) cc_final: 0.9058 (m-80) REVERT: LE 151 ILE cc_start: 0.9076 (mt) cc_final: 0.8870 (tp) REVERT: LE 264 ILE cc_start: 0.9615 (mm) cc_final: 0.9386 (tp) outliers start: 2 outliers final: 0 residues processed: 300 average time/residue: 0.4878 time to fit residues: 223.6851 Evaluate side-chains 227 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 20 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 56 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 58 GLN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 136 HIS LE 256 GLN ** Lr 6 GLN ** 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 = 0.3839 r_free = 0.3839 target = 0.077429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.066114 restraints weight = 471274.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.065580 restraints weight = 489540.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.066041 restraints weight = 428678.142| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.8685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 32994 Z= 0.301 Angle : 0.921 17.007 46133 Z= 0.468 Chirality : 0.047 0.505 5386 Planarity : 0.008 0.082 4541 Dihedral : 22.516 150.116 8982 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 34.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 2927 helix: -0.45 (0.13), residues: 1447 sheet: -1.08 (0.31), residues: 229 loop : -0.84 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP B 284 HIS 0.013 0.002 HIS E 301 PHE 0.028 0.003 PHE D 118 TYR 0.039 0.003 TYRLE 116 ARG 0.027 0.001 ARGLC 258 Details of bonding type rmsd hydrogen bonds : bond 0.10066 ( 1431) hydrogen bonds : angle 5.71323 ( 3789) covalent geometry : bond 0.00621 (32994) covalent geometry : angle 0.92141 (46133) *********************** 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 272 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 3.067 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 329 MET cc_start: 0.5861 (mmm) cc_final: 0.5287 (mmm) REVERT: D 92 LEU cc_start: 0.8436 (mt) cc_final: 0.7684 (pp) REVERT: Lh 14 LYS cc_start: 0.9679 (pptt) cc_final: 0.9199 (mmtt) REVERT: LX 73 HIS cc_start: 0.8735 (p-80) cc_final: 0.8441 (p90) REVERT: LX 116 LEU cc_start: 0.5817 (mm) cc_final: 0.5248 (mm) REVERT: LX 123 LYS cc_start: 0.8027 (ptmt) cc_final: 0.7678 (pptt) REVERT: A 75 LYS cc_start: 0.7611 (tptt) cc_final: 0.7341 (tptp) REVERT: A 80 MET cc_start: 0.8832 (mmp) cc_final: 0.8104 (mmt) REVERT: A 110 ASP cc_start: 0.8273 (m-30) cc_final: 0.7907 (m-30) REVERT: A 112 TYR cc_start: 0.9011 (m-80) cc_final: 0.8760 (m-80) REVERT: LR 25 ASP cc_start: 0.8675 (m-30) cc_final: 0.8465 (m-30) REVERT: LR 31 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8470 (tp30) REVERT: LR 52 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8105 (mmm-85) REVERT: LR 70 ARG cc_start: 0.8299 (tmm160) cc_final: 0.7558 (mmm-85) REVERT: LR 76 MET cc_start: 0.6314 (ttt) cc_final: 0.5076 (tpt) REVERT: LR 151 ARG cc_start: 0.9516 (mmp80) cc_final: 0.9202 (tpm170) REVERT: 2 28 MET cc_start: 0.6147 (tpt) cc_final: 0.5795 (tpp) REVERT: B 51 MET cc_start: 0.7733 (tpt) cc_final: 0.7494 (tpt) REVERT: B 91 ARG cc_start: 0.8882 (tpt90) cc_final: 0.8498 (tpt90) REVERT: B 119 ASP cc_start: 0.9511 (t70) cc_final: 0.9311 (t0) REVERT: B 452 MET cc_start: 0.9448 (ttp) cc_final: 0.9239 (tmm) REVERT: B 714 ARG cc_start: 0.8455 (mpt180) cc_final: 0.8097 (mpt180) REVERT: LC 95 MET cc_start: -0.0192 (mmp) cc_final: -0.0636 (tpt) REVERT: LC 221 PHE cc_start: 0.9586 (m-10) cc_final: 