Starting phenix.real_space_refine on Sat Mar 7 10:42:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9edr_47947/03_2026/9edr_47947_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9edr_47947/03_2026/9edr_47947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9edr_47947/03_2026/9edr_47947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9edr_47947/03_2026/9edr_47947.map" model { file = "/net/cci-nas-00/data/ceres_data/9edr_47947/03_2026/9edr_47947_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9edr_47947/03_2026/9edr_47947_trim.cif" } resolution = 3.8 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 96 5.16 5 C 13497 2.51 5 N 3733 2.21 5 O 4044 1.98 5 H 18811 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40189 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 16156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 16156 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 39, 'TRANS': 947} Chain breaks: 1 Chain: "G" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3133 Classifications: {'peptide': 191} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "A" Number of atoms: 6612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6612 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6602 Classifications: {'peptide': 427} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain: "C" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2194 Classifications: {'peptide': 253} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 453 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASN:plan1': 11, 'TYR:plan': 4, 'HIS:plan': 3, 'GLU:plan': 9, 'ASP:plan': 14, 'PHE:plan': 15, 'ARG:plan': 7, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 307 Chain: "I" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2391 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3009 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 4, 'TRANS': 403} Chain breaks: 5 Unresolved non-hydrogen bonds: 648 Unresolved non-hydrogen angles: 972 Unresolved non-hydrogen dihedrals: 324 Planarities with less than four sites: {'UNK:plan-1': 324} Unresolved non-hydrogen planarities: 324 Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.59, per 1000 atoms: 0.16 Number of scatterers: 40189 At special positions: 0 Unit cell: (131.12, 129.36, 207.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 8 15.00 O 4044 8.00 N 3733 7.00 C 13497 6.00 H 18811 1.00 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: 3.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5470 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 13 sheets defined 70.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'D' and resid 1 through 17 Processing helix chain 'D' and resid 19 through 32 removed outlier: 4.124A pdb=" N GLN D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLN D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 36 through 41 removed outlier: 3.887A pdb=" N LEU D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 54 Proline residue: D 49 - end of helix removed outlier: 4.232A pdb=" N SER D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 58 Processing helix chain 'D' and resid 59 through 84 removed outlier: 3.964A pdb=" N ILE D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.180A pdb=" N GLU D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 126 Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 134 through 144 removed outlier: 3.602A pdb=" N ARG D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 167 Processing helix chain 'D' and resid 170 through 174 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 181 through 194 removed outlier: 4.024A pdb=" N GLN D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.625A pdb=" N TYR D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 218 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 236 through 250 Processing helix chain 'D' and resid 255 through 277 removed outlier: 3.562A pdb=" N GLN D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 296 Processing helix chain 'D' and resid 297 through 298 No H-bonds generated for 'chain 'D' and resid 297 through 298' Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 304 through 321 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 353 through 370 Processing helix chain 'D' and resid 377 through 394 Processing helix chain 'D' and resid 397 through 415 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.746A pdb=" N ALA D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 458 through 474 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 482 through 493 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 504 through 515 removed outlier: 3.529A pdb=" N LEU D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 515 " --> pdb=" O VAL D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 535 Processing helix chain 'D' and resid 541 through 553 Processing helix chain 'D' and resid 570 through 587 Processing helix chain 'D' and resid 592 through 604 Processing helix chain 'D' and resid 611 through 626 Proline residue: D 617 - end of helix Processing helix chain 'D' and resid 630 through 640 Processing helix chain 'D' and resid 642 through 649 Processing helix chain 'D' and resid 650 through 652 No H-bonds generated for 'chain 'D' and resid 650 through 652' Processing helix chain 'D' and resid 654 through 666 Processing helix chain 'D' and resid 667 through 669 No H-bonds generated for 'chain 'D' and resid 667 through 669' Processing helix chain 'D' and resid 670 through 688 removed outlier: 3.800A pdb=" N HIS D 683 " --> pdb=" O GLY D 679 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP D 686 " --> pdb=" O ASP D 682 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL D 687 " --> pdb=" O HIS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 708 removed outlier: 3.556A pdb=" N LEU D 708 " --> pdb=" O ILE D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 734 removed outlier: 4.053A pdb=" N VAL D 723 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 741 removed outlier: 3.810A pdb=" N SER D 739 " --> pdb=" O PRO D 735 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 740 " --> pdb=" O ASP D 736 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP D 741 " --> pdb=" O PHE D 737 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 735 through 741' Processing helix chain 'D' and resid 741 through 755 removed outlier: 3.581A pdb=" N ILE D 745 " --> pdb=" O ASP D 741 " (cutoff:3.500A) Proline residue: D 747 - end of helix removed outlier: 3.554A pdb=" N ALA D 754 " --> pdb=" O THR D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 770 Processing helix chain 'D' and resid 779 through 791 Processing helix chain 'D' and resid 794 through 805 removed outlier: 3.561A pdb=" N LYS D 798 " --> pdb=" O GLU D 794 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D 799 " --> pdb=" O GLU D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 828 Processing helix chain 'D' and resid 829 through 843 Processing helix chain 'D' and resid 846 through 854 Processing helix chain 'D' and resid 855 through 860 removed outlier: 3.680A pdb=" N ASN D 859 " --> pdb=" O ILE D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 888 Processing helix chain 'D' and resid 898 through 911 removed outlier: 3.675A pdb=" N LEU D 911 " --> pdb=" O TYR D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 936 Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 941 through 965 removed outlier: 3.605A pdb=" N LEU D 945 " --> pdb=" O ASP D 941 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER D 946 " --> pdb=" O GLN D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 987 Processing helix chain 'D' and resid 988 through 994 Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.649A pdb=" N ILE G 6 " --> pdb=" O GLY G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 73 through 84 Proline residue: G 78 - end of helix removed outlier: 4.580A pdb=" N ASP G 81 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 101 through 116 Processing helix chain 'G' and resid 132 through 136 Processing helix chain 'G' and resid 138 through 157 Processing helix chain 'G' and resid 175 through 190 removed outlier: 3.888A pdb=" N THR G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.426A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 109 through 128 removed outlier: 4.777A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.235A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.765A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.592A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 5.988A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.076A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.886A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 4.186A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.110A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.494A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.617A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.503A pdb=" N SER B 176 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.654A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.157A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.198A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.509A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.569A pdb=" N LYS C 6 " --> pdb=" O ASP C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 37 Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 42 through 69 removed outlier: 4.466A pdb=" N GLU C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 226 removed outlier: 4.377A pdb=" N ASP C 226 " --> pdb=" O SER C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 268 Processing helix chain 'I' and resid 15 through 23 Processing helix chain 'I' and resid 27 through 42 Processing helix chain 'I' and resid 46 through 54 Processing helix chain 'I' and resid 58 through 73 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 77 through 85 Processing helix chain 'I' and resid 89 through 104 Processing helix chain 'I' and resid 105 through 107 No H-bonds generated for 'chain 'I' and resid 105 through 107' Processing helix chain 'I' and resid 108 through 116 Processing helix chain 'I' and resid 120 through 135 Processing helix chain 'I' and resid 137 through 149 Processing helix chain 'I' and resid 151 through 165 removed outlier: 3.605A pdb=" N ARG I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 140 through 151 Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.514A pdb=" N UNK E 173 " --> pdb=" O UNK E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.590A pdb=" N UNK E 225 " --> pdb=" O UNK E 221 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N UNK E 226 " --> pdb=" O UNK E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 247 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 312 through 322 removed outlier: 3.894A pdb=" N UNK E 316 " --> pdb=" O UNK E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 357 Processing helix chain 'E' and resid 371 through 385 Processing helix chain 'E' and resid 396 through 404 Processing helix chain 'E' and resid 435 through 437 No H-bonds generated for 'chain 'E' and resid 435 through 437' Processing helix chain 'E' and resid 449 through 461 Processing helix chain 'E' and resid 464 through 468 Processing helix chain 'E' and resid 488 through 493 Processing sheet with id=AA1, first strand: chain 'D' and resid 345 through 347 Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 60 removed outlier: 6.631A pdb=" N ILE G 17 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TRP G 68 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N CYS G 19 " --> pdb=" O TRP G 68 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE G 70 " --> pdb=" O CYS G 19 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE G 21 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA G 89 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL G 126 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL G 166 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL G 128 " --> pdb=" O VAL G 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.882A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.532A pdb=" N LEU A 318 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.079A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 12.921A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 369 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 104 removed outlier: 5.270A pdb=" N THR C 103 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA C 116 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE C 143 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU C 118 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN C 145 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU C 137 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER C 162 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N PHE C 164 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 141 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR C 166 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE C 143 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS C 168 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASN C 145 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N PHE C 183 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR C 160 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 10.588A pdb=" N ILE C 185 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N SER C 162 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU C 187 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N PHE C 164 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N ASP C 189 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR C 166 " --> pdb=" O ASP C 189 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LYS C 191 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS C 168 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE C 183 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ILE C 211 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 185 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLU C 213 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 187 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN C 208 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN C 231 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 210 " --> pdb=" O GLN C 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 110 removed outlier: 6.287A pdb=" N TYR C 108 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 125 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE C 197 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.864A pdb=" N UNK E 9 " --> pdb=" O UNK E 16 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N UNK E 16 " --> pdb=" O UNK E 9 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N UNK E 18 " --> pdb=" O UNK E 36 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N UNK E 36 " --> pdb=" O UNK E 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N UNK E 20 " --> pdb=" O UNK E 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB3, first strand: chain 'E' and resid 127 through 128 removed outlier: 6.738A pdb=" N UNK E 157 " --> pdb=" O UNK E 184 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N UNK E 234 " --> pdb=" O UNK E 208 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N UNK E 233 " --> pdb=" O UNK E 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 439 through 444 removed outlier: 8.609A pdb=" N ILE E 500 " --> pdb=" O LYS E 427 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS E 429 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL E 502 " --> pdb=" O LYS E 429 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG E 431 " --> pdb=" O VAL E 502 " (cutoff:3.500A) 1239 hydrogen bonds defined for protein. 3564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.92 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18763 1.03 - 1.24: 1326 1.24 - 1.44: 7907 1.44 - 1.64: 12426 1.64 - 1.84: 152 Bond restraints: 40574 Sorted by residual: bond pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sigma weight residual 1.610 1.844 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" O5' GTP G 501 " pdb=" PA GTP G 501 " ideal model delta sigma weight residual 1.610 1.836 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" O5' GDP B 501 " pdb=" PA GDP B 501 " ideal model delta sigma weight residual 1.610 1.738 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" O3A GDP B 501 " pdb=" PB GDP B 501 " ideal model delta sigma weight residual 1.610 1.725 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 40569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 72056 3.95 - 7.89: 217 7.89 - 11.84: 25 11.84 - 15.78: 16 15.78 - 19.73: 2 Bond angle restraints: 72316 Sorted by residual: angle pdb=" PA GDP B 501 " pdb=" O3A GDP B 501 " pdb=" PB GDP B 501 " ideal model delta sigma weight residual 120.50 140.23 -19.73 3.00e+00 1.11e-01 4.33e+01 angle pdb=" O2B GTP G 501 " pdb=" PB GTP G 501 " pdb=" O3A GTP G 501 " ideal model delta sigma weight residual 109.50 93.12 16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O2B GTP A 501 " pdb=" PB GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sigma weight residual 109.50 94.43 15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" O1B GDP B 501 " pdb=" PB GDP B 501 " pdb=" O3A GDP B 501 " ideal model delta sigma weight residual 109.50 95.12 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O1A GTP G 501 " pdb=" PA GTP G 501 " pdb=" O5' GTP G 501 " ideal model delta sigma weight residual 108.20 94.27 13.93 3.00e+00 1.11e-01 2.16e+01 ... (remaining 72311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 18783 35.32 - 70.64: 532 70.64 - 105.96: 47 105.96 - 141.28: 3 141.28 - 176.60: 6 Dihedral angle restraints: 19371 sinusoidal: 9763 harmonic: 9608 Sorted by residual: dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual -68.92 107.68 -176.60 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -123.95 -166.78 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP G 501 " pdb=" C1' GTP G 501 " pdb=" N9 GTP G 501 " pdb=" O4' GTP G 501 " ideal model delta sinusoidal sigma weight residual 104.59 -61.87 166.46 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 19368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3175 0.081 - 0.162: 242 0.162 - 0.243: 7 0.243 - 0.324: 3 0.324 - 0.405: 4 Chirality restraints: 3431 Sorted by residual: chirality pdb=" CG LEU B 263 " pdb=" CB LEU B 263 " pdb=" CD1 LEU B 263 " pdb=" CD2 LEU B 263 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C2' GDP B 501 " pdb=" C3' GDP B 501 " pdb=" O2' GDP B 501 " pdb=" C1' GDP B 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.87 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C3' GTP G 501 " pdb=" C2' GTP G 501 " pdb=" C4' GTP G 501 " pdb=" O3' GTP G 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.83 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 3428 not shown) Planarity restraints: 6089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 399 " 0.012 2.00e-02 2.50e+03 1.37e-02 5.65e+00 pdb=" CG TYR A 399 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 399 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 399 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 399 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 399 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 399 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 399 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR A 399 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR A 399 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 399 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 399 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 107 " -0.179 9.50e-02 1.11e+02 6.00e-02 4.13e+00 pdb=" NE ARG I 107 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG I 107 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG I 107 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 107 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG I 107 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG I 107 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG I 107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG I 107 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 721 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ARG D 721 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG D 721 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 722 " 0.012 2.00e-02 2.50e+03 ... (remaining 6086 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1597 2.17 - 2.78: 75827 2.78 - 3.38: 114340 3.38 - 3.99: 142711 3.99 - 4.60: 224415 Nonbonded interactions: 558890 Sorted by model distance: nonbonded pdb=" O ARG I 107 " pdb="HH11 ARG I 107 " model vdw 1.560 2.450 nonbonded pdb=" O GLU B 3 " pdb=" H GLN B 131 " model vdw 1.590 2.450 nonbonded pdb=" OE1 GLU I 48 " pdb=" H GLU I 48 " model vdw 1.599 2.450 nonbonded pdb=" O LEU B 263 " pdb="HD22 ASN B 370 " model vdw 