Starting phenix.real_space_refine on Sat Mar 7 09:29:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eds_47948/03_2026/9eds_47948_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eds_47948/03_2026/9eds_47948.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 { model { file = "/net/cci-nas-00/data/ceres_data/9eds_47948/03_2026/9eds_47948_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eds_47948/03_2026/9eds_47948_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eds_47948/03_2026/9eds_47948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eds_47948/03_2026/9eds_47948.map" } 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 95 5.16 5 C 13228 2.51 5 N 3667 2.21 5 O 3959 1.98 5 H 18121 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 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: 39078 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: "E" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3231 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 374} Link IDs: {'PTRANS': 4, 'TRANS': 451} Chain breaks: 1 Unresolved non-hydrogen bonds: 749 Unresolved non-hydrogen angles: 1122 Unresolved non-hydrogen dihedrals: 376 Planarities with less than four sites: {'UNK:plan-1': 372, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 376 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: "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: "C" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 861 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 4, 'TRANS': 168} 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: "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: 6.42, per 1000 atoms: 0.16 Number of scatterers: 39078 At special positions: 0 Unit cell: (130.24, 129.36, 210.32, 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 95 16.00 P 8 15.00 O 3959 8.00 N 3667 7.00 C 13228 6.00 H 18121 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: 3.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5408 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 16 sheets defined 69.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'D' and resid 1 through 17 Processing helix chain 'D' and resid 19 through 32 removed outlier: 4.202A pdb=" N GLN D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 4.676A 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: 4.077A 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: 4.296A 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: 4.365A pdb=" N ILE D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LYS D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.306A pdb=" N GLU D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.834A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 removed outlier: 4.795A pdb=" N ASN D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LYS D 137 " --> pdb=" O ASP D 133 " (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 193 Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.777A pdb=" N TYR D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.746A 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 Processing helix chain 'D' and resid 277 through 296 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 395 removed outlier: 3.742A pdb=" N ASP D 395 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 415 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.701A 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 514 removed outlier: 3.766A pdb=" N LEU D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 535 Processing helix chain 'D' and resid 541 through 554 removed outlier: 3.537A pdb=" N ILE D 554 " --> pdb=" O TYR D 550 " (cutoff:3.500A) 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 670 through 689 removed outlier: 3.588A pdb=" N HIS D 683 " --> pdb=" O GLY D 679 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP D 686 " --> pdb=" O ASP D 682 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL D 687 " --> pdb=" O HIS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 708 removed outlier: 3.891A pdb=" N LEU D 708 " --> pdb=" O ILE D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 734 removed outlier: 3.773A pdb=" N VAL D 723 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 741 removed outlier: 3.977A pdb=" N SER D 739 " --> pdb=" O PRO D 735 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY D 740 " --> pdb=" O ASP D 736 " (cutoff:3.500A) removed outlier: 4.340A 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: 3.819A pdb=" N ILE D 745 " --> pdb=" O ASP D 741 " (cutoff:3.500A) Proline residue: D 747 - end of helix removed outlier: 3.728A 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 Processing helix chain 'D' and resid 810 through 828 Processing helix chain 'D' and resid 829 through 844 removed outlier: 3.988A pdb=" N ILE D 844 " --> pdb=" O LEU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 854 Processing helix chain 'D' and resid 855 through 860 Processing helix chain 'D' and resid 870 through 888 Processing helix chain 'D' and resid 898 through 911 Processing helix chain 'D' and resid 914 through 936 Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 940 through 965 removed outlier: 3.938A pdb=" N ASN D 944 " --> pdb=" O ALA D 940 " (cutoff:3.500A) removed outlier: 3.714A 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 'E' and resid 67 through 72 Processing helix chain 'E' and resid 146 through 154 removed outlier: 4.126A pdb=" N UNK E 152 " --> pdb=" O UNK E 148 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N UNK E 153 " --> pdb=" O UNK E 149 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N UNK E 154 " --> pdb=" O UNK E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 175 removed outlier: 3.745A pdb=" N UNK E 171 " --> pdb=" O UNK E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.583A pdb=" N UNK E 225 " --> pdb=" O UNK E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 removed outlier: 3.742A pdb=" N UNK E 247 " --> pdb=" O UNK E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 322 removed outlier: 3.707A pdb=" N UNK E 317 " --> pdb=" O UNK E 313 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK E 320 " --> pdb=" O UNK E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 357 removed outlier: 4.051A pdb=" N UNK E 352 " --> pdb=" O UNK E 348 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK E 353 " --> pdb=" O UNK E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 384 Processing helix chain 'E' and resid 385 through 387 No H-bonds generated for 'chain 'E' and resid 385 through 387' Processing helix chain 'E' and resid 395 through 406 Processing helix chain 'E' and resid 408 through 413 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 