0.9305 (m-80) REVERT: LC 325 MET cc_start: 0.9260 (ptp) cc_final: 0.8775 (ptm) REVERT: LC 335 MET cc_start: 0.4773 (mtp) cc_final: 0.4551 (mtp) REVERT: Lr 71 ARG cc_start: 0.8063 (ptt-90) cc_final: 0.7769 (ptt180) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.5326 time to fit residues: 219.6678 Evaluate side-chains 208 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 257 optimal weight: 0.6980 chunk 202 optimal weight: 8.9990 chunk 295 optimal weight: 0.1980 chunk 160 optimal weight: 7.9990 chunk 30 optimal weight: 40.0000 chunk 233 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 247 optimal weight: 0.0770 chunk 50 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.5940 ------------------------------------------------------------------------------- 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 274 ASN E 305 ASN E 308 HIS ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.079534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.068127 restraints weight = 469565.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.067503 restraints weight = 471464.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.067777 restraints weight = 423116.458| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32994 Z= 0.146 Angle : 0.691 14.357 46133 Z= 0.352 Chirality : 0.041 0.191 5386 Planarity : 0.005 0.056 4541 Dihedral : 22.247 154.101 8982 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.89 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 2927 helix: -0.10 (0.13), residues: 1431 sheet: -0.87 (0.32), residues: 237 loop : -0.79 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 284 HIS 0.007 0.001 HISLE 190 PHE 0.031 0.002 PHELU 42 TYR 0.030 0.002 TYR B 833 ARG 0.011 0.001 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.05634 ( 1431) hydrogen bonds : angle 5.24596 ( 3789) covalent geometry : bond 0.00308 (32994) covalent geometry : angle 0.69147 (46133) *********************** 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 294 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 3.028 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 156 MET cc_start: 0.4763 (tmm) cc_final: 0.4301 (tmm) REVERT: E 306 VAL cc_start: 0.9067 (t) cc_final: 0.8769 (p) REVERT: E 329 MET cc_start: 0.5257 (mmm) cc_final: 0.4493 (mmm) REVERT: D 92 LEU cc_start: 0.8313 (mt) cc_final: 0.7673 (pp) REVERT: D 103 ILE cc_start: 0.8789 (mm) cc_final: 0.8584 (mm) REVERT: LY 119 LEU cc_start: 0.8935 (mm) cc_final: 0.8730 (mt) REVERT: Lh 14 LYS cc_start: 0.9656 (pptt) cc_final: 0.9166 (mmtt) REVERT: Lh 35 LYS cc_start: 0.9577 (mmtt) cc_final: 0.9355 (mmtt) REVERT: LX 79 PHE cc_start: 0.9708 (p90) cc_final: 0.9470 (p90) REVERT: LX 116 LEU cc_start: 0.6277 (mm) cc_final: 0.5993 (mm) REVERT: A 78 LYS cc_start: 0.8564 (mttt) cc_final: 0.8251 (pttt) REVERT: A 80 MET cc_start: 0.8675 (mmp) cc_final: 0.7794 (mmm) REVERT: A 110 ASP cc_start: 0.8188 (m-30) cc_final: 0.7756 (m-30) REVERT: A 112 TYR cc_start: 0.8990 (m-80) cc_final: 0.8666 (m-80) REVERT: LR 25 ASP cc_start: 0.8296 (m-30) cc_final: 0.8038 (m-30) REVERT: LR 31 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8435 (tp30) REVERT: LR 70 ARG cc_start: 0.8342 (tmm160) cc_final: 0.7724 (mmm-85) REVERT: LR 76 MET cc_start: 0.5352 (ttt) cc_final: 0.4256 (tpt) REVERT: 2 28 MET cc_start: 0.4694 (tpt) cc_final: 0.4412 (tpp) REVERT: 2 60 MET cc_start: 0.9375 (mmp) cc_final: 0.8909 (mmm) REVERT: B 51 MET cc_start: 0.7487 (tpt) cc_final: 0.7147 (ttt) REVERT: B 452 MET