1.600 2.450 nonbonded pdb=" O TYR D 582 " pdb=" HG1 THR D 586 " model vdw 1.631 2.450 ... (remaining 558885 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 37.660 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 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 0.234 21763 Z= 0.261 Angle : 0.921 19.730 29572 Z= 0.448 Chirality : 0.046 0.405 3431 Planarity : 0.005 0.078 3837 Dihedral : 15.213 176.602 7679 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 0.19 % Allowed : 12.29 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.09 (0.17), residues: 2506 helix: 1.27 (0.14), residues: 1423 sheet: 0.08 (0.30), residues: 276 loop : 0.17 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 698 TYR 0.039 0.002 TYR A 399 PHE 0.026 0.002 PHE D 362 TRP 0.012 0.002 TRP D 465 HIS 0.011 0.001 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00550 (21763) covalent geometry : angle 0.92097 (29572) hydrogen bonds : bond 0.10087 ( 1239) hydrogen bonds : angle 5.37402 ( 3564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 487 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 283 GLU cc_start: 0.7945 (tt0) cc_final: 0.7727 (tp30) REVERT: D 339 LYS cc_start: 0.8647 (tppt) cc_final: 0.8340 (ttmt) REVERT: D 698 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8395 (tpp80) REVERT: G 22 LEU cc_start: 0.6947 (tp) cc_final: 0.6518 (tp) REVERT: A 76 ASP cc_start: 0.7156 (t0) cc_final: 0.6915 (t70) REVERT: A 120 ASP cc_start: 0.7674 (m-30) cc_final: 0.7262 (m-30) REVERT: A 163 LYS cc_start: 0.8547 (pttm) cc_final: 0.8320 (ttpp) REVERT: B 2 ARG cc_start: 0.7041 (mtm180) cc_final: 0.6767 (mtm180) REVERT: B 73 MET cc_start: 0.8580 (mmm) cc_final: 0.8224 (mmm) REVERT: B 114 ASP cc_start: 0.6583 (m-30) cc_final: 0.6304 (t0) REVERT: B 129 CYS cc_start: 0.6992 (t) cc_final: 0.6670 (p) REVERT: C 46 LYS cc_start: 0.7670 (mttp) cc_final: 0.7468 (mttp) REVERT: I 21 LYS cc_start: 0.8645 (mmmm) cc_final: 0.8244 (mmmm) REVERT: I 143 MET cc_start: 0.5615 (mtt) cc_final: 0.5398 (mtm) outliers start: 4 outliers final: 3 residues processed: 487 average time/residue: 0.3855 time to fit residues: 278.4063 Evaluate side-chains 474 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 471 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 263 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN D 72 ASN D 306 ASN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 620 GLN ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 416 ASN ** B 423 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 = 0.4482 r_free = 0.4482 target = 0.173139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.147241 restraints weight = 120281.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.153353 restraints weight = 49388.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.157017 restraints weight = 25149.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.159215 restraints weight = 14897.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.160677 restraints weight = 10067.776| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21763 Z= 0.167 Angle : 0.560 6.445 29572 Z= 0.294 Chirality : 0.038 0.180 3431 Planarity : 0.004 0.049 3837 Dihedral : 9.487 174.353 3072 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.24 % Allowed : 11.39 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.18 (0.17), residues: 2506 helix: 1.47 (0.14), residues: 1418 sheet: -0.14 (0.31), residues: 272 loop : 0.05 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 262 TYR 0.028 0.002 TYR C 44 PHE 0.019 0.002 PHE A 138 TRP 0.009 0.001 TRP D 597 HIS 0.005 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00359 (21763) covalent geometry : angle 0.55978 (29572) hydrogen bonds : bond 0.04226 ( 1239) hydrogen bonds : angle 4.80266 ( 3564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 512 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 486 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 LYS cc_start: 0.8445 (tttt) cc_final: 0.8120 (tptt) REVERT: D 122 SER cc_start: 0.6209 (OUTLIER) cc_final: 0.5976 (p) REVERT: D 391 ASN cc_start: 0.7784 (t0) cc_final: 0.7531 (t0) REVERT: D 568 ASP cc_start: 0.7449 (m-30) cc_final: 0.7171 (m-30) REVERT: D 614 GLU cc_start: 0.7441 (mp0) cc_final: 0.7161 (mp0) REVERT: D 656 GLU cc_start: 0.8329 (mp0) cc_final: 0.8118 (mp0) REVERT: D 759 GLU cc_start: 0.8715 (tp30) cc_final: 0.8237 (tp30) REVERT: G 22 LEU cc_start: 0.6906 (tp) cc_final: 0.6358 (tp) REVERT: A 76 ASP cc_start: 0.7166 (t0) cc_final: 0.6939 (t70) REVERT: A 120 ASP cc_start: 0.7670 (m-30) cc_final: 0.7253 (m-30) REVERT: A 319 TYR cc_start: 0.6787 (m-10) cc_final: 0.6554 (m-10) REVERT: B 36 TYR cc_start: 0.7630 (t80) cc_final: 0.7294 (t80) REVERT: B 73 MET cc_start: 0.8565 (mmm) cc_final: 0.8220 (mmm) REVERT: B 114 ASP cc_start: 0.6644 (m-30) cc_final: 0.6358 (m-30) REVERT: B 129 CYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6617 (p) REVERT: B 147 MET cc_start: 0.6121 (ttm) cc_final: 0.5734 (tpp) REVERT: B 161 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6999 (m-30) REVERT: B 355 ASP cc_start: 0.7436 (m-30) cc_final: 0.7231 (m-30) REVERT: B 363 MET cc_start: 0.7019 (ttm) cc_final: 0.6633 (ttm) REVERT: C 43 SER cc_start: 0.8608 (m) cc_final: 0.7966 (p) outliers start: 26 outliers final: 17 residues processed: 491 average time/residue: 0.3737 time to fit residues: 273.2043 Evaluate side-chains 493 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 473 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 46 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 HIS ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 GLN D 734 HIS ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN B 43 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.167584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.140889 restraints weight = 119562.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.146742 restraints weight = 50984.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.150335 restraints weight = 26986.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.152564 restraints weight = 16547.