462 Processing helix chain 'E' and resid 488 through 493 Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.895A 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: 3.993A 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 138 through 157 Processing helix chain 'G' and resid 175 through 191 removed outlier: 3.548A pdb=" N CYS G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 3.712A 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: 4.469A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.555A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (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: 4.692A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.046A 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: 4.725A 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: 4.780A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.206A 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 removed outlier: 3.535A pdb=" N TYR A 282 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.902A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (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 401 removed outlier: 4.016A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.047A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.978A 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 41 through 46 removed outlier: 4.399A 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: 4.400A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.718A pdb=" N PHE B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 107 through 125 removed outlier: 4.150A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.618A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (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 removed outlier: 3.716A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) No H-bonds generated for '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 390 removed outlier: 3.955A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.201A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.766A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 23 Processing helix chain 'I' and resid 27 through 42 Processing helix chain 'I' and resid 43 through 45 No H-bonds generated for 'chain 'I' and resid 43 through 45' 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: 3.500A pdb=" N ARG I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 268 Processing sheet with id=AA1, first strand: chain 'D' and resid 345 through 347 Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 11 removed outlier: 3.962A pdb=" N UNK E 16 " --> pdb=" O UNK E 9 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N UNK E 11 " --> pdb=" O UNK E 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 20 through 23 Processing sheet with id=AA4, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'E' and resid 126 through 128 removed outlier: 3.504A pdb=" N UNK E 158 " --> pdb=" O UNK E 127 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N UNK E 208 " --> pdb=" O UNK E 234 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N UNK E 233 " --> pdb=" O UNK E 260 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N UNK E 259 " --> pdb=" O UNK E 282 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N UNK E 281 " --> pdb=" O UNK E 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AA7, first strand: chain 'E' and resid 362 through 363 Processing sheet with id=AA8, first strand: chain 'E' and resid 439 through 444 Processing sheet with id=AA9, first strand: chain 'G' and resid 53 through 60 removed outlier: 6.595A pdb=" N ILE G 17 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TRP G 68 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS G 19 " --> pdb=" O TRP G 68 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE G 70 " --> pdb=" O CYS G 19 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE G 21 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 89 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N MET G 90 " --> pdb=" O ILE G 127 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL G 129 " --> pdb=" O MET G 90 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP G 92 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASN G 131 " --> pdb=" O TRP G 92 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE G 94 " --> pdb=" O ASN G 131 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 164 " --> pdb=" O VAL G 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.898A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.657A pdb=" N CYS A 376 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 318 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 317 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 92 removed outlier: 7.708A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.054A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.477A pdb=" N PHE C 117 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 146 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASN C 119 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA C 136 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY C 161 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER C 138 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ILE C 163 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N SER C 140 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N ILE C 165 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N CYS C 142 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N ASP C 167 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG C 144 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR C 169 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 146 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 186 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 167 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE C 183 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE C 211 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 185 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU C 213 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 187 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 107 through 110 removed outlier: 6.149A pdb=" N ILE C 151 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ARG C 176 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C 153 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 197 " --> pdb=" O ASN C 221 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N CYS C 218 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU C 251 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE C 220 " --> pdb=" O GLU C 251 " (cutoff:3.500A) 1180 hydrogen bonds defined for protein. 3411 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: 9.65 Time building geometry restraints manager: 5.10 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: 18073 1.03 - 1.23: 248 1.23 - 1.43: 8703 1.43 - 1.63: 12286 1.63 - 1.83: 150 Bond restraints: 39460 Sorted by residual: bond pdb=" O5' GTP G 501 " pdb=" PA GTP G 501 " ideal model delta sigma weight residual 1.610 1.827 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sigma weight residual 1.610 1.813 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" O5' GDP B 501 " pdb=" PA GDP B 501 " ideal model delta sigma weight residual 1.610 1.729 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" O3A GDP B 501 " pdb=" PB GDP B 501 " ideal model delta sigma weight residual 1.610 1.720 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.394 0.096 2.00e-02 2.50e+03 2.29e+01 ... (remaining 39455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 70046 4.80 - 9.61: 120 9.61 - 14.41: 27 14.41 - 19.21: 5 19.21 - 24.01: 2 Bond angle restraints: 70200 Sorted by residual: angle pdb=" N VAL A 250 " pdb=" CA VAL A 250 " pdb=" C VAL A 250 " ideal model delta sigma weight residual 108.06 132.07 -24.01 1.28e+00 6.10e-01 3.52e+02 angle pdb=" N VAL A 250 " pdb=" CA VAL A 250 " pdb=" CB VAL A 250 " ideal model delta sigma weight residual 111.19 91.91 19.28 1.35e+00 5.49e-01 2.04e+02 angle pdb=" C VAL A 250 " pdb=" CA VAL A 250 " pdb=" CB VAL A 250 " ideal model delta sigma weight residual 111.80 101.20 10.60 1.54e+00 4.22e-01 4.74e+01 angle pdb=" PA GDP B 501 " pdb=" O3A GDP B 501 " pdb=" PB GDP B 501 " ideal model delta sigma weight residual 120.50 139.69 -19.19 3.00e+00 1.11e-01 4.09e+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 92.53 16.97 3.00e+00 1.11e-01 3.20e+01 ... (remaining 70195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 18307 35.18 - 70.37: 534 70.37 - 105.55: 43 105.55 - 140.73: 4 140.73 - 175.91: 6 Dihedral angle restraints: 18894 sinusoidal: 9411 harmonic: 9483 Sorted by residual: dihedral pdb=" N VAL A 250 " pdb=" C VAL A 250 " pdb=" CA VAL A 250 " pdb=" CB VAL A 250 " ideal model delta harmonic sigma weight residual 123.40 102.97 20.43 0 2.50e+00 1.60e-01 6.68e+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 -106.65 175.91 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -66.50 171.09 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 18891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2965 0.069 - 0.139: 374 0.139 - 0.208: 25 0.208 - 0.278: 10 0.278 - 0.347: 5 Chirality restraints: 3379 Sorted by residual: 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 -2.82 0.35 2.00e-01 2.50e+01 3.01e+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 -2.84 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE A 291 " pdb=" CA ILE A 291 " pdb=" CG1 ILE A 291 " pdb=" CG2 ILE A 291 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 3376 not shown) Planarity restraints: 5951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 243 " -0.278 9.50e-02 1.11e+02 4.20e-01 3.79e+03 pdb=" NE ARG A 243 " 0.253 2.00e-02 2.50e+03 pdb=" CZ ARG A 243 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 243 " -0.056 2.00e-02 2.50e+03 pdb=" NH2 ARG A 243 " -0.008 2.00e-02 2.50e+03 pdb="HH11 ARG A 243 " -0.854 2.00e-02 2.50e+03 pdb="HH12 ARG A 243 " 0.673 2.00e-02 2.50e+03 pdb="HH21 ARG A 243 " -0.383 2.00e-02 2.50e+03 pdb="HH22 ARG A 243 " 0.337 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 249 " 0.211 2.00e-02 2.50e+03 2.37e-01 8.42e+02 pdb=" CG ASN A 249 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 249 " -0.200 2.00e-02 2.50e+03 pdb=" ND2 ASN A 249 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 249 " 0.358 2.00e-02 2.50e+03 pdb="HD22 ASN A 249 " -0.352 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 351 " -0.049 2.00e-02 2.50e+03 1.00e-01 1.00e+02 pdb=" N LYS A 352 " 0.172 2.00e-02 2.50e+03 pdb=" CA LYS A 352 " -0.041 2.00e-02 2.50e+03 pdb=" H LYS A 352 " -0.081 2.00e-02 2.50e+03 ... (remaining 5948 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 846 2.11 - 2.73: 66050 2.73 - 3.36: 114055 3.36 - 3.98: 139357 3.98 - 4.60: 219707 Nonbonded interactions: 540015 Sorted by model distance: nonbonded pdb="HD21 ASN A 249 " pdb=" HG LEU A 318 " model vdw 1.489 2.270 nonbonded pdb=" OE1 GLU I 88 " pdb=" H GLU I 88 " model vdw 1.569 2.450 nonbonded pdb=" OE1 GLU I 48 " pdb=" H GLU I 48 " model vdw 1.574 2.450 nonbonded pdb=" OE1 GLU G 137 " pdb=" H GLU G 137 " model vdw 1.585 2.450 nonbonded pdb=" O TRP G 92 " pdb=" H VAL G 129 " model vdw 1.599 2.450 ... (remaining 540010 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: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.250 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.790 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 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 : 0.007 0.217 21339 Z= 0.325 Angle : 1.017 24.014 29033 Z= 0.533 Chirality : 0.049 0.347 3379 Planarity : 0.007 0.259 3779 Dihedral : 15.670 175.914 7464 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 0.59 % Allowed : 14.90 % Favored : 84.50 % Cbeta Deviations : 0.04 % 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: 2428 helix: 0.72 (0.13), residues: 1363 sheet: -0.19 (0.29), residues: 277 loop : -0.10 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 422 TYR 0.056 0.003 TYR A 24 PHE 0.045 0.003 PHE D 184 TRP 0.019 0.002 TRP A 388 HIS 0.019 0.002 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00677 (21339) covalent geometry : angle 1.01745 (29033) hydrogen bonds : bond 0.10572 ( 1180) hydrogen bonds : angle 5.97976 ( 3411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 591 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 579 time to evaluate : 0.996 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 391 ASN cc_start: 0.8023 (t0) cc_final: 0.7722 (t0) REVERT: D 590 ASP cc_start: 0.7857 (t0) cc_final: 0.7438 (t0) REVERT: D 835 GLU cc_start: 0.7872 (tp30) cc_final: 0.7602 (tp30) REVERT: D 852 GLU cc_start: 0.5314 (mt-10) cc_final: 0.4789 (mm-30) REVERT: E 471 PHE cc_start: 0.8230 (m-10) cc_final: 0.7919 (m-10) REVERT: G 181 ASP cc_start: 0.7785 (t70) cc_final: 0.7565 (t0) REVERT: A 371 VAL cc_start: 0.8860 (t) cc_final: 0.8544 (p) REVERT: B 48 ASN cc_start: 0.8374 (t0) cc_final: 0.8099 (t0) REVERT: B 139 LEU cc_start: 0.8325 (mp) cc_final: 0.8091 (mp) outliers start: 12 outliers final: 4 residues processed: 581 average time/residue: 0.3593 time to fit residues: 306.0554 Evaluate side-chains 561 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 557 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 472 HIS Chi-restraints excluded: chain B residue 60 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN D 166 ASN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 GLN D 621 GLN D 734 HIS D 993 GLN G 82 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.147951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.119210 restraints weight = 121311.