Starting phenix.real_space_refine on Fri Mar 6 10:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gj5_51382/03_2026/9gj5_51382.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gj5_51382/03_2026/9gj5_51382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gj5_51382/03_2026/9gj5_51382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gj5_51382/03_2026/9gj5_51382.map" model { file = "/net/cci-nas-00/data/ceres_data/9gj5_51382/03_2026/9gj5_51382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gj5_51382/03_2026/9gj5_51382.cif" } resolution = 4.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 364 5.49 5 S 105 5.16 5 C 17164 2.51 5 N 5439 2.21 5 O 6356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29428 Number of models: 1 Model: "" Number of chains: 14 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: "B" Number of atoms: 6880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6880 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 804} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2938 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 12, 'TRANS': 363} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'KGN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.69, per 1000 atoms: 0.19 Number of scatterers: 29428 At special positions: 0 Unit cell: (178.558, 225.032, 253.161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 364 15.00 O 6356 8.00 N 5439 7.00 C 17164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5108 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 21 sheets defined 56.4% alpha, 8.7% beta 106 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain '2' and resid 12 through 22 removed outlier: 3.802A pdb=" N LEU 2 19 " --> pdb=" O GLN 2 15 " (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: 3.582A pdb=" N GLU 2 157 " --> pdb=" O GLN 2 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS 2 170 " --> pdb=" O GLU 2 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 25 through 39 removed outlier: 3.520A pdb=" N GLN B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.688A 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: 3.594A pdb=" N TRP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.759A pdb=" N LYS B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.539A pdb=" N LEU B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 144 Processing helix chain 'B' and resid 147 through 160 removed outlier: 4.000A 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 240 through 254 Processing helix chain 'B' and resid 257 through 269 removed outlier: 3.760A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.671A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 4.145A pdb=" N LEU B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 321 removed outlier: 3.688A 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: 3.746A 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: 3.723A 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: 3.592A pdb=" N LEU B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 438 Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.907A pdb=" N ASN B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.537A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 500 through 521 removed outlier: 3.519A pdb=" N ASP B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.830A 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: 3.728A pdb=" N ASP B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 removed outlier: 3.994A pdb=" N PHE B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 587 removed outlier: 4.261A pdb=" N ASN B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 627 removed outlier: 4.009A pdb=" N GLU B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 650 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: 4.394A pdb=" N HIS B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 685 " --> pdb=" O ILE B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 701 removed outlier: 3.811A pdb=" N GLN B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 removed outlier: 3.516A pdb=" N ARG B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 740 removed outlier: 3.693A pdb=" N VAL B 732 " --> pdb=" O THR B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 757 removed outlier: 3.722A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 749 " --> pdb=" O ASN B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 771 removed outlier: 4.080A pdb=" N ARG B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER B 766 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 767 " --> pdb=" O HIS B 763 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 787 removed outlier: 3.568A pdb=" N ALA B 782 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 811 removed outlier: 4.131A pdb=" N GLY B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 831 Processing helix chain 'LC' and resid 25 through 30 Processing helix chain 'LC' and resid 33 through 45 Processing helix chain 'LC' and resid 46 through 49 removed outlier: 3.541A 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: 3.576A 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: 4.071A pdb=" N ILELC 180 " --> pdb=" O ALALC 176 " (cutoff:3.500A) Processing helix chain 'LC' and resid 192 through 196 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 removed outlier: 3.537A pdb=" N LYSLC 259 " --> pdb=" O SERLC 255 " (cutoff:3.500A) 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 Processing helix chain 'LC' and resid 331 through 368 removed outlier: 3.620A pdb=" N LYSLC 353 " --> pdb=" O LEULC 349 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLNLC 362 " --> pdb=" O ALALC 358 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALALC 363 " --> pdb=" O ALALC 359 " (cutoff:3.500A) Processing helix chain 'LE' and resid 58 through 66 removed outlier: 3.770A pdb=" N TYRLE 63 " --> pdb=" O ARGLE 59 " (cutoff:3.500A) Processing helix chain 'LE' and resid 132 through 136 Processing helix chain 'LE' and resid 178 through 183 Processing helix chain 'LE' and resid 190 through 192 No H-bonds generated for 'chain 'LE' and resid 190 through 192' Processing helix chain 'LE' and resid 213 through 218 Processing helix chain 'LE' and resid 243 through 262 removed outlier: 4.080A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix Processing helix chain 'LE' and resid 266 through 273 Processing helix chain 'Lk' and resid 7 through 15 removed outlier: 3.724A pdb=" N PHELk 11 " --> pdb=" O GLULk 7 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEULk 12 " --> pdb=" O ILELk 8 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEULk 13 " --> pdb=" O LYSLk 9 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 50 through 58 removed outlier: 3.857A pdb=" N GLULk 54 " --> pdb=" O LYSLk 50 " (cutoff:3.500A) removed outlier: 3.745A 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: 4.000A pdb=" N LYSLY 28 " --> pdb=" O HISLY 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILELY 29 " --> pdb=" O ILELY 25 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 75 through 78 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: 3.881A pdb=" N LYSLY 117 " --> pdb=" O LYSLY 113 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLNLY 127 " --> pdb=" O ALALY 123 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 11 removed outlier: 3.760A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLYLh 11 " --> pdb=" O ARGLh 7 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 37 removed outlier: 3.753A pdb=" N LEULh 17 " --> pdb=" O LYSLh 13 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEULh 18 " --> pdb=" O LYSLh 14 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYSLh 19 " --> pdb=" O GLULh 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYSLh 35 " --> pdb=" O LEULh 31 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VALLh 36 " --> pdb=" O ARGLh 32 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THRLh 37 " --> pdb=" O VALLh 33 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 45 Processing helix chain 'Lh' and resid 45 through 73 removed outlier: 4.404A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYSLh 66 " --> pdb=" O ASNLh 62 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLULh 67 " --> pdb=" O GLNLh 63 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASNLh 68 " --> pdb=" O THRLh 64 " (cutoff:3.500A) removed outlier: 3.661A 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 96 through 101 Processing helix chain 'Lh' and resid 104 through 114 Processing helix chain 'LX' and resid 83 through 92 removed outlier: 3.726A pdb=" N LYSLX 88 " --> pdb=" O GLULX 84 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILELX 90 " --> pdb=" O ALALX 86 " (cutoff:3.500A) Processing helix chain 'LX' and resid 105 through 118 removed outlier: 3.619A pdb=" N GLNLX 111 " --> pdb=" O HISLX 107 " (cutoff:3.500A) Processing helix chain 'LX' and resid 145 through 154 removed outlier: 3.593A 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: 3.927A pdb=" N ILELR 32 " --> pdb=" O GLULR 28 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 48 Processing helix chain 'LR' and resid 60 through 72 removed outlier: 3.570A pdb=" N LYSLR 72 " --> pdb=" O LEULR 68 " (cutoff:3.500A) Processing helix chain 'LR' and resid 77 through 81 removed outlier: 3.821A 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 removed outlier: 3.575A pdb=" N THRLR 94 " --> pdb=" O PROLR 90 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEULR 105 " --> pdb=" O ILELR 101 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 129 Processing helix chain 'LR' and resid 134 through 154 removed outlier: 3.508A pdb=" N GLULR 140 " --> pdb=" O ARGLR 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HISLR 141 " --> pdb=" O ILELR 137 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILELR 142 " --> pdb=" O LEULR 138 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HISLR 143 " --> pdb=" O METLR 139 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYSLR 149 " --> pdb=" O LEULR 145 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 3 through 11 Processing helix chain 'Lr' and resid 31 through 35 removed outlier: 4.105A pdb=" N ARGLr 35 " --> pdb=" O LEULr 32 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 72 through 76 Processing helix chain 'Lr' and resid 85 through 98 Processing helix chain 'Lr' and resid 106 through 122 Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.610A pdb=" N VAL A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 63 Processing helix chain 'A' and resid 136 through 157 Processing helix chain 'A' and resid 163 through 177 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.575A pdb=" N GLU A 270 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.739A pdb=" N VAL A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.816A pdb=" N LEU A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 382 Processing sheet with id=AA1, first strand: chain '2' and resid 4 through 5 removed outlier: 3.727A pdb=" N TYR 2 43 " --> pdb=" O VAL 2 56 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N VAL 2 53 " --> pdb=" O VAL 2 77 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL 2 77 " --> pdb=" O VAL 2 53 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N TYR 2 55 " --> pdb=" O LEU 2 75 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU 2 75 " --> pdb=" O TYR 2 55 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU 2 57 " --> pdb=" O THR 2 73 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY 2 70 " --> pdb=" O SER 2 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'LC' and resid 7 through 11 removed outlier: 6.846A pdb=" N ILELC 8 " --> pdb=" O LYSLC 20 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYSLC 20 " --> pdb=" O ILELC 8 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VALLC 10 " --> pdb=" O SERLC 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LC' and resid 152 through 154 removed outlier: 6.060A pdb=" N LEULC 152 " --> pdb=" O TRPLC 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'LC' and resid 187 through 189 Processing sheet with id=AA5, first strand: chain 'LE' and resid 49 through 51 removed outlier: 3.533A pdb=" N VALLE 51 " --> pdb=" O ILELE 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LE' and resid 91 through 94 Processing sheet with id=AA7, first strand: chain 'LE' and resid 187 through 189 removed outlier: 5.311A pdb=" N LEULE 174 " --> pdb=" O LEULE 165 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRLE 176 " --> pdb=" O VALLE 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VALLE 163 " --> pdb=" O THRLE 176 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THRLE 199 " --> pdb=" O ILELE 149 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILELE 151 " --> pdb=" O THRLE 197 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THRLE 197 " --> pdb=" O ILELE 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.067A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AB1, first strand: chain 'LY' and resid 79 through 82 removed outlier: 7.101A pdb=" N VALLY 79 " --> pdb=" O VALLY 73 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VALLY 73 " --> pdb=" O VALLY 79 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYRLY 81 " --> pdb=" O VALLY 71 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AB3, first strand: chain 'LX' and resid 95 through 99 removed outlier: 6.681A pdb=" N LYSLX 135 " --> pdb=" O THRLX 126 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THRLX 126 " --> pdb=" O LYSLX 135 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYRLX 137 " --> pdb=" O VALLX 124 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VALLX 124 " --> pdb=" O TYRLX 137 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARGLX 139 " --> pdb=" O ALALX 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LR' and resid 22 through 23 removed outlier: 3.723A pdb=" N ILELR 51 " --> pdb=" O TRPLR 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Lr' and resid 17 through 20 Processing sheet with id=AB6, first strand: chain 'Lr' and resid 49 through 53 Processing sheet with id=AB7, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AB8, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AB9, first strand: chain 'A' and resid 180 through 181 removed outlier: 4.099A pdb=" N VAL A 223 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AC2, first strand: chain 'A' and resid 185 through 186 removed outlier: 4.441A pdb=" N MET A 185 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 203 " --> pdb=" O MET A 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 278 through 279 1042 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 474 hydrogen bond angles 0 basepair planarities 106 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 5.51 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4565 1.32 - 1.45: 9583 1.45 - 1.57: 15675 1.57 - 1.69: 713 1.69 - 1.82: 171 Bond restraints: 30707 Sorted by residual: bond pdb=" N ILE B 713 " pdb=" CA ILE B 713 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.22e+00 bond pdb=" N MET B 712 " pdb=" CA MET B 712 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.23e-02 6.61e+03 6.27e+00 bond pdb=" N CYS B 711 " pdb=" CA CYS B 711 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.20e-02 6.94e+03 5.98e+00 bond pdb=" N MET A 276 " pdb=" CA MET A 276 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.50e-02 4.44e+03 5.41e+00 bond pdb=" CB GLU B 618 " pdb=" CG GLU B 618 " ideal model delta sigma weight residual 1.520 1.590 -0.070 3.00e-02 1.11e+03 5.41e+00 ... (remaining 30702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 42186 2.59 - 5.18: 760 5.18 - 7.76: 72 7.76 - 10.35: 14 10.35 - 12.94: 5 Bond angle restraints: 43037 Sorted by residual: angle pdb=" CA GLN A 367 " pdb=" CB GLN A 367 " pdb=" CG GLN A 367 " ideal model delta sigma weight residual 114.10 124.51 -10.41 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CB GLU B 618 " pdb=" CG GLU B 618 " pdb=" CD GLU B 618 " ideal model delta sigma weight residual 112.60 120.36 -7.76 1.70e+00 3.46e-01 2.09e+01 angle pdb=" C TYR B 451 " pdb=" N MET B 452 " pdb=" CA MET B 452 " ideal model delta sigma weight residual 121.58 113.00 8.58 1.95e+00 2.63e-01 1.94e+01 angle pdb=" O16 KGN B 901 " pdb=" P6 KGN B 901 " pdb=" O26 KGN B 901 " ideal model delta sigma weight residual 100.29 113.23 -12.94 3.00e+00 1.11e-01 1.86e+01 angle pdb=" N GLU B 611 " pdb=" CA GLU B 611 " pdb=" CB GLU B 611 " ideal model delta sigma weight residual 110.16 116.34 -6.18 1.48e+00 4.57e-01 1.74e+01 ... (remaining 43032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.84: 18207 32.84 - 65.68: 1174 65.68 - 98.52: 162 98.52 - 131.37: 25 131.37 - 164.21: 2 Dihedral angle restraints: 19570 sinusoidal: 11703 harmonic: 7867 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 77.47 122.53 1 1.50e+01 4.44e-03 6.56e+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 67.79 164.21 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 -75.74 -84.26 1 1.50e+01 4.44e-03 3.84e+01 ... (remaining 19567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.031: 5033 1.031 - 2.062: 0 2.062 - 3.093: 0 3.093 - 4.124: 0 4.124 - 5.154: 3 Chirality restraints: 5036 Sorted by residual: chirality pdb=" C1 KGN B 901 " pdb=" C2 KGN B 901 " pdb=" C6 KGN B 901 " pdb=" O11 KGN B 901 " both_signs ideal model delta sigma weight residual False 2.53 -2.62 5.15 2.00e-01 2.50e+01 6.64e+02 chirality pdb=" C2 KGN B 901 " pdb=" C1 KGN B 901 " pdb=" C3 KGN B 901 " pdb=" O12 KGN B 901 " both_signs ideal model delta sigma weight residual False -2.37 2.69 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C4 KGN B 901 " pdb=" C3 KGN B 901 " pdb=" C5 KGN B 901 " pdb=" O14 KGN B 901 " both_signs ideal model delta sigma weight residual False -2.50 2.29 -4.79 2.00e-01 2.50e+01 5.73e+02 ... (remaining 5033 not shown) Planarity restraints: 4134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 13598 " 0.023 2.00e-02 2.50e+03 3.08e-02 2.14e+01 pdb=" N1 C 13598 " -0.019 2.00e-02 2.50e+03 pdb=" C2 C 13598 " -0.073 2.00e-02 2.50e+03 pdb=" O2 C 13598 " 0.036 2.00e-02 2.50e+03 pdb=" N3 C 13598 " 0.015 2.00e-02 2.50e+03 pdb=" C4 C 13598 " -0.015 2.00e-02 2.50e+03 pdb=" N4 C 13598 " 0.021 2.00e-02 2.50e+03 pdb=" C5 C 13598 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C 13598 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 284 " 0.025 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP B 284 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B 284 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 284 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 284 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 284 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 284 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 284 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 284 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 284 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU 2 134 " 0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO 2 