Starting phenix.real_space_refine on Wed Jun 25 05:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fpz_50641/06_2025/9fpz_50641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fpz_50641/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fpz_50641/06_2025/9fpz_50641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fpz_50641/06_2025/9fpz_50641.map" model { file = "/net/cci-nas-00/data/ceres_data/9fpz_50641/06_2025/9fpz_50641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fpz_50641/06_2025/9fpz_50641.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 23.15, per 1000 atoms: 0.79 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: 7.28 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 11.28 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: 13.76 Time building geometry restraints manager: 8.67 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: 189.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.300 Check model and map are aligned: 0.240 Set scattering table: 0.270 Process input model: 80.260 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 285.770 ------------------------------------------------------------------------------- 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 : 14.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (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 TRP 0.024 0.001 TRP B 284 HIS 0.012 0.001 HIS 2 16 PHE 0.044 0.001 PHE 2 32 TYR 0.075 0.002 TYR 2 30 ARG 0.019 0.000 ARG B 70 Details of bonding type rmsd hydrogen bonds : bond 0.17994 ( 1337) hydrogen bonds : angle 6.70850 ( 3579) covalent geometry : bond 0.00334 (30687) covalent geometry : angle 0.73781 (43044) *********************** 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 : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 1.2474 time to fit residues: 544.9849 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 : 2.911 ------------------------------------------------------------------------------- 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 249 optimal weight: 0.0070 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 268 optimal weight: 0.0060 overall best weight: 3.4020 ------------------------------------------------------------------------------- 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** A 409 ASN B 480 ASN B 488 GLN B 514 HIS B 522 GLN B 620 GLN B 624 GLN B 795 ASN LC 142 HIS LC 299 GLN LE 245 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 4 HIS Lr 36 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.074277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052692 restraints weight = 162106.896| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.82 r_work: 0.3194 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30687 Z= 0.200 Angle : 0.671 14.803 43044 Z= 0.338 Chirality : 0.040 0.355 5027 Planarity : 0.005 0.084 4140 Dihedral : 21.394 167.933 8740 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % Rotamer: Outliers : 3.45 % Allowed : 18.66 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2640 helix: 0.70 (0.14), residues: 1374 sheet: -0.21 (0.34), residues: 219 loop : 0.07 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 284 HIS 0.017 0.001 HIS 2 16 PHE 0.028 0.001 PHE 2 32 TYR 0.031 0.002 TYR 2 30 ARG 0.014 0.000 ARGLY 126 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 1337) hydrogen bonds : angle 5.04740 ( 3579) covalent geometry : bond 0.00416 (30687) covalent geometry : angle 0.67099 (43044) *********************** 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 409 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 328 time to evaluate : 2.798 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 5 ASN cc_start: 0.8738 (t0) cc_final: 0.8425 (m-40) REVERT: 2 14 MET cc_start: 0.9159 (pmm) cc_final: 0.8904 (pmm) REVERT: 2 16 HIS cc_start: 0.8519 (m-70) cc_final: 0.8280 (m-70) REVERT: 2 60 MET cc_start: 0.7785 (tpt) cc_final: 0.7045 (tpt) REVERT: 2 62 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7343 (mp0) REVERT: 2 147 MET cc_start: 0.8577 (tpp) cc_final: 0.8197 (tpp) REVERT: A 294 ASP cc_start: 0.8943 (t0) cc_final: 0.8691 (t0) REVERT: A 430 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8251 (tpp) REVERT: B 282 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: B 614 ASN cc_start: 0.9562 (OUTLIER) cc_final: 0.9255 (p0) REVERT: B 692 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8583 (tt) REVERT: LC 35 ASP cc_start: 0.9315 (p0) cc_final: 0.8898 (p0) REVERT: LC 95 MET cc_start: 0.9215 (pmm) cc_final: 0.7979 (mmt) REVERT: LC 325 MET cc_start: 0.9255 (tpt) cc_final: 0.9021 (tpp) REVERT: LC 327 LYS cc_start: 0.6326 (mmpt) cc_final: 0.4324 (mptm) REVERT: LE 119 GLU cc_start: 0.8154 (mp0) cc_final: 0.7940 (pm20) REVERT: LE 240 TYR cc_start: 0.5404 (OUTLIER) cc_final: 0.2587 (t80) REVERT: Lk 30 ASP cc_start: 0.9379 (p0) cc_final: 0.9099 (p0) REVERT: LY 43 ASN cc_start: 0.9156 (t0) cc_final: 0.8948 (t0) REVERT: Lh 23 ASP cc_start: 0.9027 (p0) cc_final: 0.8717 (p0) REVERT: Lh 30 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8872 (mm-40) REVERT: Lh 111 GLU cc_start: 0.8700 (pp20) cc_final: 0.8473 (pp20) REVERT: LX 57 GLN cc_start: 0.9257 (tp40) cc_final: 0.8740 (mm110) REVERT: LX 78 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.8703 (mmmm) REVERT: LX 101 ASP cc_start: 0.9138 (t70) cc_final: 0.8822 (t0) REVERT: LX 118 ASP cc_start: 0.9235 (t0) cc_final: 0.9000 (t0) REVERT: LR 25 ASP cc_start: 0.9398 (t70) cc_final: 0.8906 (t0) REVERT: LR 28 GLU cc_start: 0.8921 (mp0) cc_final: 0.8610 (mp0) outliers start: 81 outliers final: 27 residues processed: 387 average time/residue: 1.2974 time to fit residues: 598.0260 Evaluate side-chains 321 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 2.902 ------------------------------------------------------------------------------- 