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124825 restraints weight = 49943.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128203 restraints weight = 25762.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.130275 restraints weight = 15573.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.131549 restraints weight = 10801.487| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21339 Z= 0.212 Angle : 0.619 8.348 29033 Z= 0.329 Chirality : 0.040 0.176 3379 Planarity : 0.005 0.067 3779 Dihedral : 9.802 164.830 3041 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 1.49 % Allowed : 14.01 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.57 (0.17), residues: 2428 helix: 0.93 (0.14), residues: 1367 sheet: -0.36 (0.29), residues: 287 loop : -0.09 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 243 TYR 0.024 0.002 TYR A 24 PHE 0.023 0.002 PHE A 255 TRP 0.015 0.002 TRP A 388 HIS 0.011 0.002 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00437 (21339) covalent geometry : angle 0.61942 (29033) hydrogen bonds : bond 0.04694 ( 1180) hydrogen bonds : angle 5.29111 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 602 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 572 time to evaluate : 1.026 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7025 (tm-30) REVERT: D 16 GLN cc_start: 0.7567 (tp40) cc_final: 0.7284 (mp10) REVERT: D 94 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7933 (tt0) REVERT: D 590 ASP cc_start: 0.7888 (t0) cc_final: 0.7444 (t0) REVERT: D 598 LYS cc_start: 0.9307 (mtpp) cc_final: 0.8911 (mtpp) REVERT: D 647 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8094 (ttm-80) REVERT: D 649 ILE cc_start: 0.8894 (mm) cc_final: 0.8610 (mm) REVERT: D 813 GLN cc_start: 0.7063 (mp10) cc_final: 0.6590 (mp10) REVERT: D 835 GLU cc_start: 0.7771 (tp30) cc_final: 0.7250 (tp30) REVERT: D 839 ASP cc_start: 0.8187 (m-30) cc_final: 0.7512 (m-30) REVERT: D 907 TYR cc_start: 0.6001 (t80) cc_final: 0.3935 (t80) REVERT: G 123 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7255 (mt-10) REVERT: G 181 ASP cc_start: 0.7691 (t70) cc_final: 0.7477 (t0) REVERT: A 371 VAL cc_start: 0.8921 (t) cc_final: 0.8600 (p) REVERT: B 48 ASN cc_start: 0.8355 (t0) cc_final: 0.8025 (t0) REVERT: B 161 ASP cc_start: 0.7700 (t70) cc_final: 0.7273 (t70) REVERT: I 76 ARG cc_start: 0.8330 (mtt180) cc_final: 0.8114 (mtt180) outliers start: 30 outliers final: 19 residues processed: 580 average time/residue: 0.3579 time to fit residues: 305.8665 Evaluate side-chains 571 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 552 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 646 CYS Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 134 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN G 143 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.148723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120041 restraints weight = 120996.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.125690 restraints weight = 49657.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.129089 restraints weight = 25473.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.131171 restraints weight = 15359.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.132414 restraints weight = 10609.282| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21339 Z= 0.151 Angle : 0.560 6.301 29033 Z= 0.296 Chirality : 0.039 0.165 3379 Planarity : 0.004 0.058 3779 Dihedral : 9.362 164.368 3033 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.78 % Allowed : 14.36 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.80 (0.17), residues: 2428 helix: 1.11 (0.14), residues: 1370 sheet: -0.33 (0.30), residues: 284 loop : 0.03 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 182 TYR 0.019 0.001 TYR D 71 PHE 0.022 0.001 PHE A 255 TRP 0.014 0.001 TRP A 388 HIS 0.010 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00323 (21339) covalent geometry : angle 0.55982 (29033) hydrogen bonds : bond 0.04267 ( 1180) hydrogen bonds : angle 5.05040 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 600 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 564 time to evaluate : 0.995 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 PHE cc_start: 0.6998 (m-80) cc_final: 0.6527 (m-80) REVERT: D 94 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7793 (tt0) REVERT: D 166 ASN cc_start: 0.6654 (t0) cc_final: 0.6323 (t0) REVERT: D 337 ILE cc_start: 0.7945 (mt) cc_final: 0.7591 (mp) REVERT: D 340 THR cc_start: 0.8068 (t) cc_final: 0.7866 (t) REVERT: D 419 LEU cc_start: 0.7224 (mt) cc_final: 0.6972 (mp) REVERT: D 450 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.8151 (ttp-110) REVERT: D 590 ASP cc_start: 0.7843 (t0) cc_final: 0.7483 (t0) REVERT: D 598 LYS cc_start: 0.9311 (mtpp) cc_final: 0.8917 (mtpp) REVERT: D 636 GLN cc_start: 0.7495 (mp10) cc_final: 0.7162 (mp10) REVERT: D 647 ARG cc_start: 0.8548 (ttm-80) cc_final: 0.8160 (ttm-80) REVERT: D 707 CYS cc_start: 0.9102 (m) cc_final: 0.8891 (m) REVERT: D 813 GLN cc_start: 0.7026 (mp10) cc_final: 0.6595 (mp10) REVERT: D 835 GLU cc_start: 0.7785 (tp30) cc_final: 0.7461 (tp30) REVERT: D 907 TYR cc_start: 0.5734 (t80) cc_final: 0.3693 (t80) REVERT: G 119 ARG cc_start: 0.6811 (tpt-90) cc_final: 0.6166 (tpt-90) REVERT: G 123 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7160 (mt-10) REVERT: G 181 ASP cc_start: 0.7752 (t70) cc_final: 0.7525 (t0) REVERT: A 295 CYS cc_start: 0.8410 (p) cc_final: 0.8196 (p) REVERT: A 371 VAL cc_start: 0.8900 (t) cc_final: 0.8582 (p) REVERT: A 373 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7188 (ptp-170) REVERT: B 40 SER cc_start: 0.8871 (t) cc_final: 0.8670 (t) REVERT: B 161 ASP cc_start: 0.7624 (t70) cc_final: 0.7355 (t70) outliers start: 36 outliers final: 27 residues processed: 576 average time/residue: 0.3709 time to fit residues: 314.1860 Evaluate side-chains 573 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 545 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 646 CYS Chi-restraints excluded: chain D residue 662 PHE Chi-restraints excluded: chain D residue 675 SER Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 12 optimal weight: 0.0020 chunk 153 optimal weight: 2.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN I 165 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.146683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.118298 restraints weight = 120182.