135 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO 2 135 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO 2 135 " 0.051 5.00e-02 4.00e+02 ... (remaining 4131 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 379 2.55 - 3.14: 25596 3.14 - 3.73: 55318 3.73 - 4.31: 72204 4.31 - 4.90: 104594 Nonbonded interactions: 258091 Sorted by model distance: nonbonded pdb=" OP2 G 8 75 " pdb=" OH TYRLY 74 " model vdw 1.966 3.040 nonbonded pdb=" O4 U 1 512 " pdb=" O6 G 1 647 " model vdw 1.973 2.432 nonbonded pdb=" O ARGLR 151 " pdb=" NH1 ARGLR 151 " model vdw 1.974 3.120 nonbonded pdb=" O6 G 1 493 " pdb=" N1 A 1 660 " model vdw 2.027 2.496 nonbonded pdb=" NH2 ARG 2 4 " pdb=" O ASN B 254 " model vdw 2.034 3.120 ... (remaining 258086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.190 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30707 Z= 0.238 Angle : 0.868 12.941 43037 Z= 0.464 Chirality : 0.131 5.154 5036 Planarity : 0.005 0.094 4134 Dihedral : 19.745 164.206 14462 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 30.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.76 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 2646 helix: 0.07 (0.14), residues: 1291 sheet: -0.22 (0.40), residues: 159 loop : -0.71 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 27 TYR 0.026 0.003 TYR B 495 PHE 0.044 0.003 PHE B 683 TRP 0.066 0.004 TRP B 284 HIS 0.013 0.002 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00475 (30707) covalent geometry : angle 0.86778 (43037) hydrogen bonds : bond 0.20776 ( 1316) hydrogen bonds : angle 7.37628 ( 3489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 91 MET cc_start: 0.9530 (mmp) cc_final: 0.9059 (ppp) REVERT: B 162 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7997 (tm-30) REVERT: B 464 MET cc_start: 0.3269 (ptt) cc_final: 0.2800 (ptt) REVERT: B 737 MET cc_start: 0.1194 (mpp) cc_final: 0.0906 (mpp) REVERT: B 770 MET cc_start: 0.5567 (ttt) cc_final: 0.5333 (ttm) REVERT: LC 52 TYR cc_start: 0.7183 (p90) cc_final: 0.4866 (m-80) REVERT: LC 107 THR cc_start: 0.9579 (p) cc_final: 0.9288 (p) REVERT: LC 108 TRP cc_start: 0.8795 (p90) cc_final: 0.6981 (p-90) REVERT: LC 125 CYS cc_start: 0.9680 (m) cc_final: 0.9439 (p) REVERT: LC 133 LEU cc_start: 0.9579 (tt) cc_final: 0.9153 (tt) REVERT: LC 250 CYS cc_start: 0.9105 (m) cc_final: 0.8892 (t) REVERT: LY 43 ASN cc_start: 0.8474 (t0) cc_final: 0.8089 (t0) REVERT: LY 47 MET cc_start: 0.9074 (tpt) cc_final: 0.8550 (tpt) REVERT: LX 101 ASP cc_start: 0.8416 (t0) cc_final: 0.8020 (t70) REVERT: Lr 8 MET cc_start: 0.9264 (mmp) cc_final: 0.8981 (mmm) REVERT: A 55 MET cc_start: 0.8543 (ptt) cc_final: 0.7925 (ppp) REVERT: A 259 MET cc_start: 0.9180 (tpt) cc_final: 0.8912 (tpp) REVERT: A 276 MET cc_start: 0.6552 (ttt) cc_final: 0.5677 (ttt) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1863 time to fit residues: 74.7201 Evaluate side-chains 179 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.4980 chunk 111 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 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN B 317 ASN B 423 ASN B 445 ASN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 HIS B 569 HIS B 624 GLN B 748 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 21 ASN LC 212 ASN ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 4 ASN LY 96 HIS ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 45 HIS A 147 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 367 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.053181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.044904 restraints weight = 513830.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.044816 restraints weight = 453416.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.045272 restraints weight = 345487.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.045178 restraints weight = 287292.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.045307 restraints weight = 298005.509| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30707 Z= 0.194 Angle : 0.698 12.090 43037 Z= 0.353 Chirality : 0.040 0.430 5036 Planarity : 0.006 0.151 4134 Dihedral : 22.656 165.854 8683 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 0.21 % Allowed : 4.81 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 2646 helix: 0.14 (0.13), residues: 1344 sheet: -0.51 (0.34), residues: 207 loop : -0.39 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGLY 126 TYR 0.040 0.002 TYR A 343 PHE 0.043 0.003 PHELX 79 TRP 0.037 0.002 TRP B 284 HIS 0.011 0.002 HISLR 143 Details of bonding type rmsd covalent geometry : bond 0.00389 (30707) covalent geometry : angle 0.69804 (43037) hydrogen bonds : bond 0.06626 ( 1316) hydrogen bonds : angle 5.33846 ( 3489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 247 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 33 TYR cc_start: 0.9471 (m-80) cc_final: 0.9200 (m-80) REVERT: 2 91 MET cc_start: 0.9506 (mmp) cc_final: 0.9124 (ppp) REVERT: B 9 LYS cc_start: 0.9329 (mmtt) cc_final: 0.9041 (tmtt) REVERT: B 273 MET cc_start: 0.8470 (tmm) cc_final: 0.8145 (tmm) REVERT: B 770 MET cc_start: 0.8240 (ttt) cc_final: 0.7976 (ttm) REVERT: LC 52 TYR cc_start: 0.5064 (p90) cc_final: 0.4294 (m-80) REVERT: LC 107 THR cc_start: 0.9325 (p) cc_final: 0.8919 (p) REVERT: LC 108 TRP cc_start: 0.8962 (p90) cc_final: 0.7800 (p-90) REVERT: LC 128 LEU cc_start: 0.9102 (pp) cc_final: 0.8875 (pp) REVERT: LC 133 LEU cc_start: 0.9146 (tt) cc_final: 0.8908 (tt) REVERT: LC 221 PHE cc_start: 0.9831 (m-10) cc_final: 0.9627 (m-10) REVERT: LC 250 CYS cc_start: 0.9553 (m) cc_final: 0.9073 (t) REVERT: LY 43 ASN cc_start: 0.8839 (t0) cc_final: 0.8503 (t0) REVERT: LX 79 PHE cc_start: 0.9804 (m-80) cc_final: 0.9586 (t80) REVERT: LX 98 PHE cc_start: 0.9509 (m-80) cc_final: 0.9274 (m-80) REVERT: Lr 8 MET cc_start: 0.9126 (mmp) cc_final: 0.8817 (mmm) REVERT: A 276 MET cc_start: 0.8467 (ttt) cc_final: 0.7882 (ttt) REVERT: A 343 TYR cc_start: 0.8401 (m-10) cc_final: 0.8014 (m-80) REVERT: A 347 MET cc_start: 0.6901 (pmm) cc_final: 0.6697 (pmm) outliers start: 5 outliers final: 2 residues processed: 250 average time/residue: 0.1803 time to fit residues: 72.3424 Evaluate side-chains 181 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 155 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 260 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 212 ASN ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 63 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.053762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.045209 restraints weight = 510012.