Starting phenix.real_space_refine on Fri Jun 5 08:16:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wt0_66212/06_2026/9wt0_66212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wt0_66212/06_2026/9wt0_66212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wt0_66212/06_2026/9wt0_66212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wt0_66212/06_2026/9wt0_66212.map" model { file = "/net/cci-nas-00/data/ceres_data/9wt0_66212/06_2026/9wt0_66212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wt0_66212/06_2026/9wt0_66212.cif" } resolution = 3.9 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 11976 2.51 5 N 3089 2.21 5 O 3644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18756 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3902 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 474} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 3893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3893 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 473} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3902 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 474} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 866, 7059 Classifications: {'peptide': 866} Link IDs: {'PTRANS': 33, 'TRANS': 832} Chain breaks: 1 Time building chain proxies: 4.41, per 1000 atoms: 0.24 Number of scatterers: 18756 At special positions: 0 Unit cell: (215.6, 141.9, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 3644 8.00 N 3089 7.00 C 11976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS a 51 " - pdb=" SG CYS b 316 " distance=2.02 Simple disulfide: pdb=" SG CYS a 172 " - pdb=" SG CYS A 826 " distance=2.36 Simple disulfide: pdb=" SG CYS a 316 " - pdb=" SG CYS c 51 " distance=2.04 Simple disulfide: pdb=" SG CYS b 51 " - pdb=" SG CYS c 316 " distance=2.19 Simple disulfide: pdb=" SG CYS b 172 " - pdb=" SG CYS A 912 " distance=2.87 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 331 " distance=2.02 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: 1.65 Conformation dependent library (CDL) restraints added in 928.3 milliseconds 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4390 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 26 sheets defined 41.3% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'a' and resid 22 through 45 removed outlier: 3.930A pdb=" N ILE a 30 " --> pdb=" O LEU a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 133 Processing helix chain 'a' and resid 190 through 199 removed outlier: 3.929A pdb=" N ASP a 199 " --> pdb=" O HIS a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 200 through 207 removed outlier: 3.541A pdb=" N LEU a 206 " --> pdb=" O VAL a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 213 Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 232 through 246 Processing helix chain 'a' and resid 248 through 263 Processing helix chain 'a' and resid 271 through 277 Processing helix chain 'a' and resid 281 through 285 removed outlier: 3.558A pdb=" N TYR a 284 " --> pdb=" O SER a 281 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL a 285 " --> pdb=" O SER a 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 281 through 285' Processing helix chain 'a' and resid 287 through 310 Processing helix chain 'a' and resid 355 through 373 Processing helix chain 'a' and resid 404 through 409 Processing helix chain 'a' and resid 413 through 418 Processing helix chain 'a' and resid 420 through 424 Processing helix chain 'a' and resid 440 through 444 Processing helix chain 'a' and resid 456 through 460 Processing helix chain 'a' and resid 461 through 476 removed outlier: 5.026A pdb=" N ILE a 467 " --> pdb=" O GLU a 463 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 45 removed outlier: 3.507A pdb=" N GLN b 36 " --> pdb=" O PHE b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 198 Processing helix chain 'b' and resid 200 through 207 Processing helix chain 'b' and resid 208 through 213 Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 232 through 246 Processing helix chain 'b' and resid 248 through 263 Processing helix chain 'b' and resid 269 through 274 Processing helix chain 'b' and resid 275 through 278 Processing helix chain 'b' and resid 287 through 311 removed outlier: 3.991A pdb=" N LYS b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 354 through 373 removed outlier: 4.163A pdb=" N ASN b 358 " --> pdb=" O THR b 354 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 409 Processing helix chain 'b' and resid 412 through 419 Processing helix chain 'b' and resid 420 through 424 Processing helix chain 'b' and resid 440 through 444 Processing helix chain 'b' and resid 461 through 476 Processing helix chain 'c' and resid 22 through 44 removed outlier: 3.628A pdb=" N LEU c 26 " --> pdb=" O THR c 22 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 118 Processing helix chain 'c' and resid 131 through 133 No H-bonds generated for 'chain 'c' and resid 131 through 133' Processing helix chain 'c' and resid 143 through 145 No H-bonds generated for 'chain 'c' and resid 143 through 145' Processing