Starting phenix.real_space_refine on Sun Jul 5 20:43:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gj5_51382/07_2026/9gj5_51382.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gj5_51382/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gj5_51382/07_2026/9gj5_51382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gj5_51382/07_2026/9gj5_51382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gj5_51382/07_2026/9gj5_51382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gj5_51382/07_2026/9gj5_51382.map" } 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-6108/lib/python3.11/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: 5.92, per 1000 atoms: 0.20 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: 2.47 Conformation dependent library (CDL) restraints added in 899.9 milliseconds 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: 4.52 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: 7.08 Time building geometry restraints manager: 3.32 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=" N9 G 12902 " pdb=" C4 G 12902 " ideal model delta sigma weight residual 1.375 1.341 0.034 8.00e-03 1.56e+04 1.76e+01 bond pdb=" N9 A 1 197 " pdb=" C4 A 1 197 " ideal model delta sigma weight residual 1.374 1.354 0.020 6.00e-03 2.78e+04 1.10e+01 bond pdb=" N9 A 8 82 " pdb=" C4 A 8 82 " ideal model delta sigma weight residual 1.374 1.393 -0.019 6.00e-03 2.78e+04 1.06e+01 bond pdb=" C2 G 12902 " pdb=" N3 G 12902 " ideal model delta sigma weight residual 1.323 1.299 0.024 8.00e-03 1.56e+04 9.34e+00 bond pdb=" N9 A 1 235 " pdb=" C4 A 1 235 " ideal model delta sigma weight residual 1.374 1.356 0.018 6.00e-03 2.78e+04 9.13e+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=" C2 C 13598 " pdb=" N1 C 13598 " pdb=" C6 C 13598 " ideal model delta sigma weight residual 120.30 116.69 3.61 4.00e-01 6.25e+00 8.17e+01 angle pdb=" C1' C 1 485 " pdb=" N1 C 1 485 " pdb=" C2 C 1 485 " ideal model delta sigma weight residual 118.80 128.29 -9.49 1.10e+00 8.26e-01 7.45e+01 angle pdb=" N1 C 13598 " pdb=" C6 C 13598 " pdb=" C5 C 13598 " ideal model delta sigma weight residual 121.00 124.72 -3.72 5.00e-01 4.00e+00 5.54e+01 angle pdb=" O2 C 13598 " pdb=" C2 C 13598 " pdb=" N3 C 13598 " ideal model delta sigma weight residual 121.90 116.84 5.06 7.00e-01 2.04e+00 5.23e+01 angle pdb=" N9 G 12902 " pdb=" C4 G 12902 " pdb=" N3 G 12902 " ideal model delta sigma weight residual 126.00 121.79 4.21 6.00e-01 2.78e+00 4.92e+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: 21.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.610 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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= 0.318 Angle : 0.868 12.941 43037 Z= 0.599 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/Z covalent geometry : bond 0.00475 / 0.32 (30707) covalent geometry : angle 0.86773 / 0.60 (43037) hydrogen bonds : bond 0.20776 / 13.57 ( 1316) hydrogen bonds : angle 7.37628 / 8.08 ( 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 : 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: symmetry clash revert: 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: 0.2025 time to fit residues: 80.9490 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 : 0.964 ------------------------------------------------------------------------------- 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: 30.0000 chunk 132 optimal weight: 20.0000 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: 20.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** LC 21 ASN LC 60 HIS ** LC 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 212 ASN ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 4 ASN LY 96 HIS Lh 63 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 111 GLN Lr 45 HIS A 147 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.053652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.045045 restraints weight = 513887.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.045017 restraints weight = 456277.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.045466 restraints weight = 367239.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.045367 restraints weight = 308390.