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.045149 restraints weight = 451722.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.045731 restraints weight = 352832.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.045584 restraints weight = 290148.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.045660 restraints weight = 294146.515| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30707 Z= 0.133 Angle : 0.600 10.808 43037 Z= 0.305 Chirality : 0.037 0.229 5036 Planarity : 0.005 0.134 4134 Dihedral : 22.458 166.516 8683 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2646 helix: 0.24 (0.14), residues: 1365 sheet: -0.63 (0.34), residues: 202 loop : -0.37 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 71 TYR 0.035 0.002 TYR B 138 PHE 0.034 0.002 PHE B 683 TRP 0.047 0.002 TRP B 284 HIS 0.007 0.001 HIS 2 120 Details of bonding type rmsd covalent geometry : bond 0.00274 (30707) covalent geometry : angle 0.60034 (43037) hydrogen bonds : bond 0.05092 ( 1316) hydrogen bonds : angle 4.98675 ( 3489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 243 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 28 MET cc_start: 0.7772 (ppp) cc_final: 0.7510 (ppp) REVERT: 2 33 TYR cc_start: 0.9520 (m-80) cc_final: 0.9257 (m-80) REVERT: B 9 LYS cc_start: 0.9404 (mmtt) cc_final: 0.9131 (tmtt) REVERT: B 576 GLU cc_start: 0.7416 (tp30) cc_final: 0.7005 (mm-30) REVERT: B 737 MET cc_start: -0.0000 (mpp) cc_final: -0.0267 (mmm) REVERT: B 770 MET cc_start: 0.7855 (ttt) cc_final: 0.7554 (ttm) REVERT: LC 52 TYR cc_start: 0.5052 (p90) cc_final: 0.4224 (m-80) REVERT: LC 107 THR cc_start: 0.9417 (p) cc_final: 0.9046 (p) REVERT: LC 108 TRP cc_start: 0.8970 (p90) cc_final: 0.7809 (p-90) REVERT: LC 128 LEU cc_start: 0.9134 (pp) cc_final: 0.8915 (pp) REVERT: LC 133 LEU cc_start: 0.9064 (tt) cc_final: 0.8815 (tt) REVERT: LC 221 PHE cc_start: 0.9832 (m-10) cc_final: 0.9623 (m-10) REVERT: LC 250 CYS cc_start: 0.9491 (m) cc_final: 0.9034 (t) REVERT: LE 150 LEU cc_start: 0.9664 (mt) cc_final: 0.9422 (mp) REVERT: LY 43 ASN cc_start: 0.8758 (t0) cc_final: 0.8455 (t0) REVERT: Lr 8 MET cc_start: 0.9174 (mmp) cc_final: 0.8919 (mmm) REVERT: A 55 MET cc_start: 0.9064 (ptt) cc_final: 0.8828 (ppp) REVERT: A 274 ASP cc_start: 0.9637 (m-30) cc_final: 0.9436 (p0) REVERT: A 276 MET cc_start: 0.8354 (ttt) cc_final: 0.7568 (ttt) REVERT: A 343 TYR cc_start: 0.8269 (m-10) cc_final: 0.7912 (m-80) REVERT: A 347 MET cc_start: 0.7214 (pmm) cc_final: 0.6952 (pmm) outliers start: 3 outliers final: 1 residues processed: 245 average time/residue: 0.1913 time to fit residues: 74.5686 Evaluate side-chains 173 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 251 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 265 optimal weight: 0.0970 chunk 274 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 2 ASN ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 198 ASN LC 212 ASN ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 68 ASN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 66 ASN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.052231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.044362 restraints weight = 520329.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.044251 restraints weight = 444183.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.044506 restraints weight = 378853.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.044478 restraints weight = 317762.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.044529 restraints weight = 308226.419| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30707 Z= 0.186 Angle : 0.657 11.163 43037 Z= 0.333 Chirality : 0.038 0.260 5036 Planarity : 0.005 0.131 4134 Dihedral : 22.688 167.886 8683 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2646 helix: 0.26 (0.14), residues: 1366 sheet: -0.61 (0.36), residues: 192 loop : -0.44 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGLY 126 TYR 0.020 0.002 TYR B 154 PHE 0.023 0.002 PHELC 39 TRP 0.032 0.002 TRPLR 95 HIS 0.009 0.001 HIS B 551 Details of bonding type rmsd covalent geometry : bond 0.00374 (30707) covalent geometry : angle 0.65676 (43037) hydrogen bonds : bond 0.06702 ( 1316) hydrogen bonds : angle 4.93916 ( 3489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 33 TYR cc_start: 0.9037 (m-80) cc_final: 0.8782 (m-80) REVERT: 2 91 MET cc_start: 0.9179 (mmp) cc_final: 0.8777 (ppp) REVERT: B 273 MET cc_start: 0.8526 (tmm) cc_final: 0.8242 (tmm) REVERT: B 576 GLU cc_start: 0.7993 (tp30) cc_final: 0.7395 (mm-30) REVERT: B 770 MET cc_start: 0.6524 (ttt) cc_final: 0.6204 (ttm) REVERT: LC 107 THR cc_start: 0.9635 (p) cc_final: 0.9361 (p) REVERT: LC 108 TRP cc_start: 0.8968 (p90) cc_final: 0.7305 (p-90) REVERT: LC 128 LEU cc_start: 0.9410 (pp) cc_final: 0.9161 (pp) REVERT: LC 250 CYS cc_start: 0.9253 (m) cc_final: 0.8919 (t) REVERT: LC 263 LEU cc_start: 0.9859 (mt) cc_final: 0.9634 (mt) REVERT: LE 282 TYR cc_start: 0.9377 (m-80) cc_final: 0.9138 (m-10) REVERT: LY 42 TYR cc_start: 0.9012 (m-10) cc_final: 0.8775 (m-10) REVERT: LY 43 ASN cc_start: 0.8778 (t0) cc_final: 0.8466 (t0) REVERT: LY 47 MET cc_start: 0.9481 (tpt) cc_final: 0.9252 (tpt) REVERT: LX 81 LEU cc_start: 0.9171 (mt) cc_final: 0.8911 (mt) REVERT: LX 101 ASP cc_start: 0.8547 (t70) cc_final: 0.8197 (t70) REVERT: LR 89 MET cc_start: 0.9602 (mpp) cc_final: 0.9398 (mpp) REVERT: LR 96 MET cc_start: 0.3469 (mmt) cc_final: 0.3259 (mmt) REVERT: Lr 8 MET cc_start: 0.9280 (mmp) cc_final: 0.8845 (mmm) REVERT: Lr 125 MET cc_start: 0.7622 (tmm) cc_final: 0.7246 (tmm) REVERT: A 266 PHE cc_start: 0.9602 (t80) cc_final: 0.9390 (t80) REVERT: A 276 MET cc_start: 0.8024 (ttt) cc_final: 0.7265 (ttt) REVERT: A 343 TYR cc_start: 0.9164 (m-80) cc_final: 0.8633 (m-80) REVERT: A 347 MET cc_start: 0.7480 (pmm) cc_final: 0.6887 (pmm) outliers start: 2 outliers final: 0 residues processed: 226 average time/residue: 0.1865 time to fit residues: 68.3211 Evaluate side-chains 170 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 134 optimal weight: 30.0000 chunk 251 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 208 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN B 480 ASN B 488 GLN B 514 HIS ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 14 ASN LY 96 HIS ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 111 GLN ** LR 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 100 ASN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.051721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.043271 restraints weight = 532910.