Starting phenix.real_space_refine on Mon Aug 25 16:02:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fpz_50641/08_2025/9fpz_50641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fpz_50641/08_2025/9fpz_50641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fpz_50641/08_2025/9fpz_50641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fpz_50641/08_2025/9fpz_50641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fpz_50641/08_2025/9fpz_50641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fpz_50641/08_2025/9fpz_50641.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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: 6 Type Number sf(0) Gaussians Co 2 6.85 5 P 364 5.49 5 S 111 5.16 5 C 17139 2.51 5 N 5428 2.21 5 O 6350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29394 Number of models: 1 Model: "" Number of chains: 15 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: "8" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1237 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 23, 'rna3p_pyr': 23} Link IDs: {'rna2p': 12, 'rna3p': 45} Chain: "A" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2901 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "1" Number of atoms: 6425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 6425 Classifications: {'RNA': 300} Modifications used: {'rna2p_pur': 29, 'rna2p_pyr': 25, 'rna3p_pur': 130, 'rna3p_pyr': 116} Link IDs: {'rna2p': 54, 'rna3p': 245} Chain breaks: 8 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: "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: "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: "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: "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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 5.51, per 1000 atoms: 0.19 Number of scatterers: 29394 At special positions: 0 Unit cell: (184.8, 196.56, 257.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 2 26.99 S 111 16.00 P 364 15.00 O 6350 8.00 N 5428 7.00 C 17139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 722.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5082 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 22 sheets defined 56.5% alpha, 10.2% beta 104 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain '2' and resid 12 through 22 removed outlier: 4.033A pdb=" N LEU 2 19 " --> pdb=" O GLN 2 15 " (cutoff:3.500A) removed outlier: 3.512A 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: 3.577A pdb=" N GLU 2 157 " --> pdb=" O GLN 2 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 162 through 187 removed outlier: 3.784A pdb=" N ASP A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP A 186 " --> pdb=" O TYR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.517A pdb=" N ILE A 196 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.546A pdb=" N VAL A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 25 through 39 removed outlier: 3.757A pdb=" N GLN B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 36 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 3.853A 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: 3.859A 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: 3.665A pdb=" N TRP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 removed outlier: 3.704A 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 160 removed outlier: 3.876A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 179 Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 205 through 214 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: 3.816A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.657A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 4.070A pdb=" N LEU B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 321 removed outlier: 3.822A 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: 3.666A 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: 3.893A 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: 3.762A pdb=" N LEU B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 438 removed outlier: 3.833A pdb=" N ALA B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.767A pdb=" N ASN B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.505A 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 526 removed outlier: 3.517A pdb=" N ASP B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN B 522 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) removed outlier: 3.710A 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 546 removed outlier: 3.552A pdb=" N ASP B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 550 Processing helix chain 'B' and resid 551 through 571 removed outlier: 3.553A pdb=" N ASN B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 584 removed outlier: 3.587A pdb=" N GLU B 581 " --> pdb=" O ASN B 577 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 584 " --> pdb=" O HIS B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 628 removed outlier: 3.653A pdb=" N GLU B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) 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: 4.274A pdb=" N HIS B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 703 removed outlier: 3.847A pdb=" N GLN B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 703 " --> pdb=" O PHE B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 Processing helix chain 'B' and resid 726 through 741 removed outlier: 3.817A 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: 3.577A pdb=" N ALA B 782 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 811 removed outlier: 3.598A 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 'B' and resid 834 through 838 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: 3.575A 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: 3.526A 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 155 through 161 Processing helix chain 'LC' and resid 163 through 174 Processing helix chain 'LC' and resid 176 through 186 removed outlier: 3.927A pdb=" N ILELC 180 " --> pdb=" O ALALC 176 " (cutoff:3.500A) Processing helix chain 'LC' and resid 192 through 196 removed outlier: 3.633A pdb=" N LYSLC 195 " --> pdb=" O GLYLC 192 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 222 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: 3.515A pdb=" N LEULC 328 " --> pdb=" O ILELC 324 " (cutoff:3.500A) Processing helix chain 'LC' and resid 331 through 368 removed outlier: 3.570A pdb=" N LYSLC 353 " --> pdb=" O LEULC 349 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNLC 362 " --> pdb=" O ALALC 358 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALALC 363 " --> pdb=" O ALALC 359 " (cutoff:3.500A) Processing helix chain 'LE' and resid 58 through 66 removed outlier: 3.500A 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 removed outlier: 3.596A pdb=" N PHELE 217 " --> pdb=" O THRLE 213 " (cutoff:3.500A) Processing helix chain 'LE' and resid 243 through 264 removed outlier: 3.874A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix removed outlier: 4.158A pdb=" N ILELE 264 " --> pdb=" O LYSLE 260 " (cutoff:3.500A) Processing helix chain 'LE' and resid 266 through 273 Processing helix chain 'Lk' and resid 7 through 15 removed outlier: 3.969A pdb=" N PHELk 11 " --> pdb=" O GLULk 7 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEULk 12 " --> pdb=" O ILELk 8 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEULk 13 " --> pdb=" O LYSLk 9 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 49 through 58 removed outlier: 4.064A pdb=" N ALALk 53 " --> pdb=" O ASPLk 49 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLULk 54 " --> pdb=" O LYSLk 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYSLk 55 " --> pdb=" O GLULk 51 " (cutoff:3.500A) Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 removed outlier: 3.945A 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 127 removed outlier: 3.604A pdb=" N GLULY 120 " --> pdb=" O LYSLY 116 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARGLY 126 " --> pdb=" O LYSLY 