cc_start: 0.9528 (ttp) cc_final: 0.9023 (ptp) REVERT: B 714 ARG cc_start: 0.8447 (mpt180) cc_final: 0.8146 (mpt180) REVERT: LC 95 MET cc_start: -0.0083 (mmp) cc_final: -0.0658 (tpt) REVERT: LC 101 MET cc_start: 0.2827 (tpt) cc_final: 0.2332 (tpt) REVERT: LC 189 MET cc_start: 0.9152 (mmp) cc_final: 0.8855 (mmp) REVERT: LC 221 PHE cc_start: 0.9549 (m-10) cc_final: 0.9263 (m-80) REVERT: LC 281 MET cc_start: 0.8780 (tpt) cc_final: 0.8158 (ptt) REVERT: LC 325 MET cc_start: 0.9160 (ptp) cc_final: 0.8608 (ptm) REVERT: LE 68 MET cc_start: 0.9657 (mpp) cc_final: 0.9325 (mpp) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.4927 time to fit residues: 222.2392 Evaluate side-chains 223 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 281 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN E 356 GLN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 56 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 2 ASN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 338 ASN ** LE 135 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.078420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.067312 restraints weight = 475513.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.066483 restraints weight = 515460.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.066880 restraints weight = 441828.917| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.9415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32994 Z= 0.195 Angle : 0.719 13.739 46133 Z= 0.367 Chirality : 0.041 0.352 5386 Planarity : 0.006 0.053 4541 Dihedral : 22.257 152.246 8982 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.19 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 2927 helix: -0.02 (0.13), residues: 1420 sheet: -0.88 (0.33), residues: 218 loop : -0.92 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 284 HIS 0.012 0.002 HIS 2 120 PHE 0.045 0.002 PHE E 382 TYR 0.040 0.002 TYRLC 331 ARG 0.014 0.001 ARG 2 116 Details of bonding type rmsd hydrogen bonds : bond 0.06740 ( 1431) hydrogen bonds : angle 5.33502 ( 3789) covalent geometry : bond 0.00399 (32994) covalent geometry : angle 0.71906 (46133) *********************** 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 279 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 156 MET cc_start: 0.5180 (tmm) cc_final: 0.4676 (tmm) REVERT: E 306 VAL cc_start: 0.9043 (t) cc_final: 0.8713 (p) REVERT: E 329 MET cc_start: 0.5600 (mmm) cc_final: 0.4813 (mmm) REVERT: D 92 LEU cc_start: 0.8502 (mt) cc_final: 0.7827 (pp) REVERT: Lh 14 LYS cc_start: 0.9681 (pptt) cc_final: 0.9168 (mmtt) REVERT: A 80 MET cc_start: 0.8908 (mmp) cc_final: 0.8027 (mmm) REVERT: A 110 ASP cc_start: 0.8265 (m-30) cc_final: 0.7826 (m-30) REVERT: A 112 TYR cc_start: 0.9059 (m-80) cc_final: 0.8699 (m-80) REVERT: A 121 ILE cc_start: 0.9049 (pt) cc_final: 0.8837 (pt) REVERT: LR 25 ASP cc_start: 0.8643 (m-30) cc_final: 0.8394 (m-30) REVERT: LR 31 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8524 (tp30) REVERT: LR 70 ARG cc_start: 0.8397 (tmm160) cc_final: 0.7782 (mmm-85) REVERT: LR 76 MET cc_start: 0.5610 (ttt) cc_final: 0.4702 (tpt) REVERT: 2 28 MET cc_start: 0.5462 (tpt) cc_final: 0.4871 (tpp) REVERT: 2 60 MET cc_start: 0.9310 (mmp) cc_final: 0.8899 (mmm) REVERT: B 51 MET cc_start: 0.7747 (tpt) cc_final: 0.7515 (ttt) REVERT: B 452 MET cc_start: 0.9486 (ttp) cc_final: 0.9081 (ptp) REVERT: B 691 MET cc_start: 0.9074 (mmp) cc_final: 0.8516 (mmp) REVERT: B 714 ARG cc_start: 0.8569 (mpt180) cc_final: 0.8296 (mpt180) REVERT: LC 221 PHE cc_start: 0.9646 (m-10) cc_final: 0.9423 (m-80) REVERT: LC 325 MET cc_start: 0.9155 (ptp) cc_final: 0.8646 (ptm) REVERT: LC 335 MET cc_start: 0.4614 (mtt) cc_final: 0.3968 (mtp) REVERT: LC 338 ASN cc_start: 0.9411 (m110) cc_final: 0.9015 (p0) REVERT: LE 68 MET cc_start: 0.9698 (mpp) cc_final: 0.9441 (mpp) REVERT: LE 118 THR cc_start: 0.7778 (p) cc_final: 0.7559 (t) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.5047 time to fit residues: 216.6866 Evaluate side-chains 216 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 21 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 56 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 27 HIS ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 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 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 215 ASN LC 236 ASN ** LE 135 GLN ** 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 = 0.3805 r_free = 0.3805 target = 0.075584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.064019 restraints weight = 470447.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.063518 restraints weight = 470331.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.063943 restraints weight = 404196.285| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 1.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 32994 Z= 0.273 Angle : 0.915 13.343 46133 Z= 0.469 Chirality : 0.048 0.313 5386 Planarity : 0.008 0.232 4541 Dihedral : 22.853 151.816 8982 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 36.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.76 % Favored : 93.06 % Rotamer: Outliers : 0.04 % Allowed : 1.23 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 2927 helix: -0.56 (0.13), residues: 1428 sheet: -1.42 (0.34), residues: 202 loop : -1.22 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP B 284 HIS 0.012 0.002 HIS 2 69 PHE 0.034 0.003 PHE E 382 TYR 0.073 0.004 TYRLE 57 ARG 0.015 0.001 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.09112 ( 1431) hydrogen bonds : angle 5.99215 ( 3789) covalent geometry : bond 0.00569 (32994) covalent geometry : angle 0.91465 (46133) *********************** 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 303 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 3.880 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 156 MET cc_start: 0.5076 (tmm) cc_final: 0.4416 (tmm) REVERT: E 329 MET cc_start: 0.6259 (mmm) cc_final: 0.5662 (mmm) REVERT: D 92 LEU cc_start: 0.8801 (mt) cc_final: 0.8473 (pp) REVERT: Lh 14 LYS cc_start: 0.9759 (pptt) cc_final: 0.9337 (mmtt) REVERT: LX 79 PHE cc_start: 0.9737 (p90) cc_final: 0.9494 (p90) REVERT: A 80 MET cc_start: 0.9200 (mmp) cc_final: 0.8619 (mmp) REVERT: A 110 ASP cc_start: 0.8230 (m-30) cc_final: 0.7817 (m-30) REVERT: A 112 TYR cc_start: 0.9181 (m-80) cc_final: 0.8833 (m-80) REVERT: A 121 ILE cc_start: 0.9256 (pt) cc_final: 0.8369 (pt) REVERT: LU 55 ASN cc_start: 0.8315 (p0) cc_final: 0.8104 (p0) REVERT: LR 70 ARG cc_start: 0.8399 (tmm160) cc_final: 0.8159 (mmm-85) REVERT: LR 76 MET cc_start: 0.6029 (ttt) cc_final: 0.5510 (tpt) REVERT: LR 98 ARG cc_start: 0.8369 (ppt170) cc_final: 0.7939 (ttp80) REVERT: LR 99 MET cc_start: -0.5812 (ptm) cc_final: -0.6731 (ptm) REVERT: LR 102 LEU cc_start: 0.9306 (mm) cc_final: 0.8869 (pp) REVERT: 2 12 MET cc_start: 0.8329 (ppp) cc_final: 0.8110 (ppp) REVERT: 2 28 MET cc_start: 0.5666 (tpt) cc_final: 0.5134 (tpp) REVERT: 2 30 TYR cc_start: 0.9776 (m-10) cc_final: 0.9529 (m-80) REVERT: 