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.045454 restraints weight = 304130.530| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1221 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= 0.196 Angle : 0.669 12.941 43037 Z= 0.365 Chirality : 0.041 0.254 5036 Planarity : 0.006 0.121 4134 Dihedral : 22.576 168.115 8683 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Rotamer: Outliers : 0.21 % Allowed : 4.38 % Favored : 95.40 % 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: 0.16 (0.13), residues: 1341 sheet: -0.41 (0.37), residues: 180 loop : -0.49 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARGLY 126 TYR 0.020 0.002 TYR 2 26 PHE 0.026 0.002 PHE 2 32 TRP 0.038 0.002 TRPLR 95 HIS 0.011 0.002 HISLR 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (30707) covalent geometry : angle 0.66932 / 0.37 (43037) hydrogen bonds : bond 0.07718 / 5.26 ( 1316) hydrogen bonds : angle 5.64985 / 5.79 ( 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 255 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 250 time to evaluate : 0.998 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 33 TYR cc_start: 0.9472 (m-80) cc_final: 0.9201 (m-80) REVERT: 2 60 MET cc_start: 0.9184 (mmm) cc_final: 0.8622 (mmm) REVERT: 2 91 MET cc_start: 0.9543 (mmp) cc_final: 0.9157 (ppp) REVERT: B 9 LYS cc_start: 0.9359 (mmtt) cc_final: 0.9118 (tmtt) REVERT: B 47 GLU cc_start: 0.8944 (pm20) cc_final: 0.8508 (mt-10) REVERT: B 162 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9236 (tm-30) REVERT: B 273 MET cc_start: 0.8442 (tmm) cc_final: 0.8209 (tmm) REVERT: B 737 MET cc_start: 0.0755 (mpp) cc_final: 0.0535 (mpp) REVERT: LC 52 TYR cc_start: 0.5186 (p90) cc_final: 0.4681 (m-80) REVERT: LC 107 THR cc_start: 0.9252 (p) cc_final: 0.8819 (p) REVERT: LC 108 TRP cc_start: 0.8948 (p90) cc_final: 0.7845 (p-90) REVERT: LC 133 LEU cc_start: 0.9146 (tt) cc_final: 0.8854 (tt) REVERT: LC 221 PHE cc_start: 0.9853 (m-10) cc_final: 0.9636 (m-10) REVERT: LC 250 CYS cc_start: 0.9486 (m) cc_final: 0.9005 (t) REVERT: LY 43 ASN cc_start: 0.8768 (t0) cc_final: 0.8415 (t0) REVERT: Lr 8 MET cc_start: 0.9093 (mmp) cc_final: 0.8810 (mmm) REVERT: Lr 96 MET cc_start: 0.9867 (mmp) cc_final: 0.9636 (mmt) REVERT: A 55 MET cc_start: 0.8932 (ptt) cc_final: 0.8629 (ppp) REVERT: A 129 VAL cc_start: 0.5243 (OUTLIER) cc_final: 0.4776 (m) REVERT: A 276 MET cc_start: 0.8386 (ttt) cc_final: 0.7552 (ttt) REVERT: A 343 TYR cc_start: 0.8285 (m-10) cc_final: 0.7879 (m-80) REVERT: A 347 MET cc_start: 0.7065 (pmm) cc_final: 0.6858 (pmm) outliers start: 5 outliers final: 2 residues processed: 253 average time/residue: 0.2020 time to fit residues: 81.4396 Evaluate side-chains 183 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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: 6.9990 chunk 162 optimal weight: 8.9990 chunk 260 optimal weight: 0.9990 chunk 201 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 119 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** LC 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 212 ASN ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.053728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.045378 restraints weight = 513152.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.045407 restraints weight = 453163.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.045853 restraints weight = 330046.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.045727 restraints weight = 278731.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.045884 restraints weight = 292800.681| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 30707 Z= 0.154 Angle : 0.597 10.671 43037 Z= 0.327 Chirality : 0.039 0.275 5036 Planarity : 0.005 0.130 4134 Dihedral : 22.529 169.033 8683 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 0.17 % Allowed : 3.45 % Favored : 96.38 % 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: 0.22 (0.14), residues: 1345 sheet: -0.46 (0.38), residues: 180 loop : -0.41 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGLY 126 TYR 0.027 0.002 TYR B 138 PHE 0.038 0.002 PHE B 683 TRP 0.046 0.002 TRP B 284 HIS 0.008 0.001 HISLR 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (30707) covalent