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.043913 restraints weight = 467099.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.044062 restraints weight = 350204.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.043965 restraints weight = 291570.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.044013 restraints weight = 292342.913| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30707 Z= 0.195 Angle : 0.666 10.784 43037 Z= 0.338 Chirality : 0.039 0.245 5036 Planarity : 0.005 0.139 4134 Dihedral : 22.882 167.111 8683 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2646 helix: 0.21 (0.14), residues: 1351 sheet: -0.87 (0.35), residues: 193 loop : -0.47 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGLY 126 TYR 0.020 0.002 TYR 2 137 PHE 0.030 0.002 PHE 2 32 TRP 0.058 0.003 TRP B 284 HIS 0.007 0.001 HIS B 675 Details of bonding type rmsd covalent geometry : bond 0.00392 (30707) covalent geometry : angle 0.66648 (43037) hydrogen bonds : bond 0.06367 ( 1316) hydrogen bonds : angle 4.95364 ( 3489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.771 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 28 MET cc_start: 0.7981 (ppp) cc_final: 0.7595 (ppp) REVERT: 2 33 TYR cc_start: 0.9530 (m-80) cc_final: 0.9296 (m-80) REVERT: B 273 MET cc_start: 0.8538 (tmm) cc_final: 0.8282 (tmm) REVERT: B 576 GLU cc_start: 0.8072 (tp30) cc_final: 0.7673 (mm-30) REVERT: B 770 MET cc_start: 0.8406 (ttt) cc_final: 0.8181 (ttm) REVERT: LC 107 THR cc_start: 0.9090 (p) cc_final: 0.8658 (p) REVERT: LC 108 TRP cc_start: 0.8962 (p90) cc_final: 0.7965 (p-90) REVERT: LC 250 CYS cc_start: 0.9562 (m) cc_final: 0.9007 (t) REVERT: LE 150 LEU cc_start: 0.9662 (mt) cc_final: 0.9457 (mt) REVERT: LY 43 ASN cc_start: 0.8855 (t0) cc_final: 0.8616 (t0) REVERT: LY 65 GLN cc_start: 0.8763 (mp10) cc_final: 0.8556 (mp10) REVERT: LY 91 ASN cc_start: 0.9590 (m-40) cc_final: 0.9273 (p0) REVERT: LR 149 LYS cc_start: 0.9697 (mtmm) cc_final: 0.9494 (mtmm) REVERT: Lr 8 MET cc_start: 0.9304 (mmp) cc_final: 0.9040 (mmm) REVERT: A 210 LYS cc_start: 0.9832 (pttp) cc_final: 0.9540 (tppt) REVERT: A 276 MET cc_start: 0.8558 (ttm) cc_final: 0.8322 (ttt) REVERT: A 343 TYR cc_start: 0.8352 (m-80) cc_final: 0.8027 (m-80) REVERT: A 347 MET cc_start: 0.7071 (pmm) cc_final: 0.6788 (pmm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1938 time to fit residues: 67.0780 Evaluate side-chains 160 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 214 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN B 748 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 203 GLN LC 212 ASN ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 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 = 0.3437 r_free = 0.3437 target = 0.051043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.042796 restraints weight = 535138.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.043209 restraints weight = 470598.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.043504 restraints weight = 342705.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.043390 restraints weight = 295601.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.043509 restraints weight = 289055.488| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30707 Z= 0.217 Angle : 0.707 10.260 43037 Z= 0.359 Chirality : 0.040 0.213 5036 Planarity : 0.006 0.146 4134 Dihedral : 23.110 166.276 8683 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2646 helix: 0.15 (0.14), residues: 1348 sheet: -0.95 (0.34), residues: 203 loop : -0.52 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG 2 4 TYR 0.025 0.002 TYR B 451 PHE 0.020 0.002 PHE B 683 TRP 0.041 0.003 TRP B 284 HIS 0.011 0.002 HIS B 551 Details of bonding type rmsd covalent geometry : bond 0.00431 (30707) covalent geometry : angle 0.70713 (43037) hydrogen bonds : bond 0.07312 ( 1316) hydrogen bonds : angle 5.09749 ( 3489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 MET cc_start: 0.8615 (tmm) cc_final: 0.8356 (tmm) REVERT: B 576 GLU cc_start: 0.8118 (tp30) cc_final: 0.7700 (mm-30) REVERT: B 770 MET cc_start: 0.8518 (ttt) cc_final: 0.8167 (ttt) REVERT: LC 43 ASN cc_start: 0.9463 (m110) cc_final: 0.9260 (m110) REVERT: LC 108 TRP cc_start: 0.8838 (p90) cc_final: 0.7706 (p-90) REVERT: LC 221 PHE cc_start: 0.9718 (m-80) cc_final: 0.9517 (m-80) REVERT: LC 250 CYS cc_start: 0.9587 (m) cc_final: 0.9054 (t) REVERT: LY 43 ASN cc_start: 0.9007 (t0) cc_final: 0.8760 (t0) REVERT: LY 47 MET cc_start: 0.9569 (tpt) cc_final: 0.9268 (tpt) REVERT: LY 91 ASN cc_start: 0.9547 (m-40) cc_final: 0.9213 (p0) REVERT: LX 97 VAL cc_start: 0.9446 (m) cc_final: 0.9220 (m) REVERT: Lr 8 MET cc_start: 0.9378 (mmp) cc_final: 0.9126 (mmm) REVERT: Lr 125 MET cc_start: 0.6968 (tmm) cc_final: 0.6615 (tmm) REVERT: A 276 MET cc_start: 0.8499 (ttm) cc_final: 0.8270 (ttt) REVERT: A 343 TYR cc_start: 0.8320 (m-80) cc_final: 0.8073 (m-80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1896 time to fit residues: 63.9034 Evaluate side-chains 154 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 277 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 212 ASN ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 125 ASN LR 66 ASN ** LR 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 6 GLN ** Lr 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 213 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.050780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.042449 restraints weight = 542544.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.042790 restraints weight = 469462.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.043056 restraints weight = 347400.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.042963 restraints weight = 291634.