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 A residue 430 MET Chi-restraints excluded: chain A residue 447 LEU 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 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain LX residue 42 THR 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 128 ILE Chi-restraints excluded: chain LX residue 138 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 148 ASP Chi-restraints excluded: chain Lr residue 24 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 98 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 7 optimal weight: 40.0000 chunk 85 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 49 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN B 179 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 85 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 4 HIS Lr 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.073151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.051515 restraints weight = 163100.038| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.73 r_work: 0.3165 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30687 Z= 0.248 Angle : 0.684 15.277 43044 Z= 0.346 Chirality : 0.040 0.316 5027 Planarity : 0.005 0.113 4140 Dihedral : 21.438 170.894 8711 Min Nonbonded Distance : 1.247 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 4.26 % Allowed : 18.96 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2640 helix: 0.74 (0.14), residues: 1373 sheet: -0.27 (0.33), residues: 218 loop : 0.01 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 284 HIS 0.010 0.001 HIS 2 16 PHE 0.022 0.002 PHE B 174 TYR 0.046 0.002 TYR B 451 ARG 0.014 0.001 ARGLY 126 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 1337) hydrogen bonds : angle 4.83754 ( 3579) covalent geometry : bond 0.00517 (30687) covalent geometry : angle 0.68411 (43044) *********************** 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 414 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 314 time to evaluate : 2.830 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 9 GLU cc_start: 0.8755 (pm20) cc_final: 0.8515 (pm20) REVERT: 2 14 MET cc_start: 0.9210 (pmm) cc_final: 0.8976 (pmm) REVERT: 2 16 HIS cc_start: 0.8718 (m-70) cc_final: 0.8401 (m-70) REVERT: 2 55 TYR cc_start: 0.7940 (p90) cc_final: 0.7422 (p90) REVERT: 2 147 MET cc_start: 0.8914 (tpp) cc_final: 0.8560 (mmm) REVERT: A 306 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8703 (tp30) REVERT: B 47 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: B 282 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: B 614 ASN cc_start: 0.9558 (OUTLIER) cc_final: 0.9256 (p0) REVERT: B 692 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8430 (tt) REVERT: LC 35 ASP cc_start: 0.9320 (p0) cc_final: 0.8887 (p0) REVERT: LC 62 THR cc_start: 0.8855 (p) cc_final: 0.8652 (p) REVERT: LC 86 ARG cc_start: 0.4355 (OUTLIER) cc_final: 0.1351 (mtt180) REVERT: LC 95 MET cc_start: 0.9206 (pmm) cc_final: 0.8054 (mmt) REVERT: LE 57 TYR cc_start: 0.9331 (m-10) cc_final: 0.9074 (m-10) REVERT: LE 119 GLU cc_start: 0.8103 (mp0) cc_final: 0.7881 (pm20) REVERT: LE 139 LYS cc_start: 0.5018 (OUTLIER) cc_final: 0.4317 (pttt) REVERT: LE 240 TYR cc_start: 0.5279 (OUTLIER) cc_final: 0.2259 (t80) REVERT: Lk 4 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8894 (ttmp) REVERT: Lk 57 LYS cc_start: 0.9682 (ttpp) cc_final: 0.9482 (tmmt) REVERT: LY 43 ASN cc_start: 0.9131 (t0) cc_final: 0.8922 (t0) REVERT: Lh 23 ASP cc_start: 0.9088 (p0) cc_final: 0.8666 (p0) REVERT: Lh 30 GLN cc_start: 0.9078 (mp10) cc_final: 0.8855 (mm-40) REVERT: Lh 100 GLU cc_start: 0.8494 (pp20) cc_final: 0.8162 (pp20) REVERT: Lh 101 ASN cc_start: 0.9604 (m-40) cc_final: 0.9186 (m-40) REVERT: Lh 111 GLU cc_start: 0.8753 (pp20) cc_final: 0.8511 (pp20) REVERT: LX 57 GLN cc_start: 0.9298 (tp40) cc_final: 0.8797 (mm110) REVERT: LX 63 LYS cc_start: 0.5358 (OUTLIER) cc_final: 0.4725 (mptt) REVERT: LX 78 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.8660 (mmmm) REVERT: LX 101 ASP cc_start: 0.9167 (t70) cc_final: 0.8887 (t0) REVERT: LX 118 ASP cc_start: 0.9259 (t0) cc_final: 0.9042 (t0) REVERT: LR 25 ASP cc_start: 0.9407 (t70) cc_final: 0.8975 (t0) REVERT: LR 28 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8705 (mp0) REVERT: Lr 108 MET cc_start: 0.6143 (ttt) cc_final: 0.5939 (ttt) outliers start: 100 outliers final: 37 residues processed: 389 average time/residue: 1.5397 time to fit residues: 716.4090 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 : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 7 ARG Chi-restraints excluded: chain 2 residue 110 HIS 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 A residue 378 MET 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 650 VAL 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 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 LY residue 41 LYS Chi-restraints excluded: chain LY residue 82 ILE Chi-restraints excluded: chain Lh residue 42 SER 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 28 GLU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 278 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 221 optimal weight: 0.0020 chunk 26 optimal weight: 5.