geometry : angle 0.59679 / 0.33 (43037) hydrogen bonds : bond 0.06501 / 4.38 ( 1316) hydrogen bonds : angle 5.37307 / 5.51 ( 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 253 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 0.988 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: 2 33 TYR cc_start: 0.9389 (m-80) cc_final: 0.9134 (m-80) REVERT: 2 60 MET cc_start: 0.9182 (mmm) cc_final: 0.8647 (mmm) REVERT: 2 91 MET cc_start: 0.9498 (mmp) cc_final: 0.9120 (ppp) REVERT: B 9 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9092 (tmtt) REVERT: B 273 MET cc_start: 0.8400 (tmm) cc_final: 0.8051 (tmm) REVERT: B 770 MET cc_start: 0.8099 (ttt) cc_final: 0.7781 (ttt) REVERT: LC 52 TYR cc_start: 0.4973 (p90) cc_final: 0.4369 (m-80) REVERT: LC 107 THR cc_start: 0.9342 (p) cc_final: 0.8938 (p) REVERT: LC 108 TRP cc_start: 0.8983 (p90) cc_final: 0.7795 (p-90) REVERT: LC 133 LEU cc_start: 0.9101 (tt) cc_final: 0.8831 (tt) REVERT: LC 221 PHE cc_start: 0.9855 (m-10) cc_final: 0.9636 (m-10) REVERT: LC 250 CYS cc_start: 0.9485 (m) cc_final: 0.9032 (t) REVERT: LY 43 ASN cc_start: 0.8818 (t0) cc_final: 0.8491 (t0) REVERT: LX 98 PHE cc_start: 0.9462 (m-80) cc_final: 0.9230 (m-80) REVERT: LX 144 TYR cc_start: 0.9475 (m-80) cc_final: 0.9178 (m-10) REVERT: Lr 8 MET cc_start: 0.9133 (mmp) cc_final: 0.8845 (mmm) REVERT: A 276 MET cc_start: 0.8215 (ttt) cc_final: 0.7545 (ttt) REVERT: A 343 TYR cc_start: 0.8211 (m-10) cc_final: 0.7734 (m-80) outliers start: 4 outliers final: 0 residues processed: 252 average time/residue: 0.2010 time to fit residues: 80.9638 Evaluate side-chains 178 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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: 40.0000 chunk 95 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 265 optimal weight: 0.4980 chunk 274 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 480 ASN B 488 GLN B 514 HIS 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** ** LC 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 66 ASN ** LR 143 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.053523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.045257 restraints weight = 511111.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.045394 restraints weight = 448590.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.045722 restraints weight = 333256.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.045607 restraints weight = 284985.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.045648 restraints weight = 285108.116| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30707 Z= 0.149 Angle : 0.574 9.783 43037 Z= 0.317 Chirality : 0.038 0.289 5036 Planarity : 0.005 0.135 4134 Dihedral : 22.524 169.824 8683 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.21 % 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: -0.23 (0.16), residues: 2646 helix: 0.24 (0.14), residues: 1355 sheet: -0.59 (0.36), residues: 198 loop : -0.41 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGLY 126 TYR 0.025 0.002 TYR B 138 PHE 0.026 0.002 PHE B 683 TRP 0.028 0.002 TRP B 284 HIS 0.012 0.001 HISLX 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (30707) covalent geometry : angle 0.57442 / 0.32 (43037) hydrogen bonds : bond 0.06115 / 4.15 ( 1316) hydrogen bonds : angle 5.16877 / 5.24 ( 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 238 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 1.095 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: 2 33 TYR cc_start: 0.9473 (m-80) cc_final: 0.9248 (m-80) REVERT: 2 91 MET cc_start: 0.9487 (mmp) cc_final: 0.9154 (ppp) REVERT: B 9 LYS cc_start: 0.9349 (mmtt) cc_final: 0.9057 (tmtt) REVERT: B 273 MET cc_start: 0.8275 (tmm) cc_final: 0.7987 (tmm) REVERT: B 770 MET cc_start: 0.7920 (ttt) cc_final: 0.7549 (ttt) REVERT: LC 52 TYR cc_start: 0.5056 (p90) cc_final: 0.4217 (m-80) REVERT: LC 107 THR cc_start: 0.9462 (p) cc_final: 0.9101 (p) REVERT: LC 108 TRP cc_start: 0.8990 (p90) cc_final: 0.7785 (p-90) REVERT: LC 221 PHE cc_start: 0.9835 (m-10) cc_final: 0.9630 (m-10) REVERT: LC 250 CYS cc_start: 0.9525 (m) cc_final: 0.9044 (t) REVERT: LY 43 ASN cc_start: 0.8800 (t0) cc_final: 0.8444 (t0) REVERT: LX 98 PHE cc_start: 