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.153948 restraints weight = 11408.895| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21763 Z= 0.227 Angle : 0.618 10.639 29572 Z= 0.329 Chirality : 0.041 0.182 3431 Planarity : 0.005 0.061 3837 Dihedral : 9.353 176.665 3067 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 2.33 % Allowed : 12.34 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.56 (0.17), residues: 2506 helix: 1.11 (0.13), residues: 1416 sheet: -0.61 (0.31), residues: 255 loop : -0.44 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 45 TYR 0.031 0.002 TYR C 44 PHE 0.023 0.002 PHE A 138 TRP 0.010 0.002 TRP D 597 HIS 0.011 0.002 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00488 (21763) covalent geometry : angle 0.61817 (29572) hydrogen bonds : bond 0.04521 ( 1239) hydrogen bonds : angle 4.98255 ( 3564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 542 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 493 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 LYS cc_start: 0.8608 (tttt) cc_final: 0.8306 (tmtt) REVERT: D 391 ASN cc_start: 0.7596 (t0) cc_final: 0.7300 (t0) REVERT: D 423 GLN cc_start: 0.8095 (tp40) cc_final: 0.7225 (tp40) REVERT: D 445 SER cc_start: 0.7398 (m) cc_final: 0.7170 (t) REVERT: D 731 MET cc_start: 0.8209 (mtp) cc_final: 0.7870 (mmm) REVERT: D 762 LYS cc_start: 0.8529 (tppt) cc_final: 0.8238 (tppt) REVERT: A 76 ASP cc_start: 0.7257 (t0) cc_final: 0.7033 (t70) REVERT: A 112 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8152 (ttmm) REVERT: A 120 ASP cc_start: 0.7671 (m-30) cc_final: 0.7252 (m-30) REVERT: A 319 TYR cc_start: 0.7059 (m-10) cc_final: 0.6780 (m-10) REVERT: A 429 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6773 (tp30) REVERT: B 45 GLU cc_start: 0.7685 (tt0) cc_final: 0.7453 (tt0) REVERT: B 73 MET cc_start: 0.8523 (mmm) cc_final: 0.8006 (mmm) REVERT: B 123 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7009 (mm-30) REVERT: B 129 CYS cc_start: 0.7105 (t) cc_final: 0.6847 (p) REVERT: B 131 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.6034 (mt0) REVERT: B 147 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6191 (tpt) REVERT: B 211 CYS cc_start: 0.7953 (m) cc_final: 0.7659 (p) REVERT: B 213 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7524 (mtt180) REVERT: B 355 ASP cc_start: 0.7599 (m-30) cc_final: 0.7335 (m-30) REVERT: B 363 MET cc_start: 0.6891 (ttm) cc_final: 0.6371 (ttm) REVERT: C 46 LYS cc_start: 0.7796 (mttp) cc_final: 0.7578 (mttp) REVERT: I 18 MET cc_start: 0.6894 (tmm) cc_final: 0.6653 (tmm) REVERT: I 48 GLU cc_start: 0.8034 (mp0) cc_final: 0.7831 (mp0) outliers start: 49 outliers final: 41 residues processed: 507 average time/residue: 0.3827 time to fit residues: 288.9653 Evaluate side-chains 521 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 478 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain E residue 463 PHE Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 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 = 0.4392 r_free = 0.4392 target = 0.166076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.139654 restraints weight = 120053.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.145474 restraints weight = 50797.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.149001 restraints weight = 26729.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.151204 restraints weight = 16369.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.152624 restraints weight = 11247.885| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21763 Z= 0.243 Angle : 0.609 8.184 29572 Z= 0.326 Chirality : 0.040 0.162 3431 Planarity : 0.004 0.064 3837 Dihedral : 9.235 169.429 3067 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 2.29 % Allowed : 14.67 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.17), residues: 2506 helix: 0.98 (0.13), residues: 1420 sheet: -0.94 (0.31), residues: 250 loop : -0.63 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 369 TYR 0.030 0.002 TYR C 44 PHE 0.023 0.002 PHE D 362 TRP 0.012 0.002 TRP A 346 HIS 0.009 0.002 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00521 (21763) covalent geometry : angle 0.60929 (29572) hydrogen bonds : bond 0.04492 ( 1239) hydrogen bonds : angle 5.05626 ( 3564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 530 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 482 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 GLN cc_start: 0.8516 (mt0) cc_final: 0.8240 (mt0) REVERT: D 53 LYS cc_start: 0.8656 (tttt) cc_final: 0.8345 (tmtt) REVERT: D 391 ASN cc_start: 0.7656 (t0) cc_final: 0.7318 (t0) REVERT: D 408 LEU cc_start: 0.6976 (tt) cc_final: 0.6764 (tt) REVERT: D 445 SER cc_start: 0.7438 (m) cc_final: 0.7230 (t) REVERT: D 621 GLN cc_start: 0.7735 (tp40) cc_final: 0.7340 (tp-100) REVERT: D 656 GLU cc_start: 0.8493 (mp0) cc_final: 0.8194 (pm20) REVERT: D 762 LYS cc_start: 0.8568 (tppt) cc_final: 0.8240 (tppt) REVERT: A 76 ASP cc_start: 0.7246 (t0) cc_final: 0.7022 (t70) REVERT: A 319 TYR cc_start: 0.7071 (m-10) cc_final: 0.6813 (m-10) REVERT: B 111 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6644 (mm-30) REVERT: B 123 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7125 (mm-30) REVERT: B 129 CYS cc_start: 0.7089 (t) cc_final: 0.6850 (p) REVERT: B 147 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6224 (tpt) REVERT: B 162 ARG cc_start: 0.7814 (mmp80) cc_final: 0.7572 (mmp80) REVERT: B 213 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7516 (mtt180) REVERT: B 355 ASP cc_start: 0.7649 (m-30) cc_final: 0.7413 (m-30) REVERT: C 43 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.7941 (p) REVERT: C 46 LYS cc_start: 0.7895 (mttp) cc_final: 0.7641 (mttp) REVERT: I 18 MET cc_start: 0.6878 (tmm) cc_final: 0.6639 (tmm) outliers start: 48 outliers final: 41 residues processed: 501 average time/residue: 0.3736 time to fit residues: 278.7103 Evaluate side-chains 510 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 466 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 905 LYS Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain E residue 463 PHE Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 188 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 228 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 788 HIS ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 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 = 0.4420 r_free = 0.4420 target = 0.168191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.141609 restraints weight = 119337.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.147532 restraints weight = 50057.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.151149 restraints weight = 26145.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.153352 restraints weight = 15809.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.154802 restraints weight = 10825.703| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21763 Z= 0.155 Angle : 0.550 7.930 29572 Z= 0.288 Chirality : 0.038 0.154 3431 Planarity : 0.004 0.063 3837 Dihedral : 8.978 167.364 3067 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 2.24 % Allowed : 15.39 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.62 (0.17), residues: 2506 helix: 1.25 (0.14), residues: 1427 sheet: -0.97 (0.31), residues: 253 loop : -0.49 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 372 TYR 0.024 0.002 TYR C 44 PHE 0.015 0.002 PHE D 362 TRP 0.010 0.001 TRP D 597 HIS 0.006 0.001 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00338 (21763) covalent geometry : angle 0.55002 (29572) hydrogen bonds : bond 0.03991 ( 1239) hydrogen bonds : angle 4.73451 ( 3564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 524 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 477 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 GLN cc_start: 0.8564 (tt0) cc_final: 0.8286 (tt0) REVERT: D 34 GLN cc_start: 0.8533 (mt0) cc_final: 0.8254 (mt0) REVERT: D 53 LYS cc_start: 0.8559 (tttt) cc_final: 0.8266 (tmtt) REVERT: D 219 ASP cc_start: 0.5678 (OUTLIER) cc_final: 0.5424 (t0) REVERT: D 391 ASN cc_start: 0.7741 (t0) cc_final: 0.7402 (t0) REVERT: D 445 SER cc_start: 0.7455 (m) cc_final: 0.7253 (t) REVERT: D 621 GLN cc_start: 0.7852 (tp40) cc_final: 0.7535 (tp-100) REVERT: D 656 GLU cc_start: 0.8446 (mp0) cc_final: 0.7940 (pm20) REVERT: D 730 LEU cc_start: 0.8895 (tp) cc_final: 0.8676 (tp) REVERT: D 731 MET cc_start: 0.8123 (mtp) cc_final: 0.7683 (mmm) REVERT: D 762 LYS cc_start: 0.8559 (tppt) cc_final: 0.8221 (tppt) REVERT: A 76 ASP cc_start: 0.7125 (t0) cc_final: 0.6901 (t70) REVERT: A 205 ASP cc_start: 0.7334 (t0) cc_final: 0.7035 (t70) REVERT: A 319 TYR cc_start: 0.7042 (m-10) cc_final: 0.6829 (m-10) REVERT: B 111 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6437 (mm-30) REVERT: B 129 CYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6819 (p) REVERT: B 147 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6229 (tpt) REVERT: B 161 ASP cc_start: 0.7360 (m-30) cc_final: 0.6968 (m-30) REVERT: B 211 CYS cc_start: 0.7863 (m) cc_final: 0.7654 (p) REVERT: B 213 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7443 (mtt180) REVERT: B 424 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8127 (tm-30) REVERT: C 43 SER cc_start: 0.8505 (m) cc_final: 0.7917 (p) outliers start: 47 outliers final: 33 residues processed: 495 average time/residue: 0.3585 time to fit residues: 265.7879 Evaluate side-chains 510 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 473 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain E residue 463 PHE Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 172 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 213 optimal weight: 0.0670 chunk 82 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 ASN B 165 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 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 = 0.4444 r_free = 0.4444 target = 0.169944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.143904 restraints weight = 118118.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.149630 restraints weight = 50248.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.153120 restraints weight = 26460.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.155269 restraints weight = 16070.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.156625 restraints weight = 11039.206| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21763 Z= 0.134 Angle : 0.530 7.817 29572 Z= 0.276 Chirality : 0.038 0.150 3431 Planarity : 0.004 0.048 3837 Dihedral : 8.738 163.277 3067 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.05 % Allowed : 15.91 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.85 (0.17), residues: 2506 helix: 1.44 (0.14), residues: 1435 sheet: -0.84 (0.31), residues: 259 loop : -0.41 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 162 TYR 0.021 0.001 TYR C 44 PHE 0.013 0.001 PHE D 192 TRP 0.013 0.001 TRP D 597 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00295 (21763) covalent geometry : angle 0.53007 (29572) hydrogen bonds : bond 0.03784 ( 1239) hydrogen bonds : angle 4.58946 ( 3564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 522 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 479 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 GLN cc_start: 0.8658 (tt0) cc_final: 0.8383 (tt0) REVERT: D 53 LYS cc_start: 0.8535 (tttt) cc_final: 0.8209 (tmtt) REVERT: D 391 ASN cc_start: 0.7701 (t0) cc_final: 0.7287 (t0) REVERT: D 445 SER cc_start: 0.7450 (m) cc_final: 0.7246 (t) REVERT: D 621 GLN cc_start: 0.7842 (tp40) cc_final: 0.7320 (tp-100) REVERT: D 656 GLU cc_start: 0.8525 (mp0) cc_final: 0.7983 (pm20) REVERT: D 730 LEU cc_start: 0.8855 (tp) cc_final: 0.8650 (tp) REVERT: D 731 MET cc_start: 0.8170 (mtp) cc_final: 0.7746 (mmt) REVERT: D 762 LYS cc_start: 0.8465 (tppt) cc_final: 0.8111 (tppt) REVERT: A 76 ASP cc_start: 0.7181 (t0) cc_final: 0.6940 (t70) REVERT: A 123 ARG cc_start: 0.7514 (ttm170) cc_final: 0.7251 (ttm-80) REVERT: A 262 TYR cc_start: 0.7025 (m-10) cc_final: 0.6810 (m-10) REVERT: A 319 TYR cc_start: 0.7048 (m-10) cc_final: 0.6764 (m-10) REVERT: B 111 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6394 (mm-30) REVERT: B 129 CYS cc_start: 0.7165 (t) cc_final: 0.6834 (p) REVERT: B 147 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.5826 (tpt) REVERT: B 211 CYS cc_start: 0.7931 (m) cc_final: 0.7694 (p) REVERT: B 213 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7481 (mtt180) REVERT: B 363 MET cc_start: 0.6932 (ttm) cc_final: 0.6388 (ttm) REVERT: B 366 THR cc_start: 0.8061 (m) cc_final: 0.7522 (p) REVERT: B 424 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8215 (tm-30) REVERT: C 43 SER cc_start: 0.8520 (m) cc_final: 0.7981 (p) outliers start: 43 outliers final: 37 residues processed: 495 average time/residue: 0.3599 time to fit residues: 266.4687 Evaluate side-chains 506 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 467 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 907 TYR Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain E residue 463 PHE Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 GLN ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.165852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.139300 restraints weight = 120075.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.144959 restraints weight = 52289.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.148394 restraints weight = 27953.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.150532 restraints weight = 17296.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.151918 restraints weight = 12017.584| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21763 Z= 0.257 Angle : 0.632 8.852 29572 Z= 0.339 Chirality : 0.041 0.158 3431 Planarity : 0.004 0.053 3837 Dihedral : 8.879 162.099 3067 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.10 % Allowed : 16.20 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.17), residues: 2506 helix: 1.04 (0.13), residues: 1416 sheet: -1.24 (0.31), residues: 258 loop : -0.85 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 372 TYR 0.029 0.002 TYR C 44 PHE 0.026 0.002 PHE B 20 TRP 0.017 0.002 TRP D 597 HIS 0.009 0.002 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00554 (21763) covalent geometry : angle 0.63250 (29572) hydrogen bonds : bond 0.04514 ( 1239) hydrogen bonds : angle 5.03260 ( 3564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 544 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 479 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 LYS cc_start: 0.8598 (tttt) cc_final: 0.8355 (tmtt) REVERT: D 120 TRP cc_start: 0.5570 (OUTLIER) cc_final: 0.5106 (t60) REVERT: D 391 ASN cc_start: 0.7497 (t0) cc_final: 0.7095 (t0) REVERT: D 424 ASN cc_start: 0.9222 (p0) cc_final: 0.8955 (p0) REVERT: D 445 SER cc_start: 0.7554 (m) cc_final: 0.7327 (t) REVERT: D 621 GLN cc_start: 0.7958 (tp40) cc_final: 0.7479 (tp-100) REVERT: D 762 LYS cc_start: 