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN Lh 68 ASN ** 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 = 0.3859 r_free = 0.3859 target = 0.073342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051882 restraints weight = 163664.421| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.73 r_work: 0.3177 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2027 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= 0.204 Angle : 0.667 15.105 43044 Z= 0.335 Chirality : 0.039 0.288 5027 Planarity : 0.005 0.130 4140 Dihedral : 21.457 170.630 8709 Min Nonbonded Distance : 1.225 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 4.35 % Allowed : 19.77 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2640 helix: 0.71 (0.14), residues: 1377 sheet: -0.40 (0.32), residues: 218 loop : 0.04 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 284 HIS 0.009 0.001 HIS 2 16 PHE 0.022 0.001 PHE 2 32 TYR 0.025 0.002 TYR 2 30 ARG 0.010 0.000 ARGLY 126 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 1337) hydrogen bonds : angle 4.73108 ( 3579) covalent geometry : bond 0.00428 (30687) covalent geometry : angle 0.66699 (43044) *********************** 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 420 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 318 time to evaluate : 2.977 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: 2 12 MET cc_start: 0.9235 (pp-130) cc_final: 0.8886 (pp-130) REVERT: 2 13 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.9023 (t0) REVERT: 2 14 MET cc_start: 0.9223 (pmm) cc_final: 0.8919 (pmm) REVERT: 2 16 HIS cc_start: 0.9148 (m-70) cc_final: 0.8114 (m-70) REVERT: 2 55 TYR cc_start: 0.7936 (p90) cc_final: 0.7514 (p90) REVERT: 2 98 MET cc_start: 0.8732 (tmm) cc_final: 0.8476 (ppp) REVERT: 2 129 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9084 (pm20) REVERT: 2 147 MET cc_start: 0.9225 (tpp) cc_final: 0.8570 (mmp) REVERT: A 191 MET cc_start: 0.8650 (ptt) cc_final: 0.8428 (ptt) REVERT: A 305 GLN cc_start: 0.9244 (tt0) cc_final: 0.8923 (tt0) REVERT: A 384 MET cc_start: 0.8946 (ttm) cc_final: 0.8624 (tpp) REVERT: B 47 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: B 282 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: B 465 CYS cc_start: 0.8691 (m) cc_final: 0.8466 (m) REVERT: B 614 ASN cc_start: 0.9560 (OUTLIER) cc_final: 0.9282 (p0) REVERT: B 692 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8497 (tt) REVERT: LC 35 ASP cc_start: 0.9338 (p0) cc_final: 0.8889 (p0) REVERT: LC 62 THR cc_start: 0.8885 (p) cc_final: 0.8676 (p) REVERT: LC 86 ARG cc_start: 0.4199 (OUTLIER) cc_final: 0.1148 (mtt180) REVERT: LC 95 MET cc_start: 0.9208 (pmm) cc_final: 0.8080 (mmt) REVERT: LC 189 MET cc_start: 0.9202 (mmp) cc_final: 0.8556 (ptt) REVERT: LC 288 ASP cc_start: 0.9391 (t0) cc_final: 0.9122 (t0) REVERT: LE 57 TYR cc_start: 0.9346 (m-10) cc_final: 0.9086 (m-10) REVERT: LE 119 GLU cc_start: 0.8103 (mp0) cc_final: 0.7901 (pm20) REVERT: LE 128 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.6859 (t70) REVERT: LE 139 LYS cc_start: 0.4898 (OUTLIER) cc_final: 0.4193 (pttt) REVERT: LE 240 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.2201 (t80) REVERT: LY 43 ASN cc_start: 0.9125 (t0) cc_final: 0.8876 (t0) REVERT: Lh 23 ASP cc_start: 0.9096 (p0) cc_final: 0.8737 (p0) REVERT: Lh 30 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8869 (mm-40) REVERT: Lh 100 GLU cc_start: 0.8495 (pp20) cc_final: 0.8170 (pp20) REVERT: Lh 101 ASN cc_start: 0.9582 (m-40) cc_final: 0.9142 (m-40) REVERT: Lh 111 GLU cc_start: 0.8765 (pp20) cc_final: 0.8523 (pp20) REVERT: LX 57 GLN cc_start: 0.9328 (tp40) cc_final: 0.8820 (mm110) REVERT: LX 101 ASP cc_start: 0.9168 (t70) cc_final: 0.8946 (t0) REVERT: LX 118 ASP cc_start: 0.9224 (t0) cc_final: 0.9003 (t0) REVERT: LR 28 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8576 (mm-30) outliers start: 102 outliers final: 40 residues processed: 391 average time/residue: 1.3103 time to fit residues: 607.9674 Evaluate side-chains 334 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 7 ARG Chi-restraints excluded: chain 2 residue 13 ASN Chi-restraints excluded: chain 2 residue 129 GLN 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 378 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 274 LEU 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 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 101 MET 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 128 HIS Chi-restraints excluded: chain LE residue 139 LYS Chi-restraints excluded: chain LE residue 145 THR Chi-restraints excluded: chain LE residue 240 TYR Chi-restraints excluded: chain LE residue 279 ASN 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 LY residue 41 LYS 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 88 THR Chi-restraints excluded: chain LX residue 42 THR 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 155 ILE 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 84 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 191 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 255 optimal weight: 0.0000 chunk 33 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** LC 85 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.073696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.052223 restraints weight = 161525.445| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.66 r_work: 0.3190 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30687 Z= 0.174 Angle : 0.682 13.778 43044 Z= 0.342 Chirality : 0.039 0.332 5027 Planarity : 0.005 0.135 4140 Dihedral : 21.431 170.662 8702 Min Nonbonded Distance : 1.231 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 4.52 % Allowed : 20.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2640 helix: 0.72 (0.14), residues: 1376 sheet: -0.43 (0.33), residues: 205 loop : 0.02 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 707 HIS 0.014 0.001 HIS 2 16 PHE 0.036 0.001 PHE 2 128 TYR 0.039 0.001 TYR B 451 ARG 0.019 0.000 ARGLC 201 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 1337) hydrogen bonds : angle 4.68882 ( 3579) covalent geometry : bond 0.00372 (30687) covalent geometry : angle 0.68151 (43044) *********************** 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 416 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 310 time to evaluate : 3.031 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: 2 14 MET cc_start: 0.9253 (pmm) cc_final: 0.9010 (pmm) REVERT: 2 16 HIS cc_start: 0.8871 (m-70) cc_final: 0.8450 (m170) REVERT: 2 55 TYR cc_start: 0.7961 (p90) cc_final: 0.7622 (p90) REVERT: 2 147 MET cc_start: 0.9254 (tpp) cc_final: 0.8789 (mmp) REVERT: A 191 MET cc_start: 0.8618 (ptt) cc_final: 0.8404 (ptt) REVERT: B 282 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: B 465 CYS cc_start: 0.8772 (m) cc_final: 0.8542 (m) REVERT: B 614 ASN cc_start: 0.9556 (OUTLIER) cc_final: 0.9322 (p0) REVERT: B 686 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: B 692 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8500 (mm) REVERT: LC 35 ASP cc_start: 0.9326 (p0) cc_final: 0.8868 (p0) REVERT: LC 86 ARG cc_start: 0.4320 (OUTLIER) cc_final: 0.1240 (mtt180) REVERT: LC 95 MET cc_start: 0.9214 (pmm) cc_final: 0.8089 (mmt) REVERT: LC 189 MET cc_start: 0.8872 (mmp) cc_final: 0.8141 (mtm) REVERT: LC 288 ASP cc_start: 0.9369 (t0) cc_final: 0.9065 (t0) REVERT: LE 57 TYR cc_start: 0.9333 (m-80) cc_final: 0.9063 (m-10) REVERT: LE 119 GLU cc_start: 0.8128 (mp0) cc_final: 0.7850 (pm20) REVERT: LE 128 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.6738 (t70) REVERT: LE 139 LYS cc_start: 0.4726 (OUTLIER) cc_final: 0.4032 (pttt) REVERT: LE 240 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.2119 (t80) REVERT: Lk 4 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8842 (ttmp) REVERT: Lk 30 ASP cc_start: 0.9440 (OUTLIER) cc_final: 0.9202 (p0) REVERT: LY 43 ASN cc_start: 0.9104 (t0) cc_final: 0.8850 (t0) REVERT: Lh 23 ASP cc_start: 0.9109 (p0) cc_final: 0.8803 (p0) REVERT: Lh 30 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8866 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4617 (OUTLIER) cc_final: 0.3540 (mptt) REVERT: Lh 100 GLU cc_start: 0.8532 (pp20) cc_final: 0.8254 (pp20) REVERT: Lh 101 ASN cc_start: 0.9573 (m-40) cc_final: 0.9080 (m-40) REVERT: Lh 111 GLU cc_start: 0.8758 (pp20) cc_final: 0.8528 (pp20) REVERT: LX 57 GLN cc_start: 0.9328 (tp40) cc_final: 0.8853 (mm110) REVERT: LX 101 ASP cc_start: 0.9159 (t70) cc_final: 0.8956 (t0) REVERT: LX 118 ASP cc_start: 0.9171 (t0) cc_final: 0.8942 (t0) REVERT: LR 28 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8541 (mm-30) REVERT: Lr 108 MET cc_start: 0.5995 (ttt) cc_final: 0.5784 (ttt) outliers start: 106 outliers final: 43 residues processed: 387 average time/residue: 1.2045 time to fit residues: 559.2209 Evaluate side-chains 341 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 7 ARG 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 322 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 325 VAL 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 686 GLU 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 LE residue 51 VAL Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 139 LYS 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 30 ASP Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LY residue 41 LYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 238 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 16 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS ** LC 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN LR 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.073391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.052187 restraints weight = 163080.444| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.65 r_work: 0.3186 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30687 Z= 0.205 Angle : 0.702 16.012 43044 Z= 0.351 Chirality : 0.039 0.322 5027 Planarity : 0.005 0.141 4140 Dihedral : 21.440 171.375 8702 Min Nonbonded Distance : 1.217 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 4.39 % Allowed : 21.90 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2640 helix: 0.71 (0.14), residues: 1372 sheet: -0.52 (0.34), residues: 202 loop : -0.04 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 707 HIS 0.010 0.001 HIS 2 16 PHE 0.026 0.001 PHE 2 32 TYR 0.021 0.001 TYRLX 117 ARG 0.011 0.000 ARGLY 126 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 1337) hydrogen bonds : angle 4.69681 ( 3579) covalent geometry : bond 0.00434 (30687) covalent geometry : angle 0.70227 (43044) *********************** 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 419 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 316 time to evaluate : 3.203 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 14 MET cc_start: 0.9260 (pmm) cc_final: 0.8994 (pmm) REVERT: 2 55 TYR cc_start: 0.8126 (p90) cc_final: 0.7792 (p90) REVERT: 2 98 MET cc_start: 0.8741 (tmm) cc_final: 0.8540 (ppp) REVERT: 2 147 MET cc_start: 0.9235 (tpp) cc_final: 0.8777 (mmm) REVERT: A 191 MET cc_start: 0.8580 (ptt) cc_final: 0.8378 (ptt) REVERT: A 306 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8797 (tm-30) REVERT: A 384 MET cc_start: 0.8973 (ttm) cc_final: 0.8747 (tpp) REVERT: B 51 MET cc_start: 0.8155 (tmm) cc_final: 0.7907 (ppp) REVERT: B 282 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7734 (pm20) REVERT: B 447 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7682 (mmtt) REVERT: B 465 CYS cc_start: 0.8775 (m) cc_final: 0.8558 (m) REVERT: B 530 MET cc_start: 0.6444 (ppp) cc_final: 0.5807 (ppp) REVERT: B 538 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: B 692 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8529 (mm) REVERT: LC 35 ASP cc_start: 0.9316 (p0) cc_final: 0.8855 (p0) REVERT: LC 86 ARG cc_start: 0.4373 (OUTLIER) cc_final: 0.1294 (mtt180) REVERT: LC 95 MET cc_start: 0.9214 (pmm) cc_final: 0.8122 (mmt) REVERT: LC 288 ASP cc_start: 0.9359 (t0) cc_final: 0.9043 (t0) REVERT: LE 57 TYR cc_start: 0.9340 (m-80) cc_final: 0.9077 (m-10) REVERT: LE 119 GLU cc_start: 0.8065 (mp0) cc_final: 0.7792 (pm20) REVERT: LE 128 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.6702 (t70) REVERT: LE 240 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.1954 (t80) REVERT: Lk 4 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8862 (ttmp) REVERT: Lk 30 ASP cc_start: 0.9496 (p0) cc_final: 0.9164 (p0) REVERT: LY 43 ASN cc_start: 0.9101 (t0) cc_final: 0.8867 (t0) REVERT: Lh 23 ASP cc_start: 0.9161 (p0) cc_final: 0.8886 (p0) REVERT: Lh 30 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8843 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4794 (OUTLIER) cc_final: 0.3498 (tptt) REVERT: Lh 100 GLU cc_start: 0.8481 (pp20) cc_final: 0.8196 (pp20) REVERT: Lh 101 ASN cc_start: 0.9539 (m-40) cc_final: 0.9076 (m-40) REVERT: Lh 111 GLU cc_start: 0.8751 (pp20) cc_final: 0.8505 (pp20) REVERT: LX 57 GLN cc_start: 0.9324 (tp40) cc_final: 0.8850 (mm110) REVERT: LX 101 ASP cc_start: 0.9179 (t70) cc_final: 0.8964 (t0) REVERT: LX 118 ASP cc_start: 0.9103 (t0) cc_final: 0.8870 (t0) REVERT: LR 28 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: LR 151 ARG cc_start: 0.9641 (tpp80) cc_final: 0.8933 (tpm170) outliers start: 103 outliers final: 44 residues processed: 394 average time/residue: 1.4314 time to fit residues: 679.2139 Evaluate side-chains 342 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 7 ARG 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 322 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 108 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 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 163 VAL 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 Lk residue 60 LEU Chi-restraints excluded: chain LY residue 41 LYS 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 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 LX residue 156 ILE 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 52 GLU Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 269 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 122 optimal weight: 0.0170 chunk 270 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 85 HIS ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN Lh 63 GLN ** LX 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.074782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.053482 restraints weight = 161529.367| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.85 r_work: 0.3224 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30687 Z= 0.129 Angle : 0.704 16.775 43044 Z= 0.346 Chirality : 0.039 0.386 5027 Planarity : 0.005 0.133 4140 Dihedral : 21.389 170.228 8702 Min Nonbonded Distance : 1.277 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 3.37 % Allowed : 24.24 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2640 helix: 0.68 (0.14), residues: 1370 sheet: -0.50 (0.34), residues: 199 loop : -0.07 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 707 HIS 0.017 0.001 HIS 2 16 PHE 0.022 0.001 PHE 2 32 TYR 0.039 0.001 TYR B 451 ARG 0.012 0.000 ARGLC 201 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 1337) hydrogen bonds : angle 4.62652 ( 3579) covalent geometry : bond 0.00278 (30687) covalent geometry : angle 0.70440 (43044) *********************** 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 412 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 333 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 27 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8909 (mm110) REVERT: 2 55 TYR cc_start: 0.8079 (p90) cc_final: 0.7702 (p90) REVERT: 2 147 MET cc_start: 0.9168 (tpp) cc_final: 0.8811 (mmm) REVERT: A 153 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: A 191 MET cc_start: 0.8477 (ptt) cc_final: 0.8269 (ptt) REVERT: A 384 MET cc_start: 0.8947 (ttm) cc_final: 0.8708 (tpp) REVERT: B 51 MET cc_start: 0.8000 (tmm) cc_final: 0.7674 (ppp) REVERT: B 282 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: B 447 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7666 (mmtt) REVERT: B 530 MET cc_start: 0.6420 (ppp) cc_final: 0.5753 (ppp) REVERT: B 538 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: LC 35 ASP cc_start: 0.9305 (p0) cc_final: 0.8847 (p0) REVERT: LC 86 ARG cc_start: 0.4438 (mtp-110) cc_final: 0.4182 (mtp85) REVERT: LC 95 MET cc_start: 0.9212 (pmm) cc_final: 0.8016 (mmt) REVERT: LC 189 MET cc_start: 0.9235 (mmp) cc_final: 0.7888 (ptt) REVERT: LC 283 LYS cc_start: 0.9666 (mtmm) cc_final: 0.9125 (pptt) REVERT: LC 288 ASP cc_start: 0.9352 (t0) cc_final: 0.9031 (t0) REVERT: LC 327 LYS cc_start: 0.6333 (mmpt) cc_final: 0.4523 (mptm) REVERT: LE 57 TYR cc_start: 0.9271 (m-80) cc_final: 0.9028 (m-10) REVERT: LE 119 GLU cc_start: 0.8057 (mp0) cc_final: 0.7744 (pm20) REVERT: LE 240 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.2048 (t80) REVERT: Lk 4 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8753 (ttmp) REVERT: Lk 7 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8668 (pp20) REVERT: Lk 30 ASP cc_start: 0.9469 (p0) cc_final: 0.9157 (p0) REVERT: LY 10 ASP cc_start: 0.9096 (t0) cc_final: 0.8882 (t0) REVERT: LY 43 ASN cc_start: 0.9059 (t0) cc_final: 0.8790 (t0) REVERT: Lh 23 ASP cc_start: 0.9155 (p0) cc_final: 0.8918 (p0) REVERT: Lh 30 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8856 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4615 (OUTLIER) cc_final: 0.3401 (tptt) REVERT: Lh 100 GLU cc_start: 0.8558 (pp20) cc_final: 0.8352 (pp20) REVERT: Lh 101 ASN cc_start: 0.9551 (m-40) cc_final: 0.9057 (m-40) REVERT: LX 57 GLN cc_start: 0.9327 (tp40) cc_final: 0.8851 (mm110) REVERT: LX 101 ASP cc_start: 0.9130 (t70) cc_final: 0.8786 (t0) REVERT: LX 118 ASP cc_start: 0.9085 (t0) cc_final: 0.8790 (t0) REVERT: LR 28 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8526 (mm-30) REVERT: LR 151 ARG cc_start: 0.9635 (tpp80) cc_final: 0.8924 (tpm170) outliers start: 79 outliers final: 39 residues processed: 391 average time/residue: 1.7079 time to fit residues: 800.6604 Evaluate side-chains 341 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 293 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 7 ARG Chi-restraints excluded: chain 2 residue 67 VAL 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 153 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain B residue 108 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 650 VAL Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 289 LEU Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 139 LYS 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 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 Lk residue 47 ILE Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Lh residue 30 GLN Chi-restraints excluded: chain Lh residue 86 LYS Chi-restraints excluded: chain Lh residue 88 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 156 ILE Chi-restraints excluded: chain LR residue 28 GLU Chi-restraints excluded: chain LR residue 56 THR Chi-restraints excluded: chain LR residue 89 MET Chi-restraints excluded: chain LR residue 148 ASP 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 28 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 292 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 85 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 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.074656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.053089 restraints weight = 161677.237| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.56 r_work: 0.3223 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30687 Z= 0.146 Angle : 0.719 16.854 43044 Z= 0.356 Chirality : 0.040 0.457 5027 Planarity : 0.004 0.119 4140 Dihedral : 21.353 171.401 8701 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 2.98 % Allowed : 25.44 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2640 helix: 0.67 (0.14), residues: 1374 sheet: -0.52 (0.34), residues: 199 loop : -0.07 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 707 HIS 0.010 0.001 HISLR 143 PHE 0.044 0.001 PHE 2 32 TYR 0.027 0.001 TYR 2 30 ARG 0.009 0.000 ARGLC 201 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 1337) hydrogen bonds : angle 4.63029 ( 3579) covalent geometry : bond 0.00312 (30687) covalent geometry : angle 0.71872 (43044) *********************** 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 383 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 313 time to evaluate : 2.949 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 14 MET cc_start: 0.9080 (pmm) cc_final: 0.8838 (pmm) REVERT: 2 17 CYS cc_start: 0.9439 (t) cc_final: 0.9207 (m) REVERT: 2 98 MET cc_start: 0.8704 (tmm) cc_final: 0.8444 (ppp) REVERT: 2 147 MET cc_start: 0.9234 (tpp) cc_final: 0.8722 (mmm) REVERT: A 308 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8735 (ttt) REVERT: B 51 MET cc_start: 0.8025 (tmm) cc_final: 0.7715 (ppp) REVERT: B 282 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: B 447 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7685 (mmtt) REVERT: B 485 MET cc_start: 0.6549 (ttt) cc_final: 0.6338 (tmt) REVERT: B 530 MET cc_start: 0.6621 (ppp) cc_final: 0.5929 (ppp) REVERT: B 538 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: LC 35 ASP cc_start: 0.9267 (p0) cc_final: 0.8808 (p0) REVERT: LC 86 ARG cc_start: 0.4408 (OUTLIER) cc_final: 0.3282 (mtm110) REVERT: LC 95 MET cc_start: 0.9224 (pmm) cc_final: 0.8038 (mmt) REVERT: LC 189 MET cc_start: 0.9219 (mmp) cc_final: 0.7904 (ptt) REVERT: LC 288 ASP cc_start: 0.9324 (t0) cc_final: 0.9000 (t0) REVERT: LC 327 LYS cc_start: 0.6427 (mmpt) cc_final: 0.4811 (mmtp) REVERT: LE 57 TYR cc_start: 0.9253 (m-80) cc_final: 0.9004 (m-10) REVERT: LE 119 GLU cc_start: 0.8071 (mp0) cc_final: 0.7805 (pm20) REVERT: LE 128 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.6498 (t70) REVERT: LE 240 TYR cc_start: 0.5391 (OUTLIER) cc_final: 0.2074 (t80) REVERT: Lk 4 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8839 (ttmp) REVERT: Lk 7 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8599 (pp20) REVERT: Lk 30 ASP cc_start: 0.9469 (p0) cc_final: 0.9110 (p0) REVERT: LY 43 ASN cc_start: 0.9063 (t0) cc_final: 0.8826 (t0) REVERT: Lh 23 ASP cc_start: 0.9167 (p0) cc_final: 0.8965 (p0) REVERT: Lh 30 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8812 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4647 (OUTLIER) cc_final: 0.3446 (tptt) REVERT: Lh 100 GLU cc_start: 0.8575 (pp20) cc_final: 0.8365 (pp20) REVERT: Lh 101 ASN cc_start: 0.9538 (m-40) cc_final: 0.9066 (m-40) REVERT: LX 57 GLN cc_start: 0.9318 (tp40) cc_final: 0.8883 (mm110) REVERT: LX 78 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8616 (mmmm) REVERT: LX 101 ASP cc_start: 0.9026 (t70) cc_final: 0.8803 (t0) REVERT: LX 118 ASP cc_start: 0.9066 (t0) cc_final: 0.8759 (t0) REVERT: LR 28 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8503 (mm-30) REVERT: LR 151 ARG cc_start: 0.9634 (tpp80) cc_final: 0.8933 (tpm170) outliers start: 70 outliers final: 40 residues processed: 363 average time/residue: 1.3181 time to fit residues: 574.5778 Evaluate side-chains 342 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 7 ARG Chi-restraints excluded: chain 2 residue 67 VAL Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 132 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 322 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 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 538 TYR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 728 THR 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 104 THR Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 139 LYS 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 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 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 Lh residue 116 LEU Chi-restraints excluded: chain LX residue 78 LYS 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 89 MET Chi-restraints excluded: chain LR residue 148 ASP Chi-restraints excluded: chain Lr residue 63 VAL Chi-restraints excluded: chain Lr residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 230 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 265 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 85 HIS ** 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 141 HIS ** LR 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.075003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.053893 restraints weight = 161477.359| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.81 r_work: 0.3236 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30687 Z= 0.141 Angle : 0.746 17.090 43044 Z= 0.369 Chirality : 0.040 0.412 5027 Planarity : 0.004 0.096 4140 Dihedral : 21.334 171.575 8701 Min Nonbonded Distance : 1.267 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 2.60 % Allowed : 26.25 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2640 helix: 0.59 (0.14), residues: 1376 sheet: -0.57 (0.33), residues: 209 loop : -0.05 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP B 284 HIS 0.025 0.001 HISLR 143 PHE 0.049 0.001 PHE 2 128 TYR 0.045 0.001 TYR 2 26 ARG 0.008 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 1337) hydrogen bonds : angle 4.68312 ( 3579) covalent geometry : bond 0.00306 (30687) covalent geometry : angle 0.74581 (43044) *********************** 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: 61 poor density : 320 time to evaluate : 2.891 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 14 MET cc_start: 0.9133 (pmm) cc_final: 0.8918 (pmm) REVERT: 2 28 MET cc_start: 0.8990 (pmm) cc_final: 0.8470 (ppp) REVERT: 2 147 MET cc_start: 0.9210 (tpp) cc_final: 0.8874 (mmm) REVERT: A 308 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8754 (ttt) REVERT: B 26 TYR cc_start: 0.7712 (m-80) cc_final: 0.7457 (m-80) REVERT: B 51 MET cc_start: 0.7968 (tmm) cc_final: 0.7652 (ppp) REVERT: B 447 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7580 (mmtt) REVERT: B 485 MET cc_start: 0.6579 (ttt) cc_final: 0.6326 (tmt) REVERT: B 530 MET cc_start: 0.6541 (ppp) cc_final: 0.5866 (ppp) REVERT: B 538 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: B 559 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8223 (mtp180) REVERT: B 642 LEU cc_start: 0.4940 (OUTLIER) cc_final: 0.4719 (tt) REVERT: B 699 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8944 (m-80) REVERT: LC 35 ASP cc_start: 0.9326 (p0) cc_final: 0.8905 (p0) REVERT: LC 86 ARG cc_start: 0.4437 (OUTLIER) cc_final: 0.4205 (mtp85) REVERT: LC 95 MET cc_start: 0.9236 (pmm) cc_final: 0.8039 (mmt) REVERT: LC 189 MET cc_start: 0.8759 (mmp) cc_final: 0.7898 (mtm) REVERT: LC 288 ASP cc_start: 0.9306 (t0) cc_final: 0.8985 (t0) REVERT: LC 327 LYS cc_start: 0.6425 (mmpt) cc_final: 0.4798 (mmtp) REVERT: LE 57 TYR cc_start: 0.9242 (m-80) cc_final: 0.9014 (m-10) REVERT: LE 63 TYR cc_start: 0.9100 (t80) cc_final: 0.8333 (t80) REVERT: LE 119 GLU cc_start: 0.7955 (mp0) cc_final: 0.7647 (pm20) REVERT: LE 128 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.6486 (t70) REVERT: LE 240 TYR cc_start: 0.5384 (OUTLIER) cc_final: 0.2081 (t80) REVERT: Lk 4 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8849 (ttmp) REVERT: Lk 30 ASP cc_start: 0.9486 (p0) cc_final: 0.9141 (p0) REVERT: LY 43 ASN cc_start: 0.9055 (t0) cc_final: 0.8852 (t0) REVERT: Lh 23 ASP cc_start: 0.9177 (p0) cc_final: 0.8968 (p0) REVERT: Lh 30 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8835 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.3316 (tptt) REVERT: Lh 101 ASN cc_start: 0.9546 (m-40) cc_final: 0.9098 (m-40) REVERT: LX 55 ARG cc_start: 0.7540 (tpm170) cc_final: 0.7089 (tpm-80) REVERT: LX 57 GLN cc_start: 0.9322 (tp40) cc_final: 0.8871 (mm110) REVERT: LX 78 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8636 (mmmm) REVERT: LX 88 LYS cc_start: 0.9674 (mtpt) cc_final: 0.9205 (mtpm) REVERT: LX 101 ASP cc_start: 0.9041 (t70) cc_final: 0.8800 (t0) REVERT: LX 118 ASP cc_start: 0.9077 (t0) cc_final: 0.8865 (t0) REVERT: LR 151 ARG cc_start: 0.9646 (tpp80) cc_final: 0.8882 (tpm170) outliers start: 61 outliers final: 38 residues processed: 365 average time/residue: 1.3466 time to fit residues: 588.1465 Evaluate side-chains 347 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 7 ARG Chi-restraints excluded: chain 2 residue 49 ASN Chi-restraints excluded: chain 2 residue 67 VAL Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 132 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 322 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 386 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain B residue 538 TYR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 699 PHE Chi-restraints excluded: chain B residue 728 THR 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 104 THR Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 139 LYS 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 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 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 78 LYS 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 148 ASP 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 69 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 84 optimal weight: 0.0470 chunk 229 optimal weight: 10.0000 chunk 178 optimal weight: 0.0970 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 overall best weight: 1.