0.9419 (m-80) cc_final: 0.9159 (m-80) REVERT: LX 144 TYR cc_start: 0.9431 (m-80) cc_final: 0.9143 (m-10) REVERT: Lr 8 MET cc_start: 0.9196 (mmp) cc_final: 0.8901 (mmm) REVERT: Lr 96 MET cc_start: 0.9852 (mmp) cc_final: 0.9633 (mmt) REVERT: Lr 125 MET cc_start: 0.6629 (tmm) cc_final: 0.6426 (tmm) REVERT: A 55 MET cc_start: 0.8969 (ptt) cc_final: 0.8741 (ppp) REVERT: A 276 MET cc_start: 0.8289 (ttt) cc_final: 0.7632 (ttt) REVERT: A 343 TYR cc_start: 0.8204 (m-80) cc_final: 0.7767 (m-80) REVERT: A 347 MET cc_start: 0.6791 (pmm) cc_final: 0.6574 (pmm) outliers start: 2 outliers final: 1 residues processed: 238 average time/residue: 0.1966 time to fit residues: 76.0624 Evaluate side-chains 172 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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: 10.0000 chunk 251 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 208 optimal weight: 0.9990 chunk 127 optimal weight: 30.0000 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** ** LC 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.053353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045093 restraints weight = 516075.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.045027 restraints weight = 451877.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.045465 restraints weight = 343950.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.045393 restraints weight = 287948.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.045436 restraints weight = 294706.755| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30707 Z= 0.145 Angle : 0.572 9.843 43037 Z= 0.314 Chirality : 0.038 0.268 5036 Planarity : 0.005 0.135 4134 Dihedral : 22.544 170.173 8683 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % 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: -0.20 (0.16), residues: 2646 helix: 0.31 (0.14), residues: 1356 sheet: -0.66 (0.36), residues: 198 loop : -0.42 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGLY 126 TYR 0.022 0.002 TYR B 138 PHE 0.022 0.002 PHE 2 32 TRP 0.064 0.002 TRP B 284 HIS 0.006 0.001 HIS B 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (30707) covalent geometry : angle 0.57214 / 0.31 (43037) hydrogen bonds : bond 0.05909 / 4.00 ( 1316) hydrogen bonds : angle 5.04990 / 5.15 ( 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 232 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.020 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: 2 33 TYR cc_start: 0.9460 (m-80) cc_final: 0.9202 (m-80) REVERT: 2 91 MET cc_start: 0.9479 (mmp) cc_final: 0.9119 (ppp) REVERT: B 273 MET cc_start: 0.8331 (tmm) cc_final: 0.8042 (tmm) REVERT: B 770 MET cc_start: 0.7778 (ttt) cc_final: 0.7392 (ttt) REVERT: LC 52 TYR cc_start: 0.5784 (p90) cc_final: 0.4904 (m-80) REVERT: LC 107 THR cc_start: 0.9262 (p) cc_final: 0.8871 (p) REVERT: LC 108 TRP cc_start: 0.9048 (p90) cc_final: 0.7817 (p-90) REVERT: LC 221 PHE cc_start: 0.9816 (m-10) cc_final: 0.9614 (m-10) REVERT: LC 250 CYS cc_start: 0.9539 (m) cc_final: 0.9057 (t) REVERT: LY 43 ASN cc_start: 0.8759 (t0) cc_final: 0.8477 (t0) REVERT: LX 98 PHE cc_start: 0.9337 (m-80) cc_final: 0.9111 (m-80) REVERT: LX 144 TYR cc_start: 0.9417 (m-80) cc_final: 0.9120 (m-10) REVERT: Lr 8 MET cc_start: 0.9242 (mmp) cc_final: 0.8996 (mmm) REVERT: A 276 MET cc_start: 0.8301 (ttt) cc_final: 0.7651 (ttt) REVERT: A 343 TYR cc_start: 0.8182 (m-80) cc_final: 0.7754 (m-80) REVERT: A 347 MET cc_start: 0.6820 (pmm) cc_final: 0.6590 (pmm) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1916 time to fit residues: 72.3470 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 : 0.928 ------------------------------------------------------------------------------- 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: 0.9980 chunk 233 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 129 GLN ** 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 435 GLN B 748 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 212 ASN ** LC 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 14 ASN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 66 ASN Lr 85 ASN ** 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 = 0.3482 r_free = 0.3482 target = 0.053257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.045048 restraints weight = 513813.