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.123903 restraints weight = 49473.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127274 restraints weight = 25403.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.129333 restraints weight = 15357.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.130579 restraints weight = 10647.163| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21339 Z= 0.191 Angle : 0.573 6.316 29033 Z= 0.305 Chirality : 0.039 0.203 3379 Planarity : 0.004 0.058 3779 Dihedral : 9.261 163.474 3033 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.88 % Allowed : 15.59 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.74 (0.17), residues: 2428 helix: 1.10 (0.14), residues: 1375 sheet: -0.60 (0.30), residues: 287 loop : 0.02 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.033 0.002 TYR A 24 PHE 0.023 0.001 PHE A 255 TRP 0.015 0.001 TRP A 388 HIS 0.008 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00409 (21339) covalent geometry : angle 0.57259 (29033) hydrogen bonds : bond 0.04289 ( 1180) hydrogen bonds : angle 5.09856 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 602 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 564 time to evaluate : 0.889 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7871 (tt0) REVERT: D 166 ASN cc_start: 0.6723 (t0) cc_final: 0.6395 (t0) REVERT: D 337 ILE cc_start: 0.8006 (mt) cc_final: 0.7620 (mp) REVERT: D 340 THR cc_start: 0.8201 (t) cc_final: 0.7986 (t) REVERT: D 439 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7259 (ttp-110) REVERT: D 590 ASP cc_start: 0.7814 (t0) cc_final: 0.7473 (t0) REVERT: D 598 LYS cc_start: 0.9292 (mtpp) cc_final: 0.9078 (ttmm) REVERT: D 636 GLN cc_start: 0.7502 (mp10) cc_final: 0.7188 (mp10) REVERT: D 672 GLN cc_start: 0.8991 (mp10) cc_final: 0.8567 (mp10) REVERT: D 835 GLU cc_start: 0.7745 (tp30) cc_final: 0.7458 (tp30) REVERT: D 907 TYR cc_start: 0.5864 (t80) cc_final: 0.3692 (t80) REVERT: G 111 GLU cc_start: 0.8015 (pp20) cc_final: 0.7811 (pp20) REVERT: G 119 ARG cc_start: 0.6752 (tpt-90) cc_final: 0.6238 (tpt-90) REVERT: G 123 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7159 (mt-10) REVERT: G 181 ASP cc_start: 0.7763 (t70) cc_final: 0.7535 (t0) REVERT: A 211 ASP cc_start: 0.7581 (t0) cc_final: 0.6996 (t0) REVERT: A 297 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6781 (mp0) REVERT: A 371 VAL cc_start: 0.8949 (t) cc_final: 0.8668 (p) REVERT: A 373 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7089 (ptp-170) REVERT: B 40 SER cc_start: 0.8908 (t) cc_final: 0.8696 (t) REVERT: B 48 ASN cc_start: 0.8360 (t0) cc_final: 0.7978 (t0) REVERT: I 140 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.8355 (tpp-160) outliers start: 38 outliers final: 30 residues processed: 578 average time/residue: 0.3736 time to fit residues: 314.0547 Evaluate side-chains 588 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 557 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 662 PHE Chi-restraints excluded: chain D residue 675 SER Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 67 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 210 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 chunk 144 optimal weight: 0.0170 chunk 95 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.148373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.119834 restraints weight = 120320.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.125541 restraints weight = 49411.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128957 restraints weight = 25322.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.131073 restraints weight = 15298.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.132369 restraints weight = 10569.068| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21339 Z= 0.132 Angle : 0.542 6.686 29033 Z= 0.285 Chirality : 0.038 0.179 3379 Planarity : 0.004 0.059 3779 Dihedral : 9.135 163.425 3033 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.18 % Allowed : 16.04 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.99 (0.17), residues: 2428 helix: 1.29 (0.14), residues: 1376 sheet: -0.28 (0.31), residues: 269 loop : 0.05 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 450 TYR 0.026 0.001 TYR A 24 PHE 0.021 0.001 PHE D 452 TRP 0.026 0.001 TRP G 92 HIS 0.007 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00289 (21339) covalent geometry : angle 0.54160 (29033) hydrogen bonds : bond 0.03987 ( 1180) hydrogen bonds : angle 4.88164 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 609 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 565 time to evaluate : 0.947 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLN cc_start: 0.7508 (tp40) cc_final: 0.6980 (mp10) REVERT: D 94 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7881 (tt0) REVERT: D 166 ASN cc_start: 0.6683 (t0) cc_final: 0.6316 (t0) REVERT: D 337 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7595 (mp) REVERT: D 340 THR cc_start: 0.8190 (t) cc_final: 0.7969 (t) REVERT: D 419 LEU cc_start: 0.7250 (mt) cc_final: 0.6977 (mp) REVERT: D 439 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7393 (ttp-110) REVERT: D 590 ASP cc_start: 0.7808 (t0) cc_final: 0.7480 (t0) REVERT: D 672 GLN cc_start: 0.8942 (mp10) cc_final: 0.8453 (mp10) REVERT: D 835 GLU cc_start: 0.7768 (tp30) cc_final: 0.7373 (tp30) REVERT: D 907 TYR cc_start: 0.5751 (t80) cc_final: 0.3593 (t80) REVERT: G 119 ARG cc_start: 0.6750 (tpt-90) cc_final: 0.6240 (tpt-90) REVERT: G 123 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7178 (mt-10) REVERT: G 145 ARG cc_start: 0.6871 (mtt180) cc_final: 0.6567 (mtt180) REVERT: A 371 VAL cc_start: 0.8910 (t) cc_final: 0.8604 (p) REVERT: B 46 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8191 (mtt90) REVERT: B 48 ASN cc_start: 0.8307 (t0) cc_final: 0.7885 (t0) REVERT: B 162 ARG cc_start: 0.8689 (mmt180) cc_final: 0.8207 (mmp80) REVERT: I 75 GLU cc_start: 0.8315 (pm20) cc_final: 0.7495 (tp30) REVERT: I 140 ARG cc_start: 0.8628 (tpp-160) cc_final: 0.8383 (tpp-160) outliers start: 44 outliers final: 33 residues processed: 581 average time/residue: 0.3672 time to fit residues: 312.3867 Evaluate side-chains 594 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 559 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 662 PHE Chi-restraints excluded: chain D residue 675 SER Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 216 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN D 706 ASN G 82 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.146940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.118630 restraints weight = 120184.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.124303 restraints weight = 49328.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.127735 restraints weight = 25274.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.129816 restraints weight = 15206.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.131121 restraints weight = 10512.600| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21339 Z= 0.162 Angle : 0.554 6.810 29033 Z= 0.294 Chirality : 0.038 0.164 3379 Planarity : 0.004 0.059 3779 Dihedral : 9.076 163.768 3033 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.28 % Allowed : 16.73 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.96 (0.17), residues: 2428 helix: 1.28 (0.14), residues: 1375 sheet: -0.27 (0.30), residues: 267 loop : -0.01 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 826 TYR 0.028 0.001 TYR A 24 PHE 0.026 0.001 PHE D 452 TRP 0.018 0.001 TRP G 92 HIS 0.007 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00347 (21339) covalent geometry : angle 0.55427 (29033) hydrogen bonds : bond 0.04014 ( 1180) hydrogen bonds : angle 4.92767 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 608 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 562 time to evaluate : 1.042 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLN cc_start: 0.7645 (tp40) cc_final: 0.7047 (mp10) REVERT: D 94 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7877 (tt0) REVERT: D 166 ASN cc_start: 0.6708 (t0) cc_final: 0.6317 (t0) REVERT: D 337 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7599 (mp) REVERT: D 340 THR cc_start: 0.8208 (t) cc_final: 0.7982 (t) REVERT: D 439 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7464 (ttp-110) REVERT: D 478 LEU cc_start: 0.7878 (tt) cc_final: 0.7470 (tp) REVERT: D 590 ASP cc_start: 0.7930 (t0) cc_final: 0.7582 (t0) REVERT: D 672 GLN cc_start: 0.8975 (mp10) cc_final: 0.8528 (mp10) REVERT: D 835 GLU cc_start: 0.7746 (tp30) cc_final: 0.7254 (tp30) REVERT: D 905 LYS cc_start: 0.9266 (mttp) cc_final: 0.8994 (mttp) REVERT: D 907 TYR cc_start: 0.5709 (t80) cc_final: 0.3495 (t80) REVERT: G 119 ARG cc_start: 0.6759 (tpt-90) cc_final: 0.6227 (tpt-90) REVERT: G 123 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7193 (mt-10) REVERT: G 145 ARG cc_start: 0.6928 (mtt180) cc_final: 0.6634 (mtt180) REVERT: A 371 VAL cc_start: 0.8937 (t) cc_final: 0.8654 (p) REVERT: A 415 GLU cc_start: 0.7914 (mp0) cc_final: 0.7689 (mp0) REVERT: B 48 ASN cc_start: 0.8325 (t0) cc_final: 0.7906 (t0) REVERT: B 73 MET cc_start: 0.8211 (mmm) cc_final: 0.7858 (mmm) REVERT: B 217 LEU cc_start: 0.9068 (mt) cc_final: 0.8741 (mp) REVERT: B 299 MET cc_start: 0.6838 (mmm) cc_final: 0.6487 (mmm) REVERT: I 75 GLU cc_start: 0.8382 (pm20) cc_final: 0.7554 (tp30) outliers start: 46 outliers final: 38 residues processed: 580 average time/residue: 0.3755 time to fit residues: 318.8145 Evaluate side-chains 599 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 560 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 662 PHE Chi-restraints excluded: chain D residue 675 SER Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain D residue 916 THR Chi-restraints excluded: chain D residue 991 GLN Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.146151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.118045 restraints weight = 119598.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.123695 restraints weight = 49044.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.127077 restraints weight = 25126.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.129157 restraints weight = 15153.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.130456 restraints weight = 10478.473| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21339 Z= 0.176 Angle : 0.571 7.246 29033 Z= 0.303 Chirality : 0.039 0.217 3379 Planarity : 0.004 0.059 3779 Dihedral : 9.079 164.524 3033 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.43 % Allowed : 17.33 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.89 (0.17), residues: 2428 helix: 1.27 (0.14), residues: 1375 sheet: -0.28 (0.31), residues: 263 loop : -0.14 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 86 TYR 0.028 0.002 TYR A 24 PHE 0.025 0.001 PHE D 452 TRP 0.025 0.002 TRP G 92 HIS 0.007 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00380 (21339) covalent geometry : angle 0.57062 (29033) hydrogen bonds : bond 0.04075 ( 1180) hydrogen bonds : angle 4.96160 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 624 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 575 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 16 GLN cc_start: 0.7738 (tp40) cc_final: 0.7197 (mp10) REVERT: D 94 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7889 (tt0) REVERT: D 166 ASN cc_start: 0.6700 (t0) cc_final: 0.6326 (t0) REVERT: D 337 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7674 (mp) REVERT: D 340 THR cc_start: 0.8211 (t) cc_final: 0.7964 (t) REVERT: D 439 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7585 (ttp-110) REVERT: D 478 LEU cc_start: 0.7878 (tt) cc_final: 0.7474 (tp) REVERT: D 590 ASP cc_start: 0.7937 (t0) cc_final: 0.7529 (t0) REVERT: D 598 LYS cc_start: 0.9299 (mtpp) cc_final: 0.9094 (mtpp) REVERT: D 835 GLU cc_start: 0.7755 (tp30) cc_final: 0.7236 (tp30) REVERT: D 907 TYR cc_start: 0.5580 (t80) cc_final: 0.3286 (t80) REVERT: G 96 VAL cc_start: 0.8046 (p) cc_final: 0.7371 (m) REVERT: G 97 SER cc_start: 0.7158 (OUTLIER) cc_final: 0.6633 (p) REVERT: G 119 ARG cc_start: 0.6738 (tpt-90) cc_final: 0.6195 (tpt-90) REVERT: G 123 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7269 (mt-10) REVERT: A 211 ASP cc_start: 0.7683 (t0) cc_final: 0.7039 (t0) REVERT: A 216 ASN cc_start: 0.8652 (m-40) cc_final: 0.8408 (m-40) REVERT: A 297 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6694 (mp0) REVERT: A 371 VAL cc_start: 0.8967 (t) cc_final: 0.8708 (p) REVERT: B 48 ASN cc_start: 0.8313 (t0) cc_final: 0.7909 (t0) REVERT: B 66 VAL cc_start: 0.7763 (t) cc_final: 0.7547 (m) REVERT: B 73 MET cc_start: 0.8233 (mmm) cc_final: 0.7856 (mmm) REVERT: B 138 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 162 ARG cc_start: 0.8726 (mmt180) cc_final: 0.8425 (mmt90) REVERT: B 217 LEU cc_start: 0.9118 (mt) cc_final: 0.8816 (mp) REVERT: B 299 MET cc_start: 0.6832 (mmm) cc_final: 0.6490 (mmm) REVERT: I 75 GLU cc_start: 0.8367 (pm20) cc_final: 0.7566 (tp30) REVERT: I 117 LYS cc_start: 0.7215 (tptp) cc_final: 0.7000 (tptp) REVERT: I 140 ARG cc_start: 0.8704 (tpp-160) cc_final: 0.8368 (tpp-160) outliers start: 49 outliers final: 45 residues processed: 594 average time/residue: 0.3654 time to fit residues: 317.6189 Evaluate side-chains 609 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 561 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 662 PHE Chi-restraints excluded: chain D residue 675 SER Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain D residue 991 GLN Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 85 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 206 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN I 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.147348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.118241 restraints weight = 121287.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124035 restraints weight = 50244.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.127532 restraints weight = 26003.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.129669 restraints weight = 15764.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.130984 restraints weight = 10950.730| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21339 Z= 0.144 Angle : 0.560 8.690 29033 Z= 0.294 Chirality : 0.039 0.188 3379 Planarity : 0.004 0.060 3779 Dihedral : 9.004 164.751 3033 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.38 % Allowed : 17.62 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.99 (0.17), residues: 2428 helix: 1.35 (0.14), residues: 1374 sheet: -0.22 (0.31), residues: 263 loop : -0.12 (0.24), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 145 TYR 0.027 0.002 TYR A 24 PHE 0.021 0.001 PHE D 452 TRP 0.017 0.001 TRP G 92 HIS 0.007 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00319 (21339) covalent geometry : angle 0.55965 (29033) hydrogen bonds : bond 0.03910 ( 1180) hydrogen bonds : angle 4.85413 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 618 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 570 time to evaluate : 0.915 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 16 GLN cc_start: 0.7748 (tp40) cc_final: 0.7170 (mp10) REVERT: D 94 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7885 (tt0) REVERT: D 166 ASN cc_start: 0.6664 (t0) cc_final: 0.6303 (t0) REVERT: D 337 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7740 (mp) REVERT: D 340 THR cc_start: 0.8220 (t) cc_final: 0.7975 (t) REVERT: D 439 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7559 (ttp-110) REVERT: D 478 LEU cc_start: 0.7865 (tt) cc_final: 0.7466 (tp) REVERT: D 590 ASP cc_start: 0.7914 (t0) cc_final: 0.7553 (t0) REVERT: D 835 GLU cc_start: 0.7753 (tp30) cc_final: 0.7229 (tp30) REVERT: D 907 TYR cc_start: 0.5504 (t80) cc_final: 0.3227 (t80) REVERT: G 119 ARG cc_start: 0.6721 (tpt-90) cc_final: 0.6160 (tpt-90) REVERT: G 123 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 211 ASP cc_start: 0.7665 (t0) cc_final: 0.6993 (t0) REVERT: A 216 ASN cc_start: 0.8650 (m-40) cc_final: 0.8407 (m-40) REVERT: A 297 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6643 (mp0) REVERT: A 371 VAL cc_start: 0.8939 (t) cc_final: 0.8675 (p) REVERT: B 48 ASN cc_start: 0.8270 (t0) cc_final: 0.7863 (t0) REVERT: B 73 MET cc_start: 0.8219 (mmm) cc_final: 0.7837 (mmm) REVERT: B 138 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 162 ARG cc_start: 0.8741 (mmt180) cc_final: 0.8455 (mmt90) REVERT: B 299 MET cc_start: 0.6816 (mmm) cc_final: 0.6486 (mmm) REVERT: I 75 GLU cc_start: 0.8366 (pm20) cc_final: 0.7544 (tp30) REVERT: I 117 LYS cc_start: 0.7225 (tptp) cc_final: 0.7015 (tptp) outliers start: 48 outliers final: 39 residues processed: 590 average time/residue: 0.3639 time to fit residues: 314.7534 Evaluate side-chains 604 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 563 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 662 PHE Chi-restraints excluded: chain D residue 675 SER Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain D residue 991 GLN Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 125 optimal weight: 0.0570 chunk 111 optimal weight: 1.9990 chunk 231 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 152 optimal weight: 0.0980 chunk 178 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** 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 = 0.4119 r_free = 0.4119 target = 0.147269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.118976 restraints weight = 120790.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124695 restraints weight = 49840.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.128129 restraints weight = 25633.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.130257 restraints weight = 15460.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.131575 restraints weight = 10656.384| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21339 Z= 0.141 Angle : 0.562 8.023 29033 Z= 0.296 Chirality : 0.038 0.197 3379 Planarity : 0.004 0.062 3779 Dihedral : 8.939 165.168 3033 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.33 % Allowed : 17.97 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.05 (0.17), residues: 2428 helix: 1.43 (0.14), residues: 1375 sheet: -0.35 (0.30), residues: 268 loop : -0.07 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 698 TYR 0.028 0.002 TYR A 24 PHE 0.022 0.001 PHE D 452 TRP 0.019 0.001 TRP G 92 HIS 0.007 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00312 (21339) covalent geometry : angle 0.56244 (29033) hydrogen bonds : bond 0.03844 ( 1180) hydrogen bonds : angle 4.78657 ( 3411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 620 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 573 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 16 GLN cc_start: 0.7794 (tp40) cc_final: 0.7216 (mp10) REVERT: D 56 PHE cc_start: 0.6927 (m-80) cc_final: 0.6413 (m-80) REVERT: D 94 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7735 (tt0) REVERT: D 166 ASN cc_start: 0.6650 (t0) cc_final: 0.6277 (t0) REVERT: D 337 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7772 (mp) REVERT: D 340 THR cc_start: 0.8225 (t) cc_final: 0.7974 (t) REVERT: D 343 PHE cc_start: 0.8165 (t80) cc_final: 0.7758 (t80) REVERT: D 436 ASP cc_start: 0.7878 (t0) cc_final: 0.7424 (p0) REVERT: D 478 LEU cc_start: 0.7883 (tt) cc_final: 0.7488 (tp) REVERT: D 590 ASP cc_start: 0.7899 (t0) cc_final: 0.7527 (t0) REVERT: D 835 GLU cc_start: 0.7692 (tp30) cc_final: 0.7123 (tp30) REVERT: D 905 LYS cc_start: 0.9225 (mttp) cc_final: 0.8942 (mttp) REVERT: D 907 TYR cc_start: 0.5500 (t80) cc_final: 0.3196 (t80) REVERT: G 119 ARG cc_start: 0.6693 (tpt-90) cc_final: 0.6126 (tpt-90) REVERT: G 123 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7196 (mt-10) REVERT: A 61 HIS cc_start: 0.7222 (m90) cc_final: 0.7010 (m-70) REVERT: A 211 ASP cc_start: 0.7604 (t0) cc_final: 0.6975 (t0) REVERT: A 216 ASN cc_start: 0.8641 (m-40) cc_final: 0.8364 (m-40) REVERT: A 297 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6590 (mp0) REVERT: A 371 VAL cc_start: 0.8926 (t) cc_final: 0.8663 (p) REVERT: B 48 ASN cc_start: 0.8245 (t0) cc_final: 0.7845 (t0) REVERT: B 138 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8199 (p) REVERT: B 217 LEU cc_start: 0.9138 (mt) cc_final: 0.8831 (mp) REVERT: B 299 MET cc_start: 0.6769 (mmm) cc_final: 0.6452 (mmm) REVERT: I 138 ARG cc_start: 0.7979 (tpt90) cc_final: 0.7772 (tpt90) REVERT: I 144 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7904 (tm-30) outliers start: 47 outliers final: 42 residues processed: 590 average time/residue: 0.3662 time to fit residues: 315.9340 Evaluate side-chains 606 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 562 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 662 PHE Chi-restraints excluded: chain D residue 675 SER Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain D residue 991 GLN Chi-restraints excluded: chain E residue 472 HIS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 124 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 216 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 275 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 334 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 = 0.4052 r_free = 0.4052 target = 0.142181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114363 restraints weight = 119864.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119876 restraints weight = 49838.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.123213 restraints weight = 25943.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125304 restraints weight = 15805.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.126594 restraints weight = 10973.010| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 21339 Z= 0.306 Angle : 0.684 7.595 29033 Z= 0.370 Chirality : 0.042 0.182 3379 Planarity : 0.005 0.062 3779 Dihedral : 9.203 165.872 3033 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.52 % Allowed : 18.27 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.29 (0.17), residues: 2428 helix: 0.91 (0.14), residues: 1371 sheet: -0.73 (0.30), residues: 269 loop : -0.58 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 86 TYR 0.027 0.002 TYR D 202 PHE 0.028 0.002 PHE D 192 TRP 0.020 0.002 TRP G 92 HIS 0.014 0.002 HIS D 355 Details of bonding type rmsd covalent geometry : bond 0.00647 (21339) covalent geometry : angle 0.68374 (29033) hydrogen bonds : bond 0.04668 ( 1180) hydrogen bonds : angle 5.38096 ( 3411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 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 633 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 582 time to evaluate : 1.024 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 16 GLN cc_start: 0.7934 (tp40) cc_final: 0.7315 (mp10) REVERT: D 94 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7973 (mt-10) REVERT: D 337 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 340 THR cc_start: 0.8276 (t) cc_final: 0.7937 (t) REVERT: D 419 LEU cc_start: 0.7872 (mt) cc_final: 0.7481 (mp) REVERT: D 436 ASP cc_start: 0.7905 (t0) cc_final: 0.7575 (p0) REVERT: D 478 LEU cc_start: 0.8011 (tt) cc_final: 0.7627 (tp) REVERT: D 590 ASP cc_start: 0.7878 (t0) cc_final: 0.7501 (t0) REVERT: D 819 ASP cc_start: 0.8230 (m-30) cc_final: 0.8012 (m-30) REVERT: D 835 GLU cc_start: 0.7739 (tp30) cc_final: 0.7311 (tp30) REVERT: D 907 TYR cc_start: 0.5691 (t80) cc_final: 0.3390 (t80) REVERT: G 98 LEU cc_start: 0.8167 (mt) cc_final: 0.7936 (mt) REVERT: G 119 ARG cc_start: 0.6814 (tpt-90) cc_final: 0.6322 (tpt-90) REVERT: G 123 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 48 SER cc_start: 0.8009 (t) cc_final: 0.7673 (t) REVERT: A 211 ASP cc_start: 0.7715 (t0) cc_final: 0.7127 (t0) REVERT: A 297 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6789 (mp0) REVERT: A 371 VAL cc_start: 0.9002 (t) cc_final: 0.8783 (p) REVERT: B 48 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8002 (t0) REVERT: B 73 MET cc_start: 0.8380 (mmm) cc_final: 0.8120 (mmm) REVERT: B 131 GLN cc_start: 0.7423 (tt0) cc_final: 0.6934 (tt0) REVERT: B 138 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8156 (p) REVERT: B 217 LEU cc_start: 0.9170 (mt) cc_final: 0.8885 (mp) REVERT: B 236 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6783 (t) REVERT: B 299 MET cc_start: 0.6856 (mmm) cc_final: 0.6485 (mmm) REVERT: B 307 HIS cc_start: 0.8192 (m-70) cc_final: 0.7745 (m90) REVERT: I 75 GLU cc_start: 0.8331 (pm20) cc_final: 0.7625 (tp30) REVERT: I 138 ARG cc_start: 0.8048 (tpt90) cc_final: 0.7745 (tpt90) REVERT: I 140 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.8429 (tpp-160) outliers start: 51 outliers final: 39 residues processed: 604 average time/residue: 0.3488 time to fit residues: 308.6747 Evaluate side-chains 618 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 575 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 TRP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain D residue 450 ARG Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 604 SER Chi-restraints excluded: chain D residue 662 PHE Chi-restraints excluded: chain D residue 675 SER Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 910 HIS Chi-restraints excluded: chain D residue 991 GLN Chi-restraints excluded: chain E residue 472 HIS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 163 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 102 optimal weight: 0.5980 chunk 220 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.141992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114442 restraints weight = 120206.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119877 restraints weight = 50802.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.123184 restraints weight = 26576.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125223 restraints weight = 16236.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.126490 restraints weight = 11312.432| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 21339 Z= 0.289 Angle : 0.815 59.188 29033 Z= 0.470 Chirality : 0.041 0.329 3379 Planarity : 0.005 0.062 3779 Dihedral : 9.214 165.770 3033 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.52 % Allowed : 18.56 % Favored : 78.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.25 (0.17), residues: 2428 helix: 0.89 (0.14), residues: 1370 sheet: -0.75 (0.30), residues: 269 loop : -0.61 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 77 TYR 0.023 0.002 TYR D 202 PHE 0.024 0.002 PHE D 192 TRP 0.017 0.002 TRP A 388 HIS 0.020 0.002 HIS D 894 Details of bonding type rmsd covalent geometry : bond 0.00623 (21339) covalent geometry : angle 0.81528 (29033) hydrogen bonds : bond 0.04614 ( 1180) hydrogen bonds : angle 5.36711 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8317.86 seconds wall clock time: 142 minutes 2.82 seconds (8522.82 seconds total)