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN LC 321 ASN ** LY 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.074989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.053860 restraints weight = 162385.520| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.88 r_work: 0.3234 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30687 Z= 0.150 Angle : 0.767 17.561 43044 Z= 0.380 Chirality : 0.041 0.392 5027 Planarity : 0.004 0.066 4140 Dihedral : 21.313 172.210 8701 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.47 % Allowed : 27.10 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2640 helix: 0.51 (0.14), residues: 1374 sheet: -0.56 (0.35), residues: 182 loop : -0.04 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 284 HIS 0.021 0.001 HISLR 143 PHE 0.049 0.001 PHE 2 32 TYR 0.033 0.001 TYR 2 26 ARG 0.012 0.000 ARGLC 201 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 1337) hydrogen bonds : angle 4.75633 ( 3579) covalent geometry : bond 0.00330 (30687) covalent geometry : angle 0.76666 (43044) ********************** 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 363 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 305 time to evaluate : 3.038 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 10 ASP cc_start: 0.9294 (p0) cc_final: 0.9004 (p0) REVERT: 2 13 ASN cc_start: 0.9402 (t0) cc_final: 0.9117 (m110) REVERT: 2 28 MET cc_start: 0.9028 (pmm) cc_final: 0.8522 (ppp) REVERT: 2 98 MET cc_start: 0.8759 (tmm) cc_final: 0.8421 (ppp) REVERT: 2 147 MET cc_start: 0.9163 (tpp) cc_final: 0.8880 (mmm) REVERT: A 457 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8961 (tm-30) REVERT: B 26 TYR cc_start: 0.7683 (m-80) cc_final: 0.7446 (m-80) REVERT: B 51 MET cc_start: 0.7891 (tmm) cc_final: 0.7575 (ppp) REVERT: B 447 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7690 (mmtt) REVERT: B 530 MET cc_start: 0.6467 (ppp) cc_final: 0.5826 (ppp) REVERT: B 538 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: B 642 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4989 (tt) REVERT: LC 35 ASP cc_start: 0.9324 (p0) cc_final: 0.8902 (p0) REVERT: LC 86 ARG cc_start: 0.4398 (OUTLIER) cc_final: 0.3242 (mtm110) REVERT: LC 95 MET cc_start: 0.9247 (pmm) cc_final: 0.8052 (mmt) REVERT: LC 189 MET cc_start: 0.9087 (mmp) cc_final: 0.7626 (mtm) REVERT: LC 288 ASP cc_start: 0.9314 (t0) cc_final: 0.9006 (t0) REVERT: LC 321 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8441 (t0) REVERT: LC 327 LYS cc_start: 0.6472 (mmpt) cc_final: 0.4769 (mmtp) REVERT: LE 57 TYR cc_start: 0.9269 (m-80) cc_final: 0.8966 (m-10) REVERT: LE 119 GLU cc_start: 0.7935 (mp0) cc_final: 0.7726 (pm20) REVERT: LE 128 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.6452 (t70) REVERT: Lk 4 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8876 (ttmp) REVERT: Lk 7 GLU cc_start: 0.8698 (pp20) cc_final: 0.8262 (pp20) REVERT: Lk 30 ASP cc_start: 0.9529 (p0) cc_final: 0.9151 (p0) REVERT: Lh 30 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8835 (mm-40) REVERT: Lh 86 LYS cc_start: 0.4602 (OUTLIER) cc_final: 0.3348 (tptt) REVERT: LX 57 GLN cc_start: 0.9322 (tp40) cc_final: 0.8844 (mm110) REVERT: LX 78 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8634 (mmmm) REVERT: LX 101 ASP cc_start: 0.9085 (t70) cc_final: 0.8843 (t0) REVERT: LR 28 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8548 (mm-30) REVERT: LR 151 ARG cc_start: 0.9643 (tpp80) cc_final: 0.8874 (tpm170) outliers start: 58 outliers final: 38 residues processed: 350 average time/residue: 1.2817 time to fit residues: 542.3301 Evaluate side-chains 344 residues out of total 2347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 7 ARG Chi-restraints excluded: chain 2 residue 49 ASN Chi-restraints excluded: chain 2 residue 67 VAL Chi-restraints excluded: chain 2 residue 132 GLU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 247 ILE 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 A residue 457 GLN 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 274 LEU 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 538 TYR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 650 VAL 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 LC residue 321 ASN Chi-restraints excluded: chain LE residue 51 VAL Chi-restraints excluded: chain LE residue 104 THR Chi-restraints excluded: chain LE residue 128 HIS Chi-restraints excluded: chain LE residue 145 THR 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 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 Lh residue 116 LEU Chi-restraints excluded: chain LX residue 78 LYS Chi-restraints excluded: chain LX residue 82 THR Chi-restraints excluded: chain LX residue 83 THR 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 148 ASP 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 24 optimal weight: 0.0980 chunk 135 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 95 optimal weight: 30.0000 chunk 105 optimal weight: 0.3980 chunk 150 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 85 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.075455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.054364 restraints weight = 160815.211| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.73 r_work: 0.3250 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30687 Z= 0.137 Angle : 0.774 16.834 43044 Z= 0.383 Chirality : 0.040 0.432 5027 Planarity : 0.004 0.066 4140 Dihedral : 21.280 171.943 8697 Min Nonbonded Distance : 1.278 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.47 % Allowed : 27.35 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2640 helix: 0.49 (0.14), residues: 1385 sheet: -0.53 (0.35), residues: 189 loop : -0.04 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 284 HIS 0.020 0.001 HISLR 143 PHE 0.050 0.001 PHE 2 32 TYR 0.040 0.001 TYR B 451 ARG 0.011 0.000 ARGLC 201 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1337) hydrogen bonds : angle 4.75620 ( 3579) covalent geometry : bond 0.00303 (30687) covalent geometry : angle 0.77450 (43044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41924.52 seconds wall clock time: 729 minutes 43.48 seconds (43783.48 seconds total)