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.045209 restraints weight = 452304.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045492 restraints weight = 342005.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.045406 restraints weight = 290436.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.045425 restraints weight = 286035.702| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30707 Z= 0.141 Angle : 0.569 10.461 43037 Z= 0.310 Chirality : 0.038 0.257 5036 Planarity : 0.005 0.134 4134 Dihedral : 22.539 170.278 8683 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.94 % 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: -0.21 (0.16), residues: 2646 helix: 0.29 (0.14), residues: 1369 sheet: -0.65 (0.36), residues: 193 loop : -0.42 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGLY 126 TYR 0.020 0.002 TYR 2 26 PHE 0.025 0.002 PHELX 79 TRP 0.032 0.002 TRP B 284 HIS 0.007 0.001 HIS 2 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (30707) covalent geometry : angle 0.56881 / 0.31 (43037) hydrogen bonds : bond 0.05700 / 3.87 ( 1316) hydrogen bonds : angle 4.98334 / 5.11 ( 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 231 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 1.052 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: 2 33 TYR cc_start: 0.9502 (m-80) cc_final: 0.9233 (m-80) REVERT: 2 91 MET cc_start: 0.9467 (mmp) cc_final: 0.8934 (ttp) REVERT: B 273 MET cc_start: 0.8375 (tmm) cc_final: 0.8086 (tmm) REVERT: B 576 GLU cc_start: 0.7597 (tp30) cc_final: 0.7160 (mm-30) REVERT: B 770 MET cc_start: 0.7946 (ttt) cc_final: 0.7579 (ttt) REVERT: LC 43 ASN cc_start: 0.9352 (m110) cc_final: 0.9060 (t0) REVERT: LC 52 TYR cc_start: 0.5797 (p90) cc_final: 0.4849 (m-80) REVERT: LC 107 THR cc_start: 0.9261 (p) cc_final: 0.8871 (p) REVERT: LC 108 TRP cc_start: 0.8987 (p90) cc_final: 0.7830 (p-90) REVERT: LC 250 CYS cc_start: 0.9541 (m) cc_final: 0.9039 (t) REVERT: LY 43 ASN cc_start: 0.8755 (t0) cc_final: 0.8460 (t0) REVERT: LY 77 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7954 (mtpt) REVERT: LX 81 LEU cc_start: 0.8330 (mt) cc_final: 0.8019 (mt) REVERT: LX 98 PHE cc_start: 0.9343 (m-80) cc_final: 0.9110 (m-80) REVERT: LX 144 TYR cc_start: 0.9414 (m-80) cc_final: 0.9124 (m-10) REVERT: Lr 8 MET cc_start: 0.9250 (mmp) cc_final: 0.9001 (mmm) REVERT: Lr 96 MET cc_start: 0.9824 (mmp) cc_final: 0.9621 (mmt) REVERT: Lr 125 MET cc_start: 0.6464 (tmm) cc_final: 0.6261 (tmm) REVERT: A 343 TYR cc_start: 0.8240 (m-80) cc_final: 0.7818 (m-80) REVERT: A 347 MET cc_start: 0.6782 (pmm) cc_final: 0.6561 (pmm) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.1919 time to fit residues: 72.3572 Evaluate side-chains 172 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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: 20.0000 chunk 155 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** 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** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.053201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045119 restraints weight = 516179.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.045115 restraints weight = 442196.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045488 restraints weight = 341449.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.045425 restraints weight = 289184.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.045447 restraints weight = 285840.004| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30707 Z= 0.145 Angle : 0.582 11.176 43037 Z= 0.317 Chirality : 0.038 0.257 5036 Planarity : 0.005 0.132 4134 Dihedral : 22.561 170.230 8683 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -0.21 (0.16), residues: 2646 helix: 0.30 (0.14), residues: 1364 sheet: -0.62 (0.36), residues: 192 loop : -0.45 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGLY 126 TYR 0.023 0.002 TYR 2 26 PHE 0.046 0.002 PHE B 683 TRP 0.029 0.002 TRP B 284 HIS 0.010 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (30707) covalent geometry : angle 0.58217 / 0.32 (43037) hydrogen bonds : bond 0.05791 / 3.94 ( 1316) hydrogen bonds : angle 