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLNLY 127 " --> pdb=" O ALALY 123 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 11 removed outlier: 3.757A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLYLh 11 " --> pdb=" O ARGLh 7 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 37 removed outlier: 3.531A pdb=" N LEULh 17 " --> pdb=" O LYSLh 13 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASPLh 23 " --> pdb=" O LYSLh 19 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEULh 24 " --> pdb=" O GLNLh 20 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 45 Processing helix chain 'Lh' and resid 45 through 73 removed outlier: 4.152A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLULh 67 " --> pdb=" O GLNLh 63 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASNLh 68 " --> pdb=" O THRLh 64 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEULh 69 " --> pdb=" O GLNLh 65 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 80 through 84 Processing helix chain 'Lh' and resid 88 through 94 removed outlier: 3.572A pdb=" N ARGLh 93 " --> pdb=" O ARGLh 89 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARGLh 94 " --> pdb=" O ALALh 90 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 96 through 101 removed outlier: 3.686A pdb=" N ASNLh 101 " --> pdb=" O LYSLh 97 " (cutoff:3.500A) 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 93 removed outlier: 3.789A pdb=" N LYSLX 88 " --> pdb=" O GLULX 84 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYSLX 89 " --> pdb=" O SERLX 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILELX 90 " --> pdb=" O ALALX 86 " (cutoff:3.500A) Processing helix chain 'LX' and resid 105 through 118 Processing helix chain 'LX' and resid 145 through 154 removed outlier: 3.550A pdb=" N VALLX 149 " --> pdb=" O ASPLX 145 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 16 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: 3.978A pdb=" N ILELR 32 " --> pdb=" O GLULR 28 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 removed outlier: 3.755A pdb=" N LYSLR 46 " --> pdb=" O ARGLR 42 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 72 removed outlier: 3.634A pdb=" N LYSLR 72 " --> pdb=" O LEULR 68 " (cutoff:3.500A) Processing helix chain 'LR' and resid 77 through 81 removed outlier: 3.835A 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: 3.703A pdb=" N HISLR 141 " --> pdb=" O ILELR 137 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILELR 142 " --> pdb=" O LEULR 138 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HISLR 143 " --> pdb=" O METLR 139 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 3 through 11 removed outlier: 3.692A pdb=" N VALLr 9 " --> pdb=" O LEULr 5 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 31 through 35 removed outlier: 4.264A 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 99 Processing helix chain 'Lr' and resid 106 through 122 removed outlier: 3.547A pdb=" N LYSLr 122 " --> pdb=" O LEULr 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 4 through 5 removed outlier: 3.504A pdb=" N ARG 2 4 " --> pdb=" O ILE 2 44 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR 2 43 " --> pdb=" O TYR 2 55 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR 2 55 " --> pdb=" O TYR 2 43 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA 2 45 " --> pdb=" O VAL 2 53 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N VAL 2 53 " --> pdb=" O VAL 2 77 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL 2 77 " --> pdb=" O VAL 2 53 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR 2 55 " --> pdb=" O LEU 2 75 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU 2 75 " --> pdb=" O TYR 2 55 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU 2 57 " --> pdb=" O THR 2 73 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLY 2 70 " --> pdb=" O SER 2 108 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS 2 110 " --> pdb=" O GLY 2 70 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE 2 72 " --> pdb=" O HIS 2 110 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N ARG 2 112 " --> pdb=" O ILE 2 72 " (cutoff:3.500A) removed outlier: 13.332A pdb=" N SER 2 74 " --> pdb=" O ARG 2 112 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA 2 144 " --> pdb=" O GLU 2 134 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS 2 148 " --> pdb=" O ILE 2 130 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE 2 130 " --> pdb=" O LYS 2 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.736A pdb=" N HIS A 460 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.736A pdb=" N HIS A 460 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL A 360 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 225 removed outlier: 6.210A pdb=" N ALA A 218 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N HIS A 255 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLY A 253 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 252 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 263 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 254 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 230 removed outlier: 6.659A pdb=" N LEU A 447 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 315 Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.895A pdb=" N HIS A 382 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'LC' and resid 7 through 11 removed outlier: 4.975A pdb=" N LYSLC 20 " --> pdb=" O VALLC 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'LC' and resid 64 through 65 Processing sheet with id=AB1, first strand: chain 'LC' and resid 152 through 154 removed outlier: 6.331A pdb=" N LEULC 152 " --> pdb=" O TRPLC 252 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N CYSLC 208 " --> pdb=" O ILELC 251 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THRLC 253 " --> pdb=" O CYSLC 208 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILELC 210 " --> pdb=" O THRLC 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'LC' and resid 187 through 189 Processing sheet with id=AB3, first strand: chain 'LE' and resid 49 through 51 removed outlier: 3.618A pdb=" N VALLE 51 " --> pdb=" O ILELE 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LE' and resid 91 through 94 removed outlier: 3.640A pdb=" N LYSLE 94 " --> pdb=" O ARGLE 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARGLE 105 " --> pdb=" O LYSLE 94 " (cutoff:3.500A) Processing sheet with id=AB5, 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: 4.380A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILELE 149 " --> pdb=" O THRLE 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.327A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AB8, first strand: chain 'LY' and resid 79 through 82 removed outlier: 6.787A pdb=" N VALLY 79 " --> pdb=" O VALLY 73 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VALLY 73 " --> pdb=" O VALLY 79 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYRLY 81 " --> pdb=" O VALLY 71 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AC1, first strand: chain 'LX' and resid 77 through 80 removed outlier: 6.973A pdb=" N ILELX 99 " --> pdb=" O LYSLX 78 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VALLX 97 " --> pdb=" O PROLX 80 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYSLX 123 " --> pdb=" O ARGLX 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'LR' and resid 22 through 24 removed outlier: 3.672A pdb=" N ILELR 51 " --> pdb=" O TRPLR 23 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Lr' and resid 17 through 20 Processing sheet with id=AC4, first strand: chain 'Lr' and resid 49 through 53 1078 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 272 hydrogen bonds 462 hydrogen bond angles 0 basepair planarities 104 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8140 1.34 - 1.46: 7990 1.46 - 1.58: 13671 1.58 - 1.70: 712 1.70 - 1.82: 174 Bond restraints: 30687 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 1.49e+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 1.31e+01 bond pdb=" C1 IHP B 901 " pdb=" O11 IHP B 901 " ideal model delta sigma weight residual 1.392 1.464 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C6 IHP B 901 " pdb=" O16 IHP B 901 " ideal model delta sigma weight residual 1.394 1.464 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C4 IHP B 901 " pdb=" O14 IHP B 901 " ideal model delta sigma weight residual 1.394 1.463 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 30682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 42851 4.24 - 8.49: 172 8.49 - 12.73: 15 12.73 - 16.97: 4 16.97 - 21.21: 2 Bond angle restraints: 43044 Sorted by residual: angle pdb=" CB MET A 430 " pdb=" CG MET A 430 " pdb=" SD MET A 430 " ideal model delta sigma weight residual 112.70 91.49 21.21 3.00e+00 1.11e-01 5.00e+01 angle pdb=" CA LYS B 169 " pdb=" CB LYS B 169 " pdb=" CG LYS B 169 " ideal model delta sigma weight residual 114.10 124.75 -10.65 2.00e+00 2.50e-01 2.84e+01 angle pdb=" CB MET 2 91 " pdb=" CG MET 2 91 " pdb=" SD MET 2 91 " ideal model delta sigma weight residual 112.70 127.81 -15.11 3.00e+00 1.11e-01 2.54e+01 angle pdb=" CA LEU B 661 " pdb=" CB LEU B 661 " pdb=" CG LEU B 661 " ideal model delta sigma weight residual 116.30 133.72 -17.42 3.50e+00 8.16e-02 2.48e+01 angle pdb=" CB MET B 737 " pdb=" CG MET B 737 " pdb=" SD MET B 737 " ideal model delta sigma weight residual 112.70 127.02 -14.32 3.00e+00 1.11e-01 2.28e+01 ... (remaining 43039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 17990 32.81 - 65.61: 1341 65.61 - 98.42: 161 98.42 - 131.22: 22 131.22 - 164.03: 1 Dihedral angle restraints: 19515 sinusoidal: 11672 harmonic: 7843 Sorted by residual: 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 77.09 122.91 1 1.50e+01 4.44e-03 6.58e+01 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 232.00 67.97 164.03 1 1.70e+01 3.46e-03 6.52e+01 dihedral pdb=" O4' U 1 468 " pdb=" C1' U 1 468 " pdb=" N1 U 1 468 " pdb=" C2 U 1 468 " ideal model delta sinusoidal sigma weight residual -160.00 -75.98 -84.02 1 1.50e+01 4.44e-03 3.82e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.024: 5024 1.024 - 2.047: 0 2.047 - 3.071: 0 3.071 - 4.094: 0 4.094 - 5.118: 3 Chirality restraints: 5027 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 2.60 -5.12 2.00e-01 2.50e+01 6.55e+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 2.66 -5.08 2.00e-01 2.50e+01 6.44e+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 -2.62 4.93 2.00e-01 2.50e+01 6.08e+02 ... (remaining 5024 not shown) Planarity restraints: 4140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 30 " 0.028 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR 2 30 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 30 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 30 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 30 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 30 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR 2 30 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR 2 30 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 451 " 0.023 2.00e-02 2.50e+03 2.38e-02 1.13e+01 pdb=" CG TYR B 451 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR B 451 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 451 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 451 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 451 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 451 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 451 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 26 " 0.026 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR 2 26 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 26 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 26 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 26 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 26 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR 2 26 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR 2 26 " -0.004 2.00e-02 2.50e+03 ... (remaining 4137 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 1 1.99 - 2.72: 1940 2.72 - 3.45: 44062 3.45 - 4.17: 79716 4.17 - 4.90: 123679 Nonbonded interactions: 249398 Sorted by model distance: nonbonded pdb="CO CO A 501 " pdb="CO CO A 502 " model vdw 1.268 1.400 nonbonded pdb=" O2' C 1 196 " pdb=" NH2 ARGLY 126 " model vdw 2.075 3.120 nonbonded pdb=" OD2 ASP A 262 " pdb="CO CO A 502 " model vdw 2.093 2.220 nonbonded pdb=" OG1 THR A 151 " pdb=" OE1 GLU A 153 " model vdw 2.094 3.040 nonbonded pdb=" OE2 GLU A 364 " pdb="CO CO A 501 " model vdw 2.110 2.220 ... (remaining 249393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 33.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.270 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.003 0.077 30687 Z= 0.163 Angle : 0.738 21.213 43044 Z= 0.373 Chirality : 0.129 5.118 5027 Planarity : 0.004 0.097 4140 Dihedral : 20.319 164.031 14433 Min Nonbonded Distance : 1.268 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 1.41 % Allowed : 22.37 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.16), residues: 2640 helix: 0.56 (0.14), residues: 1336 sheet: -0.02 (0.38), residues: 189 loop : 0.12 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 70 TYR 0.075 0.002 TYR 2 30 PHE 0.044 0.001 PHE 2 32 TRP 0.024 0.001 TRP B 284 HIS 0.012 0.001 HIS 2 16 Details of bonding type rmsd covalent geometry : bond 0.00334 (30687) covalent geometry : angle 0.73781 (43044) hydrogen bonds : bond 0.17994 ( 1337) hydrogen bonds : angle 6.70850 ( 3579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 343 time to evaluate : 0.644 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: 2 5 ASN cc_start: 0.6995 (t0) cc_final: 0.6727 (m-40) REVERT: 2 13 ASN cc_start: 0.8055 (m110) cc_final: 0.7717 (m110) REVERT: 2 62 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6836 (mp0) REVERT: A 294 ASP cc_start: 0.9040 (t0) cc_final: 0.8818 (t0) REVERT: A 384 MET cc_start: 0.9052 (ttm) cc_final: 0.8453 (tpp) REVERT: A 455 THR cc_start: 0.9719 (m) cc_final: 0.9413 (p) REVERT: B 274 LEU cc_start: 0.9630 (mt) cc_final: 0.9425 (pp) REVERT: B 530 MET cc_start: 0.6664 (ppp) cc_final: 0.5662 (ppp) REVERT: LC 86 ARG cc_start: 0.4197 (OUTLIER) cc_final: 0.1429 (mtt180) REVERT: LC 95 MET cc_start: 0.9129 (pmm) cc_final: 0.7900 (mmt) REVERT: LC 189 MET cc_start: 0.9483 (mmp) cc_final: 0.8627 (ptt) REVERT: LC 201 ARG cc_start: 0.9077 (mtp-110) cc_final: 0.8726 (mmp-170) REVERT: LC 262 GLU cc_start: 0.9047 (mp0) cc_final: 0.8760 (mp0) REVERT: LC 283 LYS cc_start: 0.9506 (mtmm) cc_final: 0.9031 (pptt) REVERT: LE 119 GLU cc_start: 0.8173 (mp0) cc_final: 0.7890 (pm20) REVERT: LE 240 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.2684 (t80) REVERT: Lk 7 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8376 (pp20) REVERT: Lk 30 ASP cc_start: 0.9080 (p0) cc_final: 0.8759 (p0) REVERT: LY 43 ASN cc_start: 0.9229 (t0) cc_final: 0.8627 (t0) REVERT: LY 124 LYS cc_start: 0.8598 (tmmt) cc_final: 0.8394 (tmmm) REVERT: Lh 23 ASP cc_start: 0.9139 (p0) cc_final: 0.8524 (p0) REVERT: Lh 30 GLN cc_start: 0.8926 (mp10) cc_final: 0.8700 (mm-40) REVERT: Lh 101 ASN cc_start: 0.9570 (m-40) cc_final: 0.9304 (m-40) REVERT: LX 55 ARG cc_start: 0.7600 (tpm170) cc_final: 0.7177 (tpm-80) REVERT: LX 101 ASP cc_start: 0.9058 (t0) cc_final: 0.8792 (t0) REVERT: LX 118 ASP cc_start: 0.8572 (t0) cc_final: 0.8325 (t0) REVERT: LX 156 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.7928 (tp) REVERT: LR 25 ASP cc_start: 0.9379 (t70) cc_final: 0.8870 (t0) REVERT: LR 28 GLU cc_start: 0.8815 (mp0) cc_final: 0.8586 (mp0) REVERT: Lr 77 TYR cc_start: 0.9133 (m-80) cc_final: 0.8903 (m-80) outliers start: 33 outliers final: 26 residues processed: 364 average time/residue: 0.5312 time to fit residues: 230.8828 Evaluate side-chains 328 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 103 ASN Chi-restraints excluded: chain 2 residue 110 HIS Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LE residue 154 THR Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lk residue 54 GLU Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain LY residue 107 THR Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lh residue 49 VAL Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain LX residue 82 THR Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LX residue 156 ILE Chi-restraints excluded: chain LR residue 63 CYS Chi-restraints excluded: chain Lr residue 24 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 480 ASN B 488 GLN B 514 HIS ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 GLN B 624 GLN B 795 ASN LC 299 GLN LE 245 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 34 ASN Lr 36 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.075705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.053720 restraints weight = 160889.631| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.61 r_work: 0.3240 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30687 Z= 0.132 Angle : 0.652 14.876 43044 Z= 0.326 Chirality : 0.039 0.326 5027 Planarity : 0.004 0.080 4140 Dihedral : 21.350 166.874 8740 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 3.07 % Allowed : 18.75 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.16), residues: 2640 helix: 0.64 (0.14), residues: 1374 sheet: -0.18 (0.34), residues: 219 loop : 0.06 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGLY 126 TYR 0.031 0.001 TYR 2 30 PHE 0.027 0.001 PHE 2 32 TRP 0.020 0.001 TRP B 284 HIS 0.017 0.001 HIS 2 16 Details of bonding type rmsd covalent geometry : bond 0.00274 (30687) covalent geometry : angle 0.65191 (43044) hydrogen bonds : bond 0.04875 ( 1337) hydrogen bonds : angle 4.97561 ( 3579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 352 time to evaluate : 0.955 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: 2 5 ASN cc_start: 0.8675 (t0) cc_final: 0.8370 (m-40) REVERT: 2 13 ASN cc_start: 0.9054 (m110) cc_final: 0.8836 (m110) REVERT: 2 14 MET cc_start: 0.9136 (pmm) cc_final: 0.8920 (pmm) REVERT: 2 27 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8828 (mm110) REVERT: 2 55 TYR cc_start: 0.8109 (p90) cc_final: 0.7850 (p90) REVERT: 2 62 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7424 (mp0) REVERT: 2 96 ARG cc_start: 0.8833 (ttt180) cc_final: 0.8615 (tmm-80) REVERT: 2 147 MET cc_start: 0.8587 (tpp) cc_final: 0.8343 (mmm) REVERT: A 384 MET cc_start: 0.8788 (ttm) cc_final: 0.8545 (tpp) REVERT: B 282 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: B 614 ASN cc_start: 0.9562 (OUTLIER) cc_final: 0.9229 (p0) REVERT: B 692 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8628 (tt) REVERT: LC 35 ASP cc_start: 0.9241 (p0) cc_final: 0.8814 (p0) REVERT: LC 95 MET cc_start: 0.9228 (pmm) cc_final: 0.7922 (mmt) REVERT: LC 144 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9063 (pp) REVERT: LC 283 LYS cc_start: 0.9577 (mtmm) cc_final: 0.9100 (pptt) REVERT: LC 325 MET cc_start: 0.9182 (tpt) cc_final: 0.8973 (tpp) REVERT: LC 327 LYS cc_start: 0.6249 (mmpt) cc_final: 0.4426 (mptm) REVERT: LE 119 GLU cc_start: 0.8123 (mp0) cc_final: 0.7899 (pm20) REVERT: Lk 19 ASP cc_start: 0.8789 (p0) cc_final: 0.8474 (p0) REVERT: Lk 30 ASP cc_start: 0.9328 (p0) cc_final: 0.9030 (p0) REVERT: LY 43 ASN cc_start: 0.9158 (t0) cc_final: 0.8931 (t0) REVERT: Lh 23 ASP cc_start: 0.8920 (p0) cc_final: 0.8570 (p0) REVERT: Lh 30 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8841 (mm-40) REVERT: LX 57 GLN cc_start: 0.9198 (tp40) cc_final: 0.8716 (mm110) REVERT: LX 78 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8580 (mmmm) REVERT: LX 101 ASP cc_start: 0.9071 (t0) cc_final: 0.8745 (t0) REVERT: LX 118 ASP cc_start: 0.9155 (t0) cc_final: 0.8913 (t0) REVERT: LR 25 ASP cc_start: 0.9310 (t70) cc_final: 0.8854 (t70) outliers start: 72 outliers final: 20 residues processed: 407 average time/residue: 0.5531 time to fit residues: 267.2257 Evaluate side-chains 319 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 293 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 110 HIS Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain LC residue 144 ILE Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain LX residue 78 LYS Chi-restraints excluded: chain LX residue 82 THR Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain Lr residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 35 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 283 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 522 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.072460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.050485 restraints weight = 165776.237| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.59 r_work: 0.3155 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 30687 Z= 0.328 Angle : 0.740 14.830 43044 Z= 0.375 Chirality : 0.042 0.292 5027 Planarity : 0.005 0.116 4140 Dihedral : 21.440 172.311 8704 Min Nonbonded Distance : 1.237 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 4.69 % Allowed : 19.13 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.16), residues: 2640 helix: 0.68 (0.14), residues: 1380 sheet: -0.30 (0.34), residues: 209 loop : -0.02 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARGLY 126 TYR 0.049 0.002 TYR B 451 PHE 0.025 0.002 PHE 2 128 TRP 0.015 0.002 TRP B 151 HIS 0.015 0.002 HIS 2 16 Details of bonding type rmsd covalent geometry : bond 0.00679 (30687) covalent geometry : angle 0.73970 (43044) hydrogen bonds : bond 0.05296 ( 1337) hydrogen bonds : angle 4.89466 ( 3579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 307 time to evaluate : 0.883 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: 2 13 ASN cc_start: 0.9147 (m110) cc_final: 0.8866 (m110) REVERT: 2 14 MET cc_start: 0.9233 (pmm) cc_final: 0.8994 (pmm) REVERT: 2 55 TYR cc_start: 0.8379 (p90) cc_final: 0.7859 (p90) REVERT: 2 147 MET cc_start: 0.8985 (tpp) cc_final: 0.8606 (mmm) REVERT: A 305 GLN cc_start: 0.9277 (tt0) cc_final: 0.9072 (tt0) REVERT: A 306 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: B 47 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: B 84 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8841 (p-80) REVERT: B 282 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: B 614 ASN cc_start: 0.9539 (OUTLIER) cc_final: 0.9162 (p0) REVERT: B 692 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8451 (tt) REVERT: LC 35 ASP cc_start: 0.9303 (p0) cc_final: 0.8861 (p0) REVERT: LC 86 ARG cc_start: 0.4456 (OUTLIER) cc_final: 0.1362 (mtt180) REVERT: LC 95 MET cc_start: 0.9209 (pmm) cc_final: 0.8127 (mmt) REVERT: LE 57 TYR cc_start: 0.9342 (m-10) cc_final: 0.9077 (m-10) REVERT: LE 119 GLU cc_start: 0.8074 (mp0) cc_final: 0.7813 (pm20) REVERT: LE 139 LYS cc_start: 0.5044 (OUTLIER) cc_final: 0.4005 (pttt) REVERT: Lk 4 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8874 (ttmp) REVERT: LY 124 LYS cc_start: 0.9222 (tmmm) cc_final: 0.8870 (tmmm) REVERT: Lh 23 ASP cc_start: 0.9062 (p0) cc_final: 0.8681 (p0) REVERT: Lh 30 GLN cc_start: 0.9053 (mp10) cc_final: 0.8833 (mm-40) REVERT: LX 57 GLN cc_start: 0.9276 (tp40) cc_final: 0.8783 (mm110) REVERT: LX 63 LYS cc_start: 0.5366 (OUTLIER) cc_final: 0.4769 (mptt) REVERT: LX 78 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.8755 (mmmm) REVERT: LX 101 ASP cc_start: 0.9176 (t70) cc_final: 0.8911 (t0) REVERT: LX 118 ASP cc_start: 0.9242 (t0) cc_final: 0.9039 (t0) REVERT: LR 25 ASP cc_start: 0.9424 (t70) cc_final: 0.9087 (t0) REVERT: LR 28 GLU cc_start: 0.9063 (mp0) cc_final: 0.8848 (mp0) outliers start: 110 outliers final: 38 residues processed: 386 average time/residue: 0.5291 time to fit residues: 243.3724 Evaluate side-chains 331 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 282 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LC residue 319 LEU Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 139 LYS Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 4 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LY residue 41 LYS Chi-restraints excluded: chain LY residue 82 ILE Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain LX residue 42 THR Chi-restraints excluded: chain LX residue 63 LYS Chi-restraints excluded: chain LX residue 78 LYS Chi-restraints excluded: chain LX residue 102 VAL Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain LR residue 134 ASN Chi-restraints excluded: chain LR residue 148 ASP Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 232 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 225 optimal weight: 0.6980 chunk 178 optimal weight: 0.0870 chunk 251 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN Lr 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.074160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.052180 restraints weight = 160475.009| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.56 r_work: 0.3204 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30687 Z= 0.141 Angle : 0.649 15.467 43044 Z= 0.324 Chirality : 0.039 0.323 5027 Planarity : 0.004 0.130 4140 Dihedral : 21.425 169.830 8700 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 3.75 % Allowed : 20.32 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 2640 helix: 0.73 (0.14), residues: 1380 sheet: -0.36 (0.35), residues: 193 loop : -0.01 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGLC 201 TYR 0.025 0.001 TYR 2 30 PHE 0.019 0.001 PHE 2 32 TRP 0.019 0.001 TRP B 284 HIS 0.009 0.001 HISLE 128 Details of bonding type rmsd covalent geometry : bond 0.00306 (30687) covalent geometry : angle 0.64885 (43044) hydrogen bonds : bond 0.04246 ( 1337) hydrogen bonds : angle 4.68376 ( 3579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 331 time to evaluate : 0.990 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: 2 47 ASP cc_start: 0.6369 (p0) cc_final: 0.5477 (p0) REVERT: 2 55 TYR cc_start: 0.8425 (p90) cc_final: 0.7838 (p90) REVERT: 2 98 MET cc_start: 0.8756 (tmm) cc_final: 0.8549 (pp-130) REVERT: 2 99 ILE cc_start: 0.9192 (mm) cc_final: 0.8958 (mm) REVERT: 2 147 MET cc_start: 0.9130 (tpp) cc_final: 0.8656 (mmm) REVERT: A 191 MET cc_start: 0.8652 (ptt) cc_final: 0.8337 (ptt) REVERT: B 47 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: B 84 HIS cc_start: 0.9115 (OUTLIER) cc_final: 0.8895 (p-80) REVERT: B 282 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: B 611 GLU cc_start: 0.9558 (tp30) cc_final: 0.9139 (pm20) REVERT: B 614 ASN cc_start: 0.9503 (OUTLIER) cc_final: 0.9285 (p0) REVERT: B 692 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8446 (tt) REVERT: LC 35 ASP cc_start: 0.9321 (p0) cc_final: 0.8862 (p0) REVERT: LC 86 ARG cc_start: 0.4434 (OUTLIER) cc_final: 0.4099 (mtp85) REVERT: LC 95 MET cc_start: 0.9210 (pmm) cc_final: 0.8009 (mmt) REVERT: LC 283 LYS cc_start: 0.9642 (mtmm) cc_final: 0.9096 (pptt) REVERT: LC 288 ASP cc_start: 0.9374 (t0) cc_final: 0.9067 (t0) REVERT: LC 327 LYS cc_start: 0.6270 (mmpt) cc_final: 0.4523 (mptm) REVERT: LE 57 TYR cc_start: 0.9314 (m-10) cc_final: 0.9066 (m-10) REVERT: LE 119 GLU cc_start: 0.8097 (mp0) cc_final: 0.7830 (pm20) REVERT: LE 240 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.2152 (t80) REVERT: Lk 4 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8876 (ttmp) REVERT: LY 124 LYS cc_start: 0.9179 (tmmm) cc_final: 0.8970 (tmmm) REVERT: Lh 23 ASP cc_start: 0.9053 (p0) cc_final: 0.8660 (p0) REVERT: Lh 30 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8859 (mm-40) REVERT: LX 57 GLN cc_start: 0.9291 (tp40) cc_final: 0.8785 (mm110) REVERT: LX 101 ASP cc_start: 0.9136 (t70) cc_final: 0.8897 (t0) REVERT: LX 118 ASP cc_start: 0.9218 (t0) cc_final: 0.8999 (t0) REVERT: LR 25 ASP cc_start: 0.9369 (t70) cc_final: 0.8972 (t0) REVERT: LR 28 GLU cc_start: 0.9003 (mp0) cc_final: 0.8736 (mp0) outliers start: 88 outliers final: 31 residues processed: 392 average time/residue: 0.5537 time to fit residues: 256.8362 Evaluate side-chains 332 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 110 HIS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LC residue 174 LEU Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain LE residue 279 ASN Chi-restraints excluded: chain Lk residue 4 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain LX residue 42 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 220 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN LC 321 ASN Lh 68 ASN Lr 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.073469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051622 restraints weight = 163176.173| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.51 r_work: 0.3185 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30687 Z= 0.202 Angle : 0.683 13.933 43044 Z= 0.343 Chirality : 0.039 0.322 5027 Planarity : 0.005 0.136 4140 Dihedral : 21.398 171.157 8697 Min Nonbonded Distance : 1.222 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 4.09 % Allowed : 20.84 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.16), residues: 2640 helix: 0.77 (0.14), residues: 1372 sheet: -0.41 (0.34), residues: 199 loop : -0.08 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGLC 201 TYR 0.021 0.002 TYR 2 30 PHE 0.025 0.001 PHE 2 32 TRP 0.023 0.001 TRP B 707 HIS 0.008 0.001 HISLE 128 Details of bonding type rmsd covalent geometry : bond 0.00426 (30687) covalent geometry : angle 0.68300 (43044) hydrogen bonds : bond 0.04377 ( 1337) hydrogen bonds : angle 4.67934 ( 3579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 302 time to evaluate : 0.985 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: 2 10 ASP cc_start: 0.9189 (p0) cc_final: 0.8918 (p0) REVERT: 2 129 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9172 (pm20) REVERT: 2 147 MET cc_start: 0.9191 (tpp) cc_final: 0.8690 (mmm) REVERT: A 191 MET cc_start: 0.8650 (ptt) cc_final: 0.8427 (ptt) REVERT: A 384 MET cc_start: 0.8917 (ttm) cc_final: 0.8606 (tpp) REVERT: B 166 MET cc_start: 0.8810 (pmm) cc_final: 0.8594 (pmm) REVERT: B 282 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7595 (pm20) REVERT: B 614 ASN cc_start: 0.9505 (OUTLIER) cc_final: 0.9237 (p0) REVERT: B 692 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8471 (mm) REVERT: LC 35 ASP cc_start: 0.9271 (p0) cc_final: 0.8809 (p0) REVERT: LC 86 ARG cc_start: 0.4464 (OUTLIER) cc_final: 0.1307 (mtt180) REVERT: LC 95 MET cc_start: 0.9206 (pmm) cc_final: 0.8072 (mmt) REVERT: LC 288 ASP cc_start: 0.9360 (t0) cc_final: 0.9065 (t0) REVERT: LC 321 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8427 (t0) REVERT: LE 57 TYR cc_start: 0.9296 (m-10) cc_final: 0.9051 (m-10) REVERT: LE 119 GLU cc_start: 0.8080 (mp0) cc_final: 0.7810 (pm20) REVERT: LE 240 TYR cc_start: 0.5322 (OUTLIER) cc_final: 0.2072 (t80) REVERT: Lk 4 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8891 (ttmp) REVERT: Lh 23 ASP cc_start: 0.9080 (p0) cc_final: 0.8792 (p0) REVERT: Lh 30 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8836 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4712 (OUTLIER) cc_final: 0.3632 (mptt) REVERT: Lh 100 GLU cc_start: 0.8459 (pp20) cc_final: 0.8083 (pp20) REVERT: Lh 101 ASN cc_start: 0.9623 (m-40) cc_final: 0.9206 (m-40) REVERT: LX 57 GLN cc_start: 0.9291 (tp40) cc_final: 0.8825 (mm110) REVERT: LX 101 ASP cc_start: 0.9143 (t70) cc_final: 0.8942 (t0) REVERT: LX 118 ASP cc_start: 0.9166 (t0) cc_final: 0.8938 (t0) REVERT: LR 25 ASP cc_start: 0.9388 (t70) cc_final: 0.9071 (t0) REVERT: LR 144 LYS cc_start: 0.9053 (mppt) cc_final: 0.8830 (mptt) outliers start: 96 outliers final: 41 residues processed: 376 average time/residue: 0.5455 time to fit residues: 245.4550 Evaluate side-chains 337 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 129 GLN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LC residue 179 ASP Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LC residue 321 ASN Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 145 THR Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain Lk residue 4 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 68 ASN Chi-restraints excluded: chain Lh residue 86 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain LX residue 42 THR Chi-restraints excluded: chain LX residue 82 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 1.9990 chunk 104 optimal weight: 40.0000 chunk 185 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 253 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN Lh 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.073367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051978 restraints weight = 163065.316| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.80 r_work: 0.3183 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30687 Z= 0.209 Angle : 0.702 16.238 43044 Z= 0.351 Chirality : 0.040 0.366 5027 Planarity : 0.005 0.137 4140 Dihedral : 21.429 171.317 8697 Min Nonbonded Distance : 1.217 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 3.88 % Allowed : 22.62 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.16), residues: 2640 helix: 0.76 (0.14), residues: 1371 sheet: -0.50 (0.35), residues: 195 loop : -0.10 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGLY 126 TYR 0.054 0.002 TYR B 451 PHE 0.035 0.001 PHE 2 128 TRP 0.028 0.001 TRP B 707 HIS 0.016 0.001 HIS 2 110 Details of bonding type rmsd covalent geometry : bond 0.00440 (30687) covalent geometry : angle 0.70222 (43044) hydrogen bonds : bond 0.04372 ( 1337) hydrogen bonds : angle 4.69413 ( 3579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 313 time to evaluate : 0.748 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: 2 55 TYR cc_start: 0.8182 (p90) cc_final: 0.7595 (p90) REVERT: 2 147 MET cc_start: 0.9229 (tpp) cc_final: 0.8980 (mmm) REVERT: B 282 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: B 447 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7630 (tptt) REVERT: B 614 ASN cc_start: 0.9508 (OUTLIER) cc_final: 0.9278 (p0) REVERT: B 692 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8519 (mm) REVERT: LC 35 ASP cc_start: 0.9320 (p0) cc_final: 0.8856 (p0) REVERT: LC 86 ARG cc_start: 0.4460 (OUTLIER) cc_final: 0.1292 (mtt180) REVERT: LC 95 MET cc_start: 0.9225 (pmm) cc_final: 0.8125 (mmt) REVERT: LC 288 ASP cc_start: 0.9377 (t0) cc_final: 0.9071 (t0) REVERT: LE 57 TYR cc_start: 0.9332 (m-80) cc_final: 0.9081 (m-10) REVERT: LE 119 GLU cc_start: 0.8081 (mp0) cc_final: 0.7801 (pm20) REVERT: LE 128 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.6760 (t70) REVERT: LE 240 TYR cc_start: 0.5332 (OUTLIER) cc_final: 0.2078 (t80) REVERT: Lk 4 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8889 (ttmp) REVERT: Lk 30 ASP cc_start: 0.9508 (p0) cc_final: 0.9167 (p0) REVERT: Lh 23 ASP cc_start: 0.9147 (p0) cc_final: 0.8911 (p0) REVERT: Lh 30 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8861 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4750 (OUTLIER) cc_final: 0.3470 (tptt) REVERT: Lh 100 GLU cc_start: 0.8491 (pp20) cc_final: 0.8221 (pp20) REVERT: Lh 101 ASN cc_start: 0.9628 (m-40) cc_final: 0.9211 (m-40) REVERT: LX 57 GLN cc_start: 0.9336 (tp40) cc_final: 0.8858 (mm110) REVERT: LX 101 ASP cc_start: 0.9194 (t70) cc_final: 0.8844 (t0) REVERT: LX 118 ASP cc_start: 0.9125 (t0) cc_final: 0.8899 (t0) REVERT: LR 28 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8591 (mm-30) REVERT: LR 144 LYS cc_start: 0.9105 (mppt) cc_final: 0.8876 (mptt) REVERT: LR 151 ARG cc_start: 0.9662 (tpp80) cc_final: 0.8927 (tpm170) outliers start: 91 outliers final: 42 residues processed: 383 average time/residue: 0.5459 time to fit residues: 248.8858 Evaluate side-chains 335 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 132 GLU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 145 THR Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 4 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 86 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain LX residue 42 THR Chi-restraints excluded: chain LX residue 67 ARG Chi-restraints excluded: chain LX residue 82 THR Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LX residue 145 ASP Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain LR residue 28 GLU Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 219 optimal weight: 0.0570 chunk 164 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 78 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN LC 321 ASN ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.074021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.052650 restraints weight = 161848.028| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.68 r_work: 0.3202 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 30687 Z= 0.156 Angle : 0.704 16.855 43044 Z= 0.347 Chirality : 0.039 0.390 5027 Planarity : 0.005 0.141 4140 Dihedral : 21.418 170.856 8697 Min Nonbonded Distance : 1.244 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 3.45 % Allowed : 23.73 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.16), residues: 2640 helix: 0.74 (0.14), residues: 1372 sheet: -0.53 (0.34), residues: 193 loop : -0.10 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGLC 201 TYR 0.043 0.002 TYR B 451 PHE 0.049 0.002 PHE 2 32 TRP 0.034 0.001 TRP B 707 HIS 0.009 0.001 HISLE 128 Details of bonding type rmsd covalent geometry : bond 0.00336 (30687) covalent geometry : angle 0.70367 (43044) hydrogen bonds : bond 0.04200 ( 1337) hydrogen bonds : angle 4.66309 ( 3579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 323 time to evaluate : 0.759 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: 2 5 ASN cc_start: 0.8908 (m-40) cc_final: 0.8587 (t0) REVERT: 2 10 ASP cc_start: 0.9292 (p0) cc_final: 0.8847 (p0) REVERT: 2 13 ASN cc_start: 0.9234 (m-40) cc_final: 0.8946 (m110) REVERT: 2 27 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8828 (mm110) REVERT: 2 55 TYR cc_start: 0.8258 (p90) cc_final: 0.7858 (p90) REVERT: 2 98 MET cc_start: 0.8780 (tmm) cc_final: 0.8527 (ppp) REVERT: 2 111 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8334 (m) REVERT: B 282 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: B 447 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7650 (mmtt) REVERT: B 530 MET cc_start: 0.6373 (ppp) cc_final: 0.5710 (ppp) REVERT: B 538 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: B 692 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8519 (mm) REVERT: LC 35 ASP cc_start: 0.9297 (p0) cc_final: 0.8858 (p0) REVERT: LC 86 ARG cc_start: 0.4317 (OUTLIER) cc_final: 0.3984 (mtp85) REVERT: LC 95 MET cc_start: 0.9225 (pmm) cc_final: 0.8064 (mmt) REVERT: LC 288 ASP cc_start: 0.9364 (t0) cc_final: 0.9027 (t0) REVERT: LE 57 TYR cc_start: 0.9301 (m-80) cc_final: 0.9093 (m-10) REVERT: LE 119 GLU cc_start: 0.8053 (mp0) cc_final: 0.7768 (pm20) REVERT: LE 128 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.6654 (t70) REVERT: LE 240 TYR cc_start: 0.5352 (OUTLIER) cc_final: 0.2069 (t80) REVERT: Lk 4 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8883 (ttmp) REVERT: Lk 7 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8669 (pp20) REVERT: Lk 30 ASP cc_start: 0.9482 (p0) cc_final: 0.9136 (p0) REVERT: LY 10 ASP cc_start: 0.9054 (t0) cc_final: 0.8837 (t0) REVERT: LY 86 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.9165 (pm20) REVERT: Lh 23 ASP cc_start: 0.9128 (p0) cc_final: 0.8881 (p0) REVERT: Lh 30 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8850 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4697 (OUTLIER) cc_final: 0.3408 (tptt) REVERT: Lh 100 GLU cc_start: 0.8444 (pp20) cc_final: 0.8191 (pp20) REVERT: Lh 101 ASN cc_start: 0.9600 (m-40) cc_final: 0.9186 (m-40) REVERT: LX 57 GLN cc_start: 0.9330 (tp40) cc_final: 0.8865 (mm110) REVERT: LX 101 ASP cc_start: 0.9113 (t70) cc_final: 0.8889 (t0) REVERT: LX 118 ASP cc_start: 0.9102 (t0) cc_final: 0.8882 (t0) REVERT: LR 28 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8647 (mm-30) REVERT: LR 151 ARG cc_start: 0.9645 (tpp80) cc_final: 0.8902 (tpm170) outliers start: 81 outliers final: 43 residues processed: 385 average time/residue: 0.5577 time to fit residues: 256.9094 Evaluate side-chains 346 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASN Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 132 GLU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 699 PHE Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 145 THR Chi-restraints excluded: chain