0.8511 (tppt) cc_final: 0.8161 (tppt) REVERT: G 92 TRP cc_start: 0.8272 (t-100) cc_final: 0.6102 (t-100) REVERT: A 76 ASP cc_start: 0.7203 (t0) cc_final: 0.6974 (t70) REVERT: A 102 ASN cc_start: 0.7756 (t0) cc_final: 0.7398 (t0) REVERT: A 319 TYR cc_start: 0.7315 (m-10) cc_final: 0.6854 (m-10) REVERT: A 429 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6579 (tp30) REVERT: B 111 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6624 (mm-30) REVERT: B 129 CYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6814 (p) REVERT: B 131 GLN cc_start: 0.6284 (OUTLIER) cc_final: 0.6025 (mt0) REVERT: B 147 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6368 (tpt) REVERT: B 203 ASP cc_start: 0.7096 (t0) cc_final: 0.6781 (t0) REVERT: B 355 ASP cc_start: 0.7486 (m-30) cc_final: 0.7124 (t0) REVERT: B 363 MET cc_start: 0.6838 (ttm) cc_final: 0.6538 (ttm) REVERT: B 366 THR cc_start: 0.8175 (m) cc_final: 0.7663 (p) REVERT: C 43 SER cc_start: 0.8655 (m) cc_final: 0.8255 (p) REVERT: C 52 ASP cc_start: 0.8174 (m-30) cc_final: 0.7675 (m-30) outliers start: 65 outliers final: 56 residues processed: 506 average time/residue: 0.3601 time to fit residues: 271.9606 Evaluate side-chains 528 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 467 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 593 GLN Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 907 TYR Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain E residue 463 PHE Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 HIS ** 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 = 0.4436 r_free = 0.4436 target = 0.168955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.142345 restraints weight = 119077.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.148091 restraints weight = 51145.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.151556 restraints weight = 27093.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.153677 restraints weight = 16667.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.155118 restraints weight = 11555.673| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21763 Z= 0.150 Angle : 0.564 8.052 29572 Z= 0.296 Chirality : 0.039 0.153 3431 Planarity : 0.004 0.050 3837 Dihedral : 8.581 155.048 3067 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.33 % Allowed : 17.82 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2506 helix: 1.27 (0.14), residues: 1435 sheet: -1.14 (0.31), residues: 260 loop : -0.64 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 162 TYR 0.021 0.002 TYR D 765 PHE 0.014 0.001 PHE D 615 TRP 0.016 0.001 TRP D 597 HIS 0.007 0.001 HIS D 808 Details of bonding type rmsd covalent geometry : bond 0.00329 (21763) covalent geometry : angle 0.56399 (29572) hydrogen bonds : bond 0.03957 ( 1239) hydrogen bonds : angle 4.70677 ( 3564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 532 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 483 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 LYS cc_start: 0.8639 (mttt) cc_final: 0.8245 (tppt) REVERT: D 53 LYS cc_start: 0.8512 (tttt) cc_final: 0.8232 (tmtt) REVERT: D 391 ASN cc_start: 0.7474 (t0) cc_final: 0.7233 (t0) REVERT: D 424 ASN cc_start: 0.9203 (p0) cc_final: 0.8936 (p0) REVERT: D 445 SER cc_start: 0.7537 (m) cc_final: 0.7317 (t) REVERT: D 621 GLN cc_start: 0.7903 (tp40) cc_final: 0.7420 (tp-100) REVERT: D 656 GLU cc_start: 0.8461 (mp0) cc_final: 0.8072 (pm20) REVERT: D 731 MET cc_start: 0.8136 (mtp) cc_final: 0.7665 (mmt) REVERT: D 762 LYS cc_start: 0.8486 (tppt) cc_final: 0.8125 (tppt) REVERT: A 76 ASP cc_start: 0.7136 (t0) cc_final: 0.6870 (t70) REVERT: A 123 ARG cc_start: 0.7467 (ttm170) cc_final: 0.7194 (ttm-80) REVERT: A 319 TYR cc_start: 0.7226 (m-10) cc_final: 0.6946 (m-10) REVERT: B 111 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6443 (mm-30) REVERT: B 129 CYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6813 (p) REVERT: B 131 GLN cc_start: 0.6145 (tt0) cc_final: 0.5927 (mt0) REVERT: B 147 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6300 (tpt) REVERT: B 161 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6951 (m-30) REVERT: B 195 ASN cc_start: 0.7694 (t0) cc_final: 0.7008 (t0) REVERT: B 233 MET cc_start: 0.4373 (mtt) cc_final: 0.4001 (mtt) REVERT: B 363 MET cc_start: 0.6828 (ttm) cc_final: 0.6467 (ttm) REVERT: B 366 THR cc_start: 0.8117 (m) cc_final: 0.7610 (p) REVERT: C 43 SER cc_start: 0.8627 (m) cc_final: 0.7873 (p) REVERT: C 52 ASP cc_start: 0.8122 (m-30) cc_final: 0.7637 (m-30) outliers start: 49 outliers final: 39 residues processed: 504 average time/residue: 0.3502 time to fit residues: 264.5698 Evaluate side-chains 516 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 473 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 907 TYR Chi-restraints excluded: chain D residue 934 HIS Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain E residue 463 PHE Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 179 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 228 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.166446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.140066 restraints weight = 119185.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.145648 restraints weight = 51505.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.149094 restraints weight = 27605.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.151259 restraints weight = 17055.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.152563 restraints weight = 11770.095| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21763 Z= 0.221 Angle : 0.617 8.533 29572 Z= 0.328 Chirality : 0.040 0.153 3431 Planarity : 0.004 0.053 3837 Dihedral : 8.491 146.161 3067 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.57 % Allowed : 17.96 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.26 (0.17), residues: 2506 helix: 1.11 (0.14), residues: 1421 sheet: -1.24 (0.31), residues: 257 loop : -0.90 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 372 TYR 0.026 0.002 TYR C 44 PHE 0.022 0.002 PHE B 20 TRP 0.019 0.002 TRP D 597 HIS 0.007 0.002 HIS D 78 Details of bonding type rmsd covalent geometry : bond 0.00479 (21763) covalent geometry : angle 0.61730 (29572) hydrogen bonds : bond 0.04318 ( 1239) hydrogen bonds : angle 4.96024 ( 3564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 535 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 481 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 LYS cc_start: 0.8741 (mttt) cc_final: 0.8315 (tppt) REVERT: D 53 LYS cc_start: 0.8620 (tttt) cc_final: 0.8311 (tmtt) REVERT: D 391 ASN cc_start: 0.7501 (t0) cc_final: 0.7228 (t0) REVERT: D 424 ASN cc_start: 0.9243 (p0) cc_final: 0.8976 (p0) REVERT: D 445 SER cc_start: 0.7567 (m) cc_final: 0.7325 (t) REVERT: D 594 GLU cc_start: 0.8495 (tp30) cc_final: 0.8286 (tp30) REVERT: D 621 GLN cc_start: 0.7947 (tp40) cc_final: 0.7473 (tp-100) REVERT: D 656 GLU cc_start: 0.8530 (mp0) cc_final: 0.8125 (pm20) REVERT: D 762 LYS cc_start: 0.8456 (tppt) cc_final: 0.8090 (tppt) REVERT: G 92 TRP cc_start: 0.8264 (t-100) cc_final: 0.6038 (t-100) REVERT: A 76 ASP cc_start: 0.7252 (t0) cc_final: 0.7000 (t70) REVERT: A 102 ASN cc_start: 0.7645 (t0) cc_final: 0.7327 (t0) REVERT: A 123 ARG cc_start: 0.7507 (ttm170) cc_final: 0.7228 (ttm-80) REVERT: A 262 TYR cc_start: 0.7096 (m-10) cc_final: 0.6890 (m-10) REVERT: A 319 TYR cc_start: 0.7372 (m-10) cc_final: 0.6932 (m-10) REVERT: B 111 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6585 (mm-30) REVERT: B 123 GLU cc_start: 0.7489 (tp30) cc_final: 0.7198 (tp30) REVERT: B 129 CYS cc_start: 0.7078 (t) cc_final: 0.6807 (p) REVERT: B 131 GLN cc_start: 0.6151 (OUTLIER) cc_final: 0.5935 (mt0) REVERT: B 147 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6318 (tpt) REVERT: B 161 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: B 213 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7426 (mtt180) REVERT: B 355 ASP cc_start: 0.7561 (m-30) cc_final: 0.7199 (t0) REVERT: B 366 THR cc_start: 0.8149 (m) cc_final: 0.7622 (p) REVERT: C 43 SER cc_start: 0.8718 (m) cc_final: 0.7957 (p) REVERT: C 46 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7556 (mttp) REVERT: C 52 ASP cc_start: 0.8182 (m-30) cc_final: 0.7696 (m-30) outliers start: 54 outliers final: 44 residues processed: 506 average time/residue: 0.3493 time to fit residues: 264.1038 Evaluate side-chains 525 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 476 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 907 TYR Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain E residue 463 PHE Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.167510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.141163 restraints weight = 118797.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.146824 restraints weight = 50772.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.150276 restraints weight = 26931.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.152357 restraints weight = 16536.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.153746 restraints weight = 11447.317| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21763 Z= 0.174 Angle : 0.588 8.209 29572 Z= 0.309 Chirality : 0.039 0.152 3431 Planarity : 0.004 0.052 3837 Dihedral : 8.184 138.601 3067 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.29 % Allowed : 18.68 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.39 (0.17), residues: 2506 helix: 1.23 (0.14), residues: 1422 sheet: -1.14 (0.31), residues: 258 loop : -0.87 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 372 TYR 0.021 0.002 TYR C 44 PHE 0.014 0.002 PHE B 20 TRP 0.016 0.001 TRP D 597 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00381 (21763) covalent geometry : angle 0.58849 (29572) hydrogen bonds : bond 0.04076 ( 1239) hydrogen bonds : angle 4.81352 ( 3564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Evaluate side-chains 529 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 481 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 LYS cc_start: 0.8698 (mttt) cc_final: 0.8288 (tppt) REVERT: D 53 LYS cc_start: 0.8516 (tttt) cc_final: 0.8248 (tmtt) REVERT: D 391 ASN cc_start: 0.7491 (t0) cc_final: 0.7196 (t0) REVERT: D 424 ASN cc_start: 0.9193 (p0) cc_final: 0.8924 (p0) REVERT: D 445 SER cc_start: 0.7607 (m) cc_final: 0.7347 (t) REVERT: D 621 GLN cc_start: 0.7945 (tp40) cc_final: 0.7472 (tp-100) REVERT: D 656 GLU cc_start: 0.8502 (mp0) cc_final: 0.8111 (pm20) REVERT: D 762 LYS cc_start: 0.8428 (tppt) cc_final: 0.8062 (tppt) REVERT: G 92 TRP cc_start: 0.8229 (t-100) cc_final: 0.5933 (t-100) REVERT: A 76 ASP cc_start: 0.7164 (t0) cc_final: 0.6908 (t70) REVERT: A 102 ASN cc_start: 0.7613 (t0) cc_final: 0.7319 (t0) REVERT: A 123 ARG cc_start: 0.7469 (ttm170) cc_final: 0.7193 (ttm-80) REVERT: A 210 TYR cc_start: 0.7614 (t80) cc_final: 0.7020 (t80) REVERT: A 319 TYR cc_start: 0.7269 (m-10) cc_final: 0.6923 (m-10) REVERT: B 111 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6398 (mm-30) REVERT: B 129 CYS cc_start: 0.6996 (t) cc_final: 0.6780 (p) REVERT: B 131 GLN cc_start: 0.6097 (OUTLIER) cc_final: 0.5877 (mt0) REVERT: B 147 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6347 (tpt) REVERT: B 161 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: B 213 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7359 (mtt180) REVERT: B 355 ASP cc_start: 0.7518 (m-30) cc_final: 0.7187 (t0) REVERT: B 366 THR cc_start: 0.8167 (m) cc_final: 0.7618 (p) REVERT: C 43 SER cc_start: 0.8673 (m) cc_final: 0.7890 (p) REVERT: C 46 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7542 (mttp) REVERT: C 52 ASP cc_start: 0.8150 (m-30) cc_final: 0.7773 (m-30) REVERT: I 18 MET cc_start: 0.6620 (tmm) cc_final: 0.6360 (tmm) outliers start: 48 outliers final: 40 residues processed: 501 average time/residue: 0.3659 time to fit residues: 273.3078 Evaluate side-chains 523 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 478 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 342 HIS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 907 TYR Chi-restraints excluded: chain D residue 950 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 150 GLU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain E residue 463 PHE Chi-restraints excluded: chain E residue 464 ASP Chi-restraints excluded: chain E residue 503 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 15 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 150 optimal weight: 0.4980 chunk 154 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 180 optimal weight: 0.3980 chunk 203 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 HIS ** 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 = 0.4423 r_free = 0.4423 target = 0.167693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.141230 restraints weight = 119516.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.146968 restraints weight = 51020.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.150433 restraints weight = 26977.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.152536 restraints weight = 16581.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.153968 restraints weight = 11490.780| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.206 21763 Z= 0.170 Angle : 0.737 59.198 29572 Z= 0.409 Chirality : 0.039 0.172 3431 Planarity : 0.004 0.052 3837 Dihedral : 8.178 138.644 3067 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.19 % Allowed : 18.82 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.41 (0.17), residues: 2506 helix: 1.24 (0.14), residues: 1422 sheet: -1.15 (0.31), residues: 257 loop : -0.87 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 372 TYR 0.021 0.002 TYR C 44 PHE 0.014 0.001 PHE B 20 TRP 0.041 0.002 TRP G 80 HIS 0.006 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00380 (21763) covalent geometry : angle 0.73685 (29572) hydrogen bonds : bond 0.04033 ( 1239) hydrogen bonds : angle 4.80373 ( 3564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8031.18 seconds wall clock time: 137 minutes 40.57 seconds (8260.57 seconds total)