4.95971 / 5.10 ( 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 224 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.019 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: 2 33 TYR cc_start: 0.9523 (m-80) cc_final: 0.9261 (m-80) REVERT: 2 91 MET cc_start: 0.9466 (mmp) cc_final: 0.8938 (ttp) REVERT: B 273 MET cc_start: 0.8408 (tmm) cc_final: 0.8131 (tmm) REVERT: B 576 GLU cc_start: 0.7624 (tp30) cc_final: 0.7183 (mm-30) REVERT: B 770 MET cc_start: 0.7930 (ttt) cc_final: 0.7573 (ttt) REVERT: LC 52 TYR cc_start: 0.5756 (p90) cc_final: 0.4669 (m-80) REVERT: LC 107 THR cc_start: 0.9279 (p) cc_final: 0.8859 (p) REVERT: LC 108 TRP cc_start: 0.8994 (p90) cc_final: 0.7815 (p-90) REVERT: LC 221 PHE cc_start: 0.9784 (m-10) cc_final: 0.9531 (m-10) REVERT: LC 250 CYS cc_start: 0.9560 (m) cc_final: 0.9054 (t) REVERT: LY 43 ASN cc_start: 0.8759 (t0) cc_final: 0.8448 (t0) REVERT: LY 77 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8068 (mtpt) REVERT: LX 98 PHE cc_start: 0.9260 (m-80) cc_final: 0.9047 (m-80) REVERT: LX 144 TYR cc_start: 0.9454 (m-80) cc_final: 0.9178 (m-10) REVERT: Lr 8 MET cc_start: 0.9263 (mmp) cc_final: 0.9018 (mmm) REVERT: A 276 MET cc_start: 0.8400 (ttt) cc_final: 0.7152 (ppp) REVERT: A 343 TYR cc_start: 0.8244 (m-80) cc_final: 0.7815 (m-80) REVERT: A 347 MET cc_start: 0.6688 (pmm) cc_final: 0.6469 (pmm) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1918 time to fit residues: 69.9881 Evaluate side-chains 164 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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: 3.9990 chunk 279 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** 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** ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 66 ASN Lr 100 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.053119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045201 restraints weight = 514883.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.045193 restraints weight = 438231.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.045521 restraints weight = 347286.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.045458 restraints weight = 293357.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.045477 restraints weight = 294030.629| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30707 Z= 0.138 Angle : 0.580 11.585 43037 Z= 0.314 Chirality : 0.038 0.246 5036 Planarity : 0.005 0.130 4134 Dihedral : 22.566 170.046 8683 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: -0.20 (0.16), residues: 2646 helix: 0.33 (0.14), residues: 1362 sheet: -0.77 (0.35), residues: 198 loop : -0.45 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 764 TYR 0.018 0.002 TYR B 154 PHE 0.036 0.002 PHE 2 32 TRP 0.079 0.002 TRP B 284 HIS 0.007 0.001 HIS 2 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (30707) covalent geometry : angle 0.58004 / 0.31 (43037) hydrogen bonds : bond 0.05566 / 3.78 ( 1316) hydrogen bonds : angle 4.93324 / 5.07 ( 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 226 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.968 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: 2 33 TYR cc_start: 0.9502 (m-80) cc_final: 0.9237 (m-80) REVERT: 2 91 MET cc_start: 0.9444 (mmp) cc_final: 0.8860 (tmm) REVERT: B 273 MET cc_start: 0.8490 (tmm) cc_final: 0.8202 (tmm) REVERT: B 576 GLU cc_start: 0.7889 (tp30) cc_final: 0.7421 (mm-30) REVERT: B 770 MET cc_start: 0.8000 (ttt) cc_final: 0.7676 (ttt) REVERT: LC 43 ASN cc_start: 0.9360 (m110) cc_final: 0.9122 (t0) REVERT: LC 52 TYR cc_start: 0.5995 (p90) cc_final: 0.4850 (m-80) REVERT: LC 107 THR cc_start: 0.9273 (p) cc_final: 0.8822 (p) REVERT: LC 108 TRP cc_start: 0.8963 (p90) cc_final: 0.7730 (p-90) REVERT: LC 221 PHE cc_start: 0.9778 (m-10) cc_final: 0.9523 (m-10) REVERT: LC 250 CYS cc_start: 0.9560 (m) cc_final: 0.9057 (t) REVERT: LY 43 ASN cc_start: 0.8772 (t0) cc_final: 0.8440 (t0) REVERT: LY 62 TYR cc_start: 0.9073 (m-10) cc_final: 0.8694 (t80) REVERT: LY 77 LYS cc_start: 0.8232 (mtpt) cc_final: 0.8005 (mtpt) REVERT: LX 98 PHE cc_start: 0.9238 (m-80) cc_final: 0.9011 (m-80) REVERT: LX 144 TYR cc_start: 0.9418 (m-80) cc_final: 0.9120 (m-10) REVERT: Lr 8 MET