2 60 MET cc_start: 0.9375 (mmp) cc_final: 0.8865 (mmm) REVERT: 2 91 MET cc_start: 0.7001 (tmm) cc_final: 0.6776 (tmm) REVERT: B 51 MET cc_start: 0.8024 (tpt) cc_final: 0.7604 (mtp) REVERT: B 431 MET cc_start: 0.7320 (mmp) cc_final: 0.7115 (mmm) REVERT: B 452 MET cc_start: 0.9329 (ttp) cc_final: 0.8561 (ptp) REVERT: B 691 MET cc_start: 0.8550 (mmp) cc_final: 0.8149 (mmm) REVERT: LC 43 ASN cc_start: 0.9046 (t0) cc_final: 0.8838 (t0) REVERT: LC 138 MET cc_start: 0.9620 (tmm) cc_final: 0.9337 (tmm) REVERT: LC 310 HIS cc_start: 0.7879 (m-70) cc_final: 0.7583 (m-70) REVERT: LC 325 MET cc_start: 0.9041 (ptp) cc_final: 0.8602 (ptm) REVERT: LC 335 MET cc_start: 0.4878 (mtt) cc_final: 0.4616 (mtp) REVERT: LE 68 MET cc_start: 0.9685 (mpp) cc_final: 0.9466 (mpp) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.5070 time to fit residues: 239.2927 Evaluate side-chains 216 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 249 optimal weight: 20.0000 chunk 260 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 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 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 56 GLN ** LY 86 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** LX 105 ASN A 87 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 61 GLN LC 236 ASN ** LC 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 256 GLN ** Lr 36 ASN ** 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 = 0.3790 r_free = 0.3790 target = 0.074718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.063258 restraints weight = 477474.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.062799 restraints weight = 473764.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.063029 restraints weight = 435397.269| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 1.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 32994 Z= 0.271 Angle : 0.886 18.795 46133 Z= 0.455 Chirality : 0.047 0.368 5386 Planarity : 0.007 0.132 4541 Dihedral : 22.939 150.906 8982 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 35.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.90 % Favored : 92.96 % Rotamer: Outliers : 0.12 % Allowed : 0.81 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 2927 helix: -0.64 (0.13), residues: 1434 sheet: -1.61 (0.34), residues: 206 loop : -1.42 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRPLC 108 HIS 0.011 0.002 HISLr 4 PHE 0.044 0.003 PHE E 382 TYR 0.040 0.003 TYRLC 331 ARG 0.016 0.001 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.08536 ( 1431) hydrogen bonds : angle 6.00509 ( 3789) covalent geometry : bond 0.00560 (32994) covalent geometry : angle 0.88612 (46133) ********************** 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 292 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 4.807 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 156 MET cc_start: 0.4957 (tmm) cc_final: 0.4291 (tmm) REVERT: E 306 VAL cc_start: 0.9090 (t) cc_final: 0.8799 (p) REVERT: E 329 MET cc_start: 0.6392 (mmm) cc_final: 0.5787 (mmm) REVERT: D 92 LEU cc_start: 0.8782 (mt) cc_final: 0.8381 (pp) REVERT: LX 77 ILE cc_start: 0.7637 (tp) cc_final: 0.7257 (tp) REVERT: LX 79 PHE cc_start: 0.9724 (p90) cc_final: 0.9475 (p90) REVERT: A 80 MET cc_start: 0.8998 (mmp) cc_final: 0.8479 (mmm) REVERT: A 110 ASP cc_start: 0.8409 (m-30) cc_final: 0.8004 (m-30) REVERT: A 112 TYR cc_start: 0.9175 (m-80) cc_final: 0.8807 (m-80) REVERT: A 121 ILE cc_start: 0.9422 (pt) cc_final: 0.8653 (pt) REVERT: LU 97 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7576 (mtt180) REVERT: LR 31 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8974 (tp30) REVERT: LR 70 ARG cc_start: 0.8431 (tmm160) cc_final: 0.8001 (mmm-85) REVERT: LR 76 MET cc_start: 0.5946 (ttt) cc_final: 0.5617 (tpt) REVERT: LR 137 ILE cc_start: 0.9534 (mp) cc_final: 0.8714 (mp) REVERT: 2 28 MET cc_start: 0.7665 (tpt) cc_final: 0.6528 (tpp) REVERT: 2 60 MET cc_start: 0.9297 (mmp) cc_final: 0.8928 (mmm) REVERT: B 51 MET cc_start: 0.8127 (tpt) cc_final: 0.7591 (ptp) REVERT: B 431 MET cc_start: 0.7539 (mmp) cc_final: 0.7315 (mmm) REVERT: B 452 MET cc_start: 0.9350 (ttp) cc_final: 0.8702 (ptp) REVERT: B 528 TYR cc_start: 0.7609 (t80) cc_final: 0.7407 (t80) REVERT: B 691 MET cc_start: 0.9044 (mmp) cc_final: 0.8544 (mmp) REVERT: LC 325 MET cc_start: 0.8889 (ptp) cc_final: 0.8466 (ptm) REVERT: LC 335 MET cc_start: 0.5018 (mtt) cc_final: 0.4798 (mtp) REVERT: LE 68 MET cc_start: 0.9629 (mpp) cc_final: 0.9414 (mpp) REVERT: LE 112 MET cc_start: 0.7781 (mtt) cc_final: 0.7372 (ppp) REVERT: Lr 125 MET cc_start: 0.1370 (mmm) cc_final: 0.0982 (mmm) outliers start: 3 outliers final: 1 residues processed: 292 average time/residue: 0.6494 time to fit residues: 292.6941 Evaluate side-chains 211 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 39 optimal weight: 30.0000 chunk 206 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 312 optimal weight: 0.6980 chunk 275 optimal weight: 0.2980 chunk 67 optimal weight: 10.0000 chunk 147 optimal weight: 0.0270 chunk 112 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 overall best weight: 1.8042 ------------------------------------------------------------------------------- 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 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 86 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** LX 105 ASN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 141 HIS ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN 2 161 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** 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 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 215 ASN LC 278 ASN ** Lr 36 ASN ** 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 = 0.3844 r_free = 0.3844 target = 0.077377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.065631 restraints weight = 460861.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.065769 restraints weight = 442775.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.066024 restraints weight = 371332.095| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 1.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32994 Z= 0.154 Angle : 0.748 14.332 46133 Z= 0.384 Chirality : 0.043 0.266 5386 Planarity : 0.005 0.072 4541 Dihedral : 22.420 151.600 8982 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.75 % Favored : 95.11 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 2927 helix: -0.36 (0.13), residues: 1434 sheet: -1.19 (0.33), residues: 234 loop : -1.19 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP B 284 HIS 0.011 0.001 HISLr 4 PHE 0.032 0.002 PHE E 382 TYR 0.034 0.002 TYR 2 122 ARG 0.013 0.001 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.05655 ( 1431) hydrogen bonds : angle 5.52206 ( 3789) covalent geometry : bond 0.00324 (32994) covalent geometry : angle 0.74835 (46133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13850.73 seconds wall clock time: 244 minutes 46.48 seconds (14686.48 seconds total)