LE residue 163 VAL Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain LE residue 279 ASN Chi-restraints excluded: chain Lk residue 4 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LY residue 86 GLN Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 86 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain LX residue 42 THR Chi-restraints excluded: chain LX residue 82 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LR residue 28 GLU Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain LR residue 140 GLU Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 17 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 81 HIS A 167 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 86 ASN ** LR 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.070944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.049788 restraints weight = 166102.479| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.80 r_work: 0.3126 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 30687 Z= 0.432 Angle : 0.901 16.604 43044 Z= 0.453 Chirality : 0.046 0.338 5027 Planarity : 0.007 0.157 4140 Dihedral : 21.657 173.611 8697 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 3.49 % Allowed : 24.80 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.16), residues: 2640 helix: 0.47 (0.14), residues: 1366 sheet: -0.54 (0.37), residues: 183 loop : -0.29 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARGLY 126 TYR 0.033 0.003 TYR 2 122 PHE 0.051 0.002 PHE 2 32 TRP 0.033 0.002 TRP B 707 HIS 0.019 0.002 HISLC 85 Details of bonding type rmsd covalent geometry : bond 0.00893 (30687) covalent geometry : angle 0.90089 (43044) hydrogen bonds : bond 0.06034 ( 1337) hydrogen bonds : angle 5.13260 ( 3579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 292 time to evaluate : 1.027 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: 2 5 ASN cc_start: 0.8981 (m-40) cc_final: 0.8758 (t0) REVERT: 2 10 ASP cc_start: 0.9250 (p0) cc_final: 0.8734 (p0) REVERT: 2 13 ASN cc_start: 0.9264 (m-40) cc_final: 0.9007 (m110) REVERT: 2 122 TYR cc_start: 0.8948 (p90) cc_final: 0.8740 (p90) REVERT: 2 124 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8782 (p0) REVERT: 2 147 MET cc_start: 0.8473 (tpp) cc_final: 0.8026 (tpp) REVERT: B 44 GLU cc_start: 0.8984 (pm20) cc_final: 0.8722 (tp30) REVERT: B 51 MET cc_start: 0.8116 (tmm) cc_final: 0.7812 (ppp) REVERT: B 530 MET cc_start: 0.6666 (ppp) cc_final: 0.5981 (ppp) REVERT: B 538 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: B 586 ASN cc_start: 0.8757 (t0) cc_final: 0.8364 (p0) REVERT: B 692 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8497 (mp) REVERT: LC 86 ARG cc_start: 0.4347 (OUTLIER) cc_final: 0.2516 (ptt90) REVERT: LC 95 MET cc_start: 0.9227 (pmm) cc_final: 0.8235 (tpt) REVERT: LC 288 ASP cc_start: 0.9397 (t0) cc_final: 0.9051 (t0) REVERT: LE 57 TYR cc_start: 0.9410 (m-80) cc_final: 0.9140 (m-10) REVERT: LE 128 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.6651 (t70) REVERT: Lk 4 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8887 (ttmp) REVERT: Lk 30 ASP cc_start: 0.9512 (p0) cc_final: 0.9195 (p0) REVERT: Lk 40 ARG cc_start: 0.4991 (OUTLIER) cc_final: 0.4627 (pmt170) REVERT: LY 43 ASN cc_start: 0.9171 (t0) cc_final: 0.8707 (t0) REVERT: LY 86 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.9305 (pm20) REVERT: LY 124 LYS cc_start: 0.9617 (OUTLIER) cc_final: 0.9326 (tmmm) REVERT: Lh 23 ASP cc_start: 0.9235 (p0) cc_final: 0.8994 (p0) REVERT: Lh 30 GLN cc_start: 0.9108 (mp10) cc_final: 0.8890 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4706 (OUTLIER) cc_final: 0.3494 (mptt) REVERT: LX 78 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.8856 (mmmm) REVERT: LX 101 ASP cc_start: 0.9245 (t70) cc_final: 0.9003 (t0) REVERT: LX 111 GLN cc_start: 0.9428 (mm-40) cc_final: 0.9061 (tp-100) REVERT: LR 27 ASN cc_start: 0.9550 (p0) cc_final: 0.9321 (p0) REVERT: LR 28 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8799 (mm-30) REVERT: LR 151 ARG cc_start: 0.9658 (tpp80) cc_final: 0.8961 (tpm170) outliers start: 82 outliers final: 45 residues processed: 357 average time/residue: 0.5554 time to fit residues: 235.9085 Evaluate side-chains 331 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASN Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 124 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 145 THR Chi-restraints excluded: chain LE residue 163 VAL Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain Lk residue 4 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 40 ARG Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Lk residue 69 LEU Chi-restraints excluded: chain LY residue 86 GLN Chi-restraints excluded: chain LY residue 124 LYS Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 86 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain LX residue 42 THR Chi-restraints excluded: chain LX residue 67 ARG Chi-restraints excluded: chain LX residue 78 LYS Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 102 VAL Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LX residue 145 ASP Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain LR residue 28 GLU Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 155 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.072542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051245 restraints weight = 162007.517| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.49 r_work: 0.3171 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30687 Z= 0.216 Angle : 0.796 16.463 43044 Z= 0.397 Chirality : 0.043 0.378 5027 Planarity : 0.005 0.159 4140 Dihedral : 21.631 169.675 8696 Min Nonbonded Distance : 1.233 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.90 % Allowed : 25.73 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 2640 helix: 0.58 (0.14), residues: 1361 sheet: -0.71 (0.36), residues: 181 loop : -0.20 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 70 TYR 0.042 0.002 TYR B 451 PHE 0.050 0.002 PHE 2 32 TRP 0.034 0.002 TRP B 707 HIS 0.016 0.001 HISLR 143 Details of bonding type rmsd covalent geometry : bond 0.00460 (30687) covalent geometry : angle 0.79554 (43044) hydrogen bonds : bond 0.04584 ( 1337) hydrogen bonds : angle 4.94694 ( 3579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 313 time to evaluate : 0.969 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: 2 5 ASN cc_start: 0.8953 (m-40) cc_final: 0.8696 (t0) REVERT: 2 10 ASP cc_start: 0.9278 (p0) cc_final: 0.8831 (p0) REVERT: 2 12 MET cc_start: 0.9229 (pmm) cc_final: 0.8586 (pmm) REVERT: 2 13 ASN cc_start: 0.9281 (m-40) cc_final: 0.8905 (m110) REVERT: 2 27 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8782 (mm110) REVERT: 2 124 ASN cc_start: 0.9250 (m110) cc_final: 0.8847 (p0) REVERT: A 191 MET cc_start: 0.8619 (ptt) cc_final: 0.8384 (ptt) REVERT: B 51 MET cc_start: 0.8079 (tmm) cc_final: 0.7773 (ppp) REVERT: B 586 ASN cc_start: 0.8740 (t0) cc_final: 0.8299 (p0) REVERT: B 692 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8682 (mp) REVERT: LC 35 ASP cc_start: 0.9309 (p0) cc_final: 0.8822 (p0) REVERT: LC 86 ARG cc_start: 0.4465 (OUTLIER) cc_final: 0.3683 (mtm110) REVERT: LC 95 MET cc_start: 0.9225 (pmm) cc_final: 0.8106 (mmt) REVERT: LC 288 ASP cc_start: 0.9381 (t0) cc_final: 0.9064 (t0) REVERT: LE 57 TYR cc_start: 0.9331 (m-80) cc_final: 0.9055 (m-10) REVERT: LE 63 TYR cc_start: 0.9236 (t80) cc_final: 0.8437 (t80) REVERT: LE 128 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6433 (t70) REVERT: LE 240 TYR cc_start: 0.5301 (OUTLIER) cc_final: 0.1545 (t80) REVERT: Lk 4 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8946 (ttmp) REVERT: Lk 7 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8682 (pp20) REVERT: Lk 30 ASP cc_start: 0.9511 (p0) cc_final: 0.9156 (p0) REVERT: Lk 40 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.4649 (pmt170) REVERT: Lh 23 ASP cc_start: 0.9195 (p0) cc_final: 0.8979 (p0) REVERT: Lh 30 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8838 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4723 (OUTLIER) cc_final: 0.3449 (tptt) REVERT: LX 78 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8708 (mmmm) REVERT: LX 101 ASP cc_start: 0.9191 (t70) cc_final: 0.8953 (t0) REVERT: LX 111 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9021 (tp-100) REVERT: LR 28 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8787 (mp0) REVERT: LR 151 ARG cc_start: 0.9648 (tpp80) cc_final: 0.8925 (tpm170) outliers start: 68 outliers final: 43 residues processed: 368 average time/residue: 0.5657 time to fit residues: 247.2067 Evaluate side-chains 345 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASN Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 145 THR Chi-restraints excluded: chain LE residue 163 VAL Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain LE residue 279 ASN Chi-restraints excluded: chain Lk residue 4 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lk residue 40 ARG Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain LY residue 118 ILE Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 86 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain LX residue 42 THR Chi-restraints excluded: chain LX residue 78 LYS Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain LR residue 28 GLU Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Chi-restraints excluded: chain Lr residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 274 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 295 optimal weight: 0.6980 chunk 101 optimal weight: 0.0270 chunk 197 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 252 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 overall best weight: 1.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.073531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.052349 restraints weight = 160778.514| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.53 r_work: 0.3200 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30687 Z= 0.160 Angle : 0.785 17.474 43044 Z= 0.392 Chirality : 0.041 0.417 5027 Planarity : 0.005 0.149 4140 Dihedral : 21.524 169.859 8696 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 2.26 % Allowed : 26.84 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.16), residues: 2640 helix: 0.60 (0.14), residues: 1362 sheet: -0.79 (0.35), residues: 181 loop : -0.17 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGLC 201 TYR 0.026 0.001 TYR 2 55 PHE 0.038 0.001 PHE 2 128 TRP 0.040 0.002 TRP B 707 HIS 0.016 0.001 HISLR 143 Details of bonding type rmsd covalent geometry : bond 0.00350 (30687) covalent geometry : angle 0.78515 (43044) hydrogen bonds : bond 0.04350 ( 1337) hydrogen bonds : angle 4.88009 ( 3579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 317 time to evaluate : 0.698 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: 2 5 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.7826 (t0) REVERT: 2 7 ARG cc_start: 0.8943 (tpt90) cc_final: 0.8242 (mmm160) REVERT: 2 10 ASP cc_start: 0.9381 (p0) cc_final: 0.8675 (p0) REVERT: 2 13 ASN cc_start: 0.9245 (m-40) cc_final: 0.8904 (m110) REVERT: 2 27 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8872 (mm110) REVERT: 2 98 MET cc_start: 0.8824 (ppp) cc_final: 0.8294 (ppp) REVERT: 2 124 ASN cc_start: 0.9308 (m110) cc_final: 0.8885 (p0) REVERT: A 191 MET cc_start: 0.8488 (ptt) cc_final: 0.8254 (ptt) REVERT: A 306 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8933 (tm-30) REVERT: A 308 MET cc_start: 0.8797 (ptm) cc_final: 0.8581 (ttt) REVERT: A 309 GLU cc_start: 0.8657 (pm20) cc_final: 0.8384 (pm20) REVERT: B 51 MET cc_start: 0.8082 (tmm) cc_final: 0.7776 (ppp) REVERT: B 438 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: B 538 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 586 ASN cc_start: 0.8741 (t0) cc_final: 0.8315 (p0) REVERT: B 699 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8793 (m-80) REVERT: LC 35 ASP cc_start: 0.9295 (p0) cc_final: 0.8829 (p0) REVERT: LC 86 ARG cc_start: 0.4409 (OUTLIER) cc_final: 0.3744 (mtm110) REVERT: LC 95 MET cc_start: 0.9242 (pmm) cc_final: 0.8077 (mmt) REVERT: LC 189 MET cc_start: 0.9116 (mmp) cc_final: 0.8562 (ptt) REVERT: LC 288 ASP cc_start: 0.9367 (t0) cc_final: 0.9047 (t0) REVERT: LE 57 TYR cc_start: 0.9296 (m-80) cc_final: 0.8991 (m-10) REVERT: LE 63 TYR cc_start: 0.9138 (t80) cc_final: 0.8387 (t80) REVERT: LE 128 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6329 (t70) REVERT: LE 240 TYR cc_start: 0.5212 (OUTLIER) cc_final: 0.1495 (t80) REVERT: LE 279 ASN cc_start: 0.3820 (OUTLIER) cc_final: 0.3357 (m-40) REVERT: Lk 4 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8904 (ttmp) REVERT: Lk 7 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8664 (pp20) REVERT: Lh 30 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8810 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4599 (OUTLIER) cc_final: 0.3320 (mptt) REVERT: LX 55 ARG cc_start: 0.7725 (tpm170) cc_final: 0.7307 (tpm-80) REVERT: LX 78 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8599 (mmmm) REVERT: LX 101 ASP cc_start: 0.9124 (t70) cc_final: 0.8881 (t0) REVERT: LR 28 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8748 (mp0) REVERT: LR 151 ARG cc_start: 0.9635 (tpp80) cc_final: 0.8895 (tpm170) outliers start: 53 outliers final: 34 residues processed: 357 average time/residue: 0.5411 time to fit residues: 229.5606 Evaluate side-chains 344 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 297 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 5 ASN Chi-restraints excluded: chain 2 residue 49 ASN Chi-restraints excluded: chain 2 residue 73 THR Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 699 PHE Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 86 ARG Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 145 THR Chi-restraints excluded: chain LE residue 163 VAL Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain LE residue 243 THR Chi-restraints excluded: chain LE residue 279 ASN Chi-restraints excluded: chain Lk residue 4 LYS Chi-restraints excluded: chain Lk residue 10 ASP Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 86 LYS Chi-restraints excluded: chain Lh residue 88 THR Chi-restraints excluded: chain LX residue 42 THR Chi-restraints excluded: chain LX residue 78 LYS Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 116 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LR residue 22 VAL Chi-restraints excluded: chain LR residue 28 GLU Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 84 THR Chi-restraints excluded: chain Lr residue 24 THR Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 140 optimal weight: 0.0870 chunk 128 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 292 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 265 optimal weight: 0.0050 chunk 286 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 overall best weight: 3.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 93 ASN ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.073155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.052183 restraints weight = 162975.867| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.67 r_work: 0.3189 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30687 Z= 0.200 Angle : 0.802 18.742 43044 Z= 0.402 Chirality : 0.042 0.408 5027 Planarity : 0.005 0.145 4140 Dihedral : 21.520 171.559 8696 Min Nonbonded Distance : 1.213 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 2.39 % Allowed : 27.40 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2640 helix: 0.59 (0.14), residues: 1363 sheet: -0.83 (0.35), residues: 181 loop : -0.19 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARGLC 201 TYR 0.048 0.002 TYR 2 26 PHE 0.036 0.002 PHE 2 128 TRP 0.032 0.001 TRP B 707 HIS 0.016 0.001 HISLR 143 Details of bonding type rmsd covalent geometry : bond 0.00431 (30687) covalent geometry : angle 0.80193 (43044) hydrogen bonds : bond 0.04473 ( 1337) hydrogen bonds : angle 4.94672 ( 3579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17960.90 seconds wall clock time: 304 minutes 47.07 seconds (18287.07 seconds total)