cc_start: 0.9292 (mmp) cc_final: 0.9028 (mmm) REVERT: A 276 MET cc_start: 0.8597 (ttt) cc_final: 0.8297 (ttt) REVERT: A 343 TYR cc_start: 0.8336 (m-80) cc_final: 0.7924 (m-80) REVERT: A 347 MET cc_start: 0.6838 (pmm) cc_final: 0.6619 (pmm) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1927 time to fit residues: 70.9149 Evaluate side-chains 165 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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: 9.9990 chunk 286 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** 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 36 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.052857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.044076 restraints weight = 517890.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.044798 restraints weight = 459027.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.045023 restraints weight = 338018.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.044864 restraints weight = 291426.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.044962 restraints weight = 285805.061| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30707 Z= 0.150 Angle : 0.593 11.266 43037 Z= 0.323 Chirality : 0.038 0.244 5036 Planarity : 0.005 0.128 4134 Dihedral : 22.597 170.132 8683 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 0.04 % Allowed : 0.81 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.23 (0.16), residues: 2646 helix: 0.32 (0.14), residues: 1352 sheet: -0.77 (0.36), residues: 192 loop : -0.48 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGLY 126 TYR 0.037 0.002 TYR B 451 PHE 0.027 0.002 PHE B 683 TRP 0.058 0.002 TRP B 284 HIS 0.011 0.001 HIS B 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (30707) covalent geometry : angle 0.59338 / 0.32 (43037) hydrogen bonds : bond 0.05897 / 4.03 ( 1316) hydrogen bonds : angle 4.98601 / 5.11 ( 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 225 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.992 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: 2 33 TYR cc_start: 0.9557 (m-80) cc_final: 0.9297 (m-80) REVERT: 2 91 MET cc_start: 0.9466 (mmp) cc_final: 0.8896 (tmm) REVERT: B 273 MET cc_start: 0.8493 (tmm) cc_final: 0.8224 (tmm) REVERT: B 482 MET cc_start: 0.7519 (mmm) cc_final: 0.7254 (mmm) REVERT: B 576 GLU cc_start: 0.7904 (tp30) cc_final: 0.7498 (mm-30) REVERT: B 770 MET cc_start: 0.8254 (ttt) cc_final: 0.7982 (ttt) REVERT: LC 43 ASN cc_start: 0.9352 (m110) cc_final: 0.9110 (t0) REVERT: LC 107 THR cc_start: 0.9179 (p) cc_final: 0.8760 (p) REVERT: LC 108 TRP cc_start: 0.8943 (p90) cc_final: 0.7941 (p-90) REVERT: LC 221 PHE cc_start: 0.9772 (m-10) cc_final: 0.9541 (m-10) REVERT: LC 250 CYS cc_start: 0.9564 (m) cc_final: 0.9043 (t) REVERT: LY 43 ASN cc_start: 0.8775 (t0) cc_final: 0.8477 (t0) REVERT: LX 144 TYR cc_start: 0.9423 (m-80) cc_final: 0.9146 (m-10) REVERT: LR 141 HIS cc_start: 0.9264 (m90) cc_final: 0.9062 (m-70) REVERT: Lr 8 MET cc_start: 0.9295 (mmp) cc_final: 0.9045 (mmm) REVERT: A 276 MET cc_start: 0.8677 (ttt) cc_final: 0.8426 (ttt) REVERT: A 343 TYR cc_start: 0.8083 (m-80) cc_final: 0.7729 (m-80) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1963 time to fit residues: 71.3005 Evaluate side-chains 167 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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: 20.0000 chunk 54 optimal weight: 7.9990 chunk 249 optimal weight: 0.0470 chunk 83 optimal weight: 2.9990 chunk 259 optimal weight: 20.0000 chunk 236 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 162 optimal weight: 0.0170 overall best weight: 0.9718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN LY 96 HIS ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.053649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.045094 restraints weight = 507565.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.045259 restraints weight = 471916.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.045650 restraints weight = 366719.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.045598 restraints weight = 302398.