helix chain 'c' and resid 189 through 198 Processing helix chain 'c' and resid 200 through 207 Processing helix chain 'c' and resid 208 through 215 Processing helix chain 'c' and resid 226 through 230 Processing helix chain 'c' and resid 232 through 246 Processing helix chain 'c' and resid 248 through 263 Processing helix chain 'c' and resid 269 through 274 Processing helix chain 'c' and resid 275 through 277 No H-bonds generated for 'chain 'c' and resid 275 through 277' Processing helix chain 'c' and resid 287 through 311 removed outlier: 3.543A pdb=" N PHE c 310 " --> pdb=" O ILE c 306 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 355 through 373 Processing helix chain 'c' and resid 405 through 412 removed outlier: 4.585A pdb=" N SER c 412 " --> pdb=" O LEU c 408 " (cutoff:3.500A) Processing helix chain 'c' and resid 412 through 417 Processing helix chain 'c' and resid 420 through 424 Processing helix chain 'c' and resid 440 through 444 Processing helix chain 'c' and resid 461 through 476 removed outlier: 5.263A pdb=" N ILE c 467 " --> pdb=" O GLU c 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 38 Processing helix chain 'A' and resid 48 through 69 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 173 through 187 removed outlier: 4.032A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 348 through 367 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 408 through 411 Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.516A pdb=" N ALA A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 490 through 493 Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'A' and resid 514 through 526 removed outlier: 3.985A pdb=" N LYS A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 543 removed outlier: 3.749A pdb=" N GLU A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 632 through 649 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.809A pdb=" N ASN A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 772 through 780 removed outlier: 3.757A pdb=" N TYR A 776 " --> pdb=" O CYS A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 816 Processing helix chain 'A' and resid 854 through 871 Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 879 through 899 removed outlier: 4.096A pdb=" N GLN A 888 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 13 through 14 removed outlier: 14.531A pdb=" N LEU c 183 " --> pdb=" O LEU c 129 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N LEU c 129 " --> pdb=" O LEU c 183 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL c 185 " --> pdb=" O TRP c 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 55 through 59 removed outlier: 7.061A pdb=" N ILE c 62 " --> pdb=" O PRO c 58 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL c 185 " --> pdb=" O TRP c 127 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N LEU c 129 " --> pdb=" O LEU c 183 " (cutoff:3.500A) removed outlier: 14.531A pdb=" N LEU c 183 " --> pdb=" O LEU c 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'a' and resid 55 through 59 removed outlier: 7.242A pdb=" N ILE a 62 " --> pdb=" O PRO a 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'a' and resid 81 through 84 removed outlier: 3.961A pdb=" N ALA a 84 " --> pdb=" O GLY a 91 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY a 91 " --> pdb=" O ALA a 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 140 through 141 removed outlier: 5.253A pdb=" N VAL a 185 " --> pdb=" O TRP a 127 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LYS a 151 " --> pdb=" O ARG a 331 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG a 331 " --> pdb=" O LYS a 151 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA a 153 " --> pdb=" O LEU a 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 140 through 141 removed outlier: 5.253A pdb=" N VAL a 185 " --> pdb=" O TRP a 127 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR b 12 " --> pdb=" O GLN a 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 382 through 384 Processing sheet with id=AB1, first strand: chain 'b' and resid 19 through 20 Processing sheet with id=AB2, first strand: chain 'b' and resid 77 through 78 removed outlier: 6.776A pdb=" N ILE b 69 " --> pdb=" O VAL b 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 55 through 56 removed outlier: 5.157A pdb=" N VAL b 185 " --> pdb=" O TRP b 127 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU b 129 " --> pdb=" O LEU b 183 " (cutoff:3.500A) removed outlier: 14.835A pdb=" N LEU b 183 " --> pdb=" O LEU b 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 140 through 141 removed outlier: 5.157A pdb=" N VAL b 185 " --> pdb=" O TRP b 127 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU b 129 " --> pdb=" O LEU b 183 " (cutoff:3.500A) removed outlier: 14.835A pdb=" N LEU b 183 " --> pdb=" O LEU b 129 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR c 12 " --> pdb=" O GLN b 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 81 through 82 Processing sheet with id=AB6, first strand: chain 'b' and resid 382 through 386 Processing sheet with id=AB7, first