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.043060 restraints weight = 291407.673| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 30707 Z= 0.243 Angle : 0.768 11.723 43037 Z= 0.391 Chirality : 0.042 0.302 5036 Planarity : 0.006 0.154 4134 Dihedral : 23.415 164.779 8683 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2646 helix: -0.05 (0.14), residues: 1332 sheet: -1.28 (0.35), residues: 194 loop : -0.65 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGLY 126 TYR 0.022 0.003 TYR 2 137 PHE 0.053 0.003 PHE 2 32 TRP 0.037 0.003 TRP B 284 HIS 0.013 0.002 HIS 2 161 Details of bonding type rmsd covalent geometry : bond 0.00491 (30707) covalent geometry : angle 0.76848 (43037) hydrogen bonds : bond 0.08005 ( 1316) hydrogen bonds : angle 5.23606 ( 3489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.949 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: symmetry clash revert: symmetry clash REVERT: 2 28 MET cc_start: 0.7689 (ppp) cc_final: 0.7312 (ppp) REVERT: 2 33 TYR cc_start: 0.9707 (t80) cc_final: 0.9456 (t80) REVERT: B 273 MET cc_start: 0.8563 (tmm) cc_final: 0.8306 (tmm) REVERT: B 431 MET cc_start: 0.1408 (mmp) cc_final: 0.0996 (mmt) REVERT: B 737 MET cc_start: 0.1516 (tpt) cc_final: 0.1299 (tpp) REVERT: B 770 MET cc_start: 0.8606 (ttt) cc_final: 0.8377 (ttt) REVERT: LC 43 ASN cc_start: 0.9513 (m110) cc_final: 0.9309 (m110) REVERT: LC 108 TRP cc_start: 0.8618 (p90) cc_final: 0.7461 (p-90) REVERT: LC 221 PHE cc_start: 0.9568 (m-80) cc_final: 0.9366 (m-80) REVERT: LC 250 CYS cc_start: 0.9602 (m) cc_final: 0.9074 (t) REVERT: LE 150 LEU cc_start: 0.9599 (mt) cc_final: 0.9293 (mp) REVERT: LY 43 ASN cc_start: 0.9039 (t0) cc_final: 0.8777 (t0) REVERT: LY 65 GLN cc_start: 0.8636 (mp10) cc_final: 0.8409 (mp10) REVERT: LY 91 ASN cc_start: 0.9529 (m-40) cc_final: 0.9278 (p0) REVERT: LX 97 VAL cc_start: 0.9420 (m) cc_final: 0.9112 (m) REVERT: Lr 8 MET cc_start: 0.9170 (mmp) cc_final: 0.8946 (mmp) REVERT: Lr 125 MET cc_start: 0.6924 (tmm) cc_final: 0.6546 (tmm) REVERT: A 276 MET cc_start: 0.8621 (ttm) cc_final: 0.8401 (ttt) REVERT: A 343 TYR cc_start: 0.8146 (m-80) cc_final: 0.7901 (m-80) REVERT: A 347 MET cc_start: 0.6904 (pmm) cc_final: 0.6640 (pmm) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1878 time to fit residues: 62.8882 Evaluate side-chains 148 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 255 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.051177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.043254 restraints weight = 534873.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.043463 restraints weight = 463787.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.043761 restraints weight = 355446.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.043626 restraints weight = 307534.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.043687 restraints weight = 291661.216| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30707 Z= 0.194 Angle : 0.714 10.842 43037 Z= 0.363 Chirality : 0.041 0.339 5036 Planarity : 0.005 0.150 4134 Dihedral : 23.315 162.598 8683 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 25.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2646 helix: 0.04 (0.14), residues: 1330 sheet: -1.25 (0.36), residues: 191 loop : -0.67 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGLY 126 TYR 0.021 0.002 TYR A 343 PHE 0.038 0.002 PHE B 683 TRP 0.033 0.002 TRPLR 95 HIS 0.010 0.001 HISLR 143 Details of bonding type rmsd covalent geometry : bond 0.00395 (30707) covalent geometry : angle 0.71431 (43037) hydrogen bonds : bond 0.06997 ( 1316) hydrogen bonds : angle 5.20243 ( 3489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.049 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 33 TYR cc_start: 0.9752 (t80) cc_final: 0.9503 (m-80) REVERT: B 273 MET cc_start: 0.8601 (tmm) cc_final: 0.8335 (tmm) REVERT: B 464 MET cc_start: 0.6811 (ptt) cc_final: 0.6444 (ptt) REVERT: B 770 MET cc_start: 0.8577 (ttt) cc_final: 0.8357 (ttt) REVERT: LC 108 TRP cc_start: 0.8555 (p90) cc_final: 0.7362 (p-90) REVERT: LC 221 PHE cc_start: 0.9632 (m-10) cc_final: 0.9411 (m-80) REVERT: LC 250 CYS cc_start: 0.9665 (m) cc_final: 0.9176 (t) REVERT: LE 150 LEU cc_start: 0.9601 (mt) cc_final: 0.9394 (mt) REVERT: LY 30 MET cc_start: 0.9232 (mmp) cc_final: 0.9029 (mmm) REVERT: LY 42 TYR cc_start: 0.9128 (m-10) cc_final: 0.8822 (m-10) REVERT: LY 43 ASN cc_start: 0.9115 (t0) cc_final: 0.8873 (t0) REVERT: LY 91 ASN cc_start: 0.9682 (m-40) cc_final: 0.9382 (p0) REVERT: LX 97 VAL cc_start: 0.9449 (m) cc_final: 0.9121 (m) REVERT: LR 141 HIS cc_start: 0.9286 (m-70) cc_final: 0.9076 (m90) REVERT: Lr 8 MET cc_start: 0.9185 (mmp) cc_final: 0.8930 (mmm) REVERT: Lr 125 MET cc_start: 0.7206 (tmm) cc_final: 0.6873 (tmm) REVERT: A 276 MET cc_start: 0.8535 (ttm) cc_final: 0.8260 (ttt) REVERT: A 347 MET cc_start: 0.7201 (pmm) cc_final: 0.6891 (pmm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1893 time to fit residues: 61.2037 Evaluate side-chains 149 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 217 optimal weight: 0.8980 chunk 286 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN LY 20 ASN LY 96 HIS ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 93 ASN ** Lr 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.052373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.044274 restraints weight = 523137.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.044415 restraints weight = 456759.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.044838 restraints weight = 344669.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.044705 restraints weight = 297420.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.044812 restraints weight = 283651.452| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30707 Z= 0.133 Angle : 0.658 12.376 43037 Z= 0.334 Chirality : 0.040 0.348 5036 Planarity : 0.005 0.133 4134 Dihedral : 22.960 161.420 8683 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 0.04 % Allowed : 0.68 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2646 helix: 0.20 (0.14), residues: 1343 sheet: -1.22 (0.35), residues: 200 loop : -0.61 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGLY 126 TYR 0.018 0.002 TYR B 809 PHE 0.031 0.002 PHE 2 32 TRP 0.073 0.002 TRP B 284 HIS 0.010 0.001 HISLR 143 Details of bonding type rmsd covalent geometry : bond 0.00278 (30707) covalent geometry : angle 0.65809 (43037) hydrogen bonds : bond 0.05496 ( 1316) hydrogen bonds : angle 4.98833 ( 3489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.710 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 28 MET cc_start: 0.8023 (ppp) cc_final: 0.7479 (ppp) REVERT: 2 33 TYR cc_start: 0.9767 (t80) cc_final: 0.9535 (t80) REVERT: B 273 MET cc_start: 0.8624 (tmm) cc_final: 0.8375 (tmm) REVERT: B 464 MET cc_start: 0.6565 (ptt) cc_final: 0.6115 (ptt) REVERT: B 770 MET cc_start: 0.8302 (ttt) cc_final: 0.8051 (ttt) REVERT: LC 43 ASN cc_start: 0.9448 (m110) cc_final: 0.9150 (m110) REVERT: LC 108 TRP cc_start: 0.8464 (p90) cc_final: 0.7327 (p-90) REVERT: LC 221 PHE cc_start: 0.9639 (m-10) cc_final: 0.9372 (m-80) REVERT: LC 250 CYS cc_start: 0.9546 (m) cc_final: 0.9118 (t) REVERT: LE 150 LEU cc_start: 0.9572 (mt) cc_final: 0.9333 (mt) REVERT: LY 30 MET cc_start: 0.9278 (mmp) cc_final: 0.9022 (mmm) REVERT: LY 43 ASN cc_start: 0.9096 (t0) cc_final: 0.8822 (t0) REVERT: LY 65 GLN cc_start: 0.8799 (mp10) cc_final: 0.8545 (mp10) REVERT: LY 91 ASN cc_start: 0.9668 (m-40) cc_final: 0.9339 (p0) REVERT: LX 81 LEU cc_start: 0.8652 (mt) cc_final: 0.8405 (mt) REVERT: LR 40 GLN cc_start: 0.9449 (mm110) cc_final: 0.9127 (mp10) REVERT: LR 141 HIS cc_start: 0.9278 (m-70) cc_final: 0.9043 (m90) REVERT: Lr 8 MET cc_start: 0.9204 (mmp) cc_final: 0.8872 (mmp) REVERT: Lr 38 PHE cc_start: 0.9275 (t80) cc_final: 0.8916 (t80) REVERT: Lr 125 MET cc_start: 0.7221 (tmm) cc_final: 0.6900 (tmm) REVERT: A 274 ASP cc_start: 0.9681 (m-30) cc_final: 0.9407 (p0) REVERT: A 276 MET cc_start: 0.8502 (ttm) cc_final: 0.8195 (ttt) REVERT: A 347 MET cc_start: 0.7261 (pmm) cc_final: 0.6826 (pmm) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1830 time to fit residues: 63.8212 Evaluate side-chains 161 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 10 optimal weight: 50.0000 chunk 54 optimal weight: 8.9990 chunk 249 optimal weight: 2.9990 chunk 83 optimal weight: 0.0070 chunk 259 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 40.0000 chunk 81 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 GLN ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 828 HIS ** LC 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN ** LE 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 121 GLN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.051476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.043886 restraints weight = 530137.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.044125 restraints weight = 451723.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.044255 restraints weight = 342041.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.044184 restraints weight = 286075.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.044217 restraints weight = 286377.184| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30707 Z= 0.193 Angle : 0.703 11.775 43037 Z= 0.357 Chirality : 0.040 0.347 5036 Planarity : 0.005 0.135 4134 Dihedral : 23.128 162.398 8683 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2646 helix: 0.15 (0.14), residues: 1342 sheet: -1.20 (0.36), residues: 189 loop : -0.71 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGLY 126 TYR 0.020 0.002 TYRLX 137 PHE 0.035 0.002 PHE B 683 TRP 0.064 0.003 TRP B 284 HIS 0.011 0.001 HIS 2 120 Details of bonding type rmsd covalent geometry : bond 0.00394 (30707) covalent geometry : angle 0.70316 (43037) hydrogen bonds : bond 0.07101 ( 1316) hydrogen bonds : angle 5.12505 ( 3489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.909 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 33 TYR cc_start: 0.9772 (t80) cc_final: 0.9531 (t80) REVERT: B 273 MET cc_start: 0.8665 (tmm) cc_final: 0.8421 (tmm) REVERT: B 464 MET cc_start: 0.6528 (ptt) cc_final: 0.6121 (ptt) REVERT: B 737 MET cc_start: 0.2282 (tpt) cc_final: 0.2062 (tpp) REVERT: B 770 MET cc_start: 0.8447 (ttt) cc_final: 0.8172 (ttt) REVERT: LC 43 ASN cc_start: 0.9456 (m110) cc_final: 0.9193 (m110) REVERT: LC 108 TRP cc_start: 0.8480 (p90) cc_final: 0.7307 (p-90) REVERT: LC 221 PHE cc_start: 0.9595 (m-10) cc_final: 0.9352 (m-80) REVERT: LC 250 CYS cc_start: 0.9489 (m) cc_final: 0.9098 (t) REVERT: LE 150 LEU cc_start: 0.9571 (mt) cc_final: 0.9362 (mt) REVERT: LY 30 MET cc_start: 0.9286 (mmp) cc_final: 0.9073 (mmm) REVERT: LY 43 ASN cc_start: 0.9163 (t0) cc_final: 0.8909 (t0) REVERT: LY 65 GLN cc_start: 0.8898 (mp10) cc_final: 0.8636 (mp10) REVERT: LY 91 ASN cc_start: 0.9671 (m-40) cc_final: 0.9371 (p0) REVERT: Lr 8 MET cc_start: 0.9199 (mmp) cc_final: 0.8938 (mmm) REVERT: Lr 125 MET cc_start: 0.7357 (tmm) cc_final: 0.7001 (tmm) REVERT: A 276 MET cc_start: 0.8621 (ttm) cc_final: 0.8363 (ttt) REVERT: A 347 MET cc_start: 0.7292 (pmm) cc_final: 0.6958 (pmm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1892 time to fit residues: 61.1506 Evaluate side-chains 154 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 140 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 197 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 164 optimal weight: 0.0470 chunk 252 optimal weight: 20.0000 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 43 ASN LC 212 ASN LE 284 HIS LY 96 HIS ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lr 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 121 GLN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.053009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.044693 restraints weight = 518968.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.044957 restraints weight = 452840.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.045376 restraints weight = 352427.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.045287 restraints weight = 304739.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.045386 restraints weight = 278097.705| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30707 Z= 0.126 Angle : 0.650 12.626 43037 Z= 0.331 Chirality : 0.039 0.360 5036 Planarity : 0.005 0.120 4134 Dihedral : 22.763 162.072 8683 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2646 helix: 0.25 (0.14), residues: 1348 sheet: -1.05 (0.35), residues: 200 loop : -0.57 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGLY 126 TYR 0.028 0.002 TYR 2 145 PHE 0.029 0.002 PHE B 683 TRP 0.065 0.002 TRP B 284 HIS 0.010 0.001 HIS 2 120 Details of bonding type rmsd covalent geometry : bond 0.00265 (30707) covalent geometry : angle 0.65025 (43037) hydrogen bonds : bond 0.05339 ( 1316) hydrogen bonds : angle 4.94047 ( 3489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.49 seconds wall clock time: 101 minutes 14.06 seconds (6074.06 seconds total)