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.045765 restraints weight = 291360.528| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 30707 Z= 0.121 Angle : 0.583 11.646 43037 Z= 0.315 Chirality : 0.039 0.248 5036 Planarity : 0.005 0.128 4134 Dihedral : 22.496 169.616 8683 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.20 (0.16), residues: 2646 helix: 0.35 (0.14), residues: 1353 sheet: -0.71 (0.36), residues: 200 loop : -0.47 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGLY 126 TYR 0.029 0.002 TYR B 451 PHE 0.041 0.002 PHE B 683 TRP 0.059 0.002 TRP B 284 HIS 0.010 0.001 HIS 2 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (30707) covalent geometry : angle 0.58278 / 0.32 (43037) hydrogen bonds : bond 0.04753 / 3.15 ( 1316) hydrogen bonds : angle 4.87810 / 5.06 ( 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 225 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.993 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: 2 28 MET cc_start: 0.8024 (ppp) cc_final: 0.7491 (ppp) REVERT: 2 33 TYR cc_start: 0.9512 (m-80) cc_final: 0.9244 (m-80) REVERT: 2 91 MET cc_start: 0.9438 (mmp) cc_final: 0.8870 (tmm) REVERT: B 273 MET cc_start: 0.8526 (tmm) cc_final: 0.8254 (tmm) REVERT: B 482 MET cc_start: 0.7148 (mmm) cc_final: 0.6892 (mmm) REVERT: B 576 GLU cc_start: 0.7965 (tp30) cc_final: 0.7573 (mm-30) REVERT: LC 43 ASN cc_start: 0.9391 (m110) cc_final: 0.9134 (t0) REVERT: LC 107 THR cc_start: 0.9244 (p) cc_final: 0.8850 (p) REVERT: LC 108 TRP cc_start: 0.8954 (p90) cc_final: 0.7899 (p-90) REVERT: LC 221 PHE cc_start: 0.9782 (m-10) cc_final: 0.9552 (m-10) REVERT: LC 250 CYS cc_start: 0.9558 (m) cc_final: 0.9070 (t) REVERT: LY 43 ASN cc_start: 0.8820 (t0) cc_final: 0.8535 (t0) REVERT: LX 144 TYR cc_start: 0.9436 (m-80) cc_final: 0.9198 (m-10) REVERT: LR 141 HIS cc_start: 0.9306 (m90) cc_final: 0.9095 (m-70) REVERT: Lr 8 MET cc_start: 0.9226 (mmp) cc_final: 0.8971 (mmp) REVERT: A 276 MET cc_start: 0.8637 (ttt) cc_final: 0.8342 (ttt) REVERT: A 343 TYR cc_start: 0.7996 (m-80) cc_final: 0.7672 (m-80) REVERT: A 347 MET cc_start: 0.6949 (pmm) cc_final: 0.6633 (pmm) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1948 time to fit residues: 71.2563 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 : 0.992 ------------------------------------------------------------------------------- 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: 1.9990 chunk 102 optimal weight: 5.9990 chunk 125 optimal weight: 30.0000 chunk 197 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 186 optimal weight: 0.4980 chunk 185 optimal weight: 0.4980 chunk 153 optimal weight: 0.0370 chunk 164 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 142 GLN B 748 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 299 GLN ** Lh 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 36 ASN ** 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 = 0.3493 r_free = 0.3493 target = 0.053768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.045194 restraints weight = 511188.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.045335 restraints weight = 487433.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.045794 restraints weight = 367966.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.045730 restraints weight = 316979.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.045887 restraints weight = 289659.081| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 30707 Z= 0.118 Angle : 0.562 11.661 43037 Z= 0.304 Chirality : 0.037 0.253 5036 Planarity : 0.005 0.118 4134 Dihedral : 22.387 169.875 8683 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 0.04 % Allowed : 0.34 % 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: -0.13 (0.16), residues: 2646 helix: 0.39 (0.14), residues: 1354 sheet: -0.66 (0.36), residues: 200 loop : -0.43 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGLY 126 TYR 0.028 0.001 TYR B 451 PHE 0.040 0.002 PHE B 683 TRP 0.055 0.002 TRP B 284 HIS 0.010 0.001 HIS 2 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (30707) covalent geometry : angle 0.56153 / 0.30 (43037) hydrogen bonds : bond 0.04925 / 3.28 ( 1316) hydrogen bonds : angle 4.83470 / 5.04 ( 3489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5980.80 seconds wall clock time: 105 minutes 7.33 seconds (6307.33 seconds total)