strand: chain 'c' and resid 77 through 78 removed outlier: 6.763A pdb=" N ILE c 69 " --> pdb=" O VAL c 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 81 through 83 Processing sheet with id=AB9, first strand: chain 'c' and resid 382 through 386 Processing sheet with id=AC1, first strand: chain 'A' and resid 114 through 121 removed outlier: 6.725A pdb=" N GLU A 164 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS A 117 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 162 " --> pdb=" O CYS A 117 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE A 119 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG A 160 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG A 121 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 158 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A 159 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLU A 198 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 161 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AC3, first strand: chain 'A' and resid 296 through 305 removed outlier: 6.496A pdb=" N ASN A 210 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 302 " --> pdb=" O CYS A 208 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N CYS A 208 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU A 304 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 206 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA A 201 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS A 329 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A 203 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 296 through 305 removed outlier: 6.496A pdb=" N ASN A 210 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 302 " --> pdb=" O CYS A 208 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N CYS A 208 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU A 304 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 206 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR A 335 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 207 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN A 337 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 209 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE A 339 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 211 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AC6, first strand: chain 'A' and resid 598 through 603 Processing sheet with id=AC7, first strand: chain 'A' and resid 736 through 739 removed outlier: 6.932A pdb=" N VAL A 789 " --> pdb=" O LYS A 824 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS A 826 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 791 " --> pdb=" O CYS A 826 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 828 " --> pdb=" O ILE A 791 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 793 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 838 through 839 794 hydrogen bonds defined for protein. 2169 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: 3.71 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3149 1.24 - 1.39: 4679 1.39 - 1.53: 10045 1.53 - 1.67: 1183 1.67 - 1.82: 71 Bond restraints: 19127 Sorted by residual: bond pdb=" CG1 ILE A 462 " pdb=" CD1 ILE A 462 " ideal model delta sigma weight residual 1.513 1.100 0.413 3.90e-02 6.57e+02 1.12e+02 bond pdb=" CB HIS a 326 " pdb=" CG HIS a 326 " ideal model delta sigma weight residual 1.497 1.390 0.107 1.40e-02 5.10e+03 5.85e+01 bond pdb=" CG HIS a 182 " pdb=" CD2 HIS a 182 " ideal model delta sigma weight residual 1.354 1.279 0.075 1.10e-02 8.26e+03 4.69e+01 bond pdb=" C PHE A 383 " pdb=" N ALA A 384 " ideal model delta sigma weight residual 1.333 1.428 -0.095 1.49e-02 4.50e+03 4.07e+01 bond pdb=" CG1 ILE A 70 " pdb=" CD1 ILE A 70 " ideal model delta sigma weight residual 1.513 1.278 0.235 3.90e-02 6.57e+02 3.64e+01 ... (remaining 19122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 24166 2.98 - 5.96: 1562 5.96 - 8.94: 139 8.94 - 11.92: 17 11.92 - 14.91: 4 Bond angle restraints: 25888 Sorted by residual: angle pdb=" N GLY c 120 " pdb=" CA GLY c 120 " pdb=" C GLY c 120 " ideal model delta sigma weight residual 112.18 97.27 14.91 1.34e+00 5.57e-01 1.24e+02 angle pdb=" N GLY b 52 " pdb=" CA GLY b 52 " pdb=" C GLY b 52 " ideal model delta sigma weight residual 111.54 124.43 -12.89 1.36e+00 5.41e-01 8.98e+01 angle pdb=" N LEU c 119 " pdb=" CA LEU c 119 " pdb=" C LEU c 119 " ideal model delta sigma weight residual 110.61 100.07 10.54 1.25e+00 6.40e-01 7.12e+01 angle pdb=" N VAL a 149 " pdb=" CA VAL a 149 " pdb=" C VAL a 149 " ideal model delta sigma weight residual 113.20 105.43 7.77 9.60e-01 1.09e+00 6.55e+01 angle pdb=" N GLY A 81 " pdb=" CA GLY A 81 " pdb=" C GLY A 81 " ideal model delta sigma weight residual 111.95 119.45 -7.50 9.50e-01 1.11e+00 6.23e+01 ... (remaining 25883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11039 17.84 - 35.69: 371 35.69 - 53.53: 68 53.53 - 71.38: 37 71.38 - 89.22: 15 Dihedral angle restraints: 11530 sinusoidal: 4710 harmonic: 6820 Sorted by residual: dihedral pdb=" CB CYS b 172 " pdb=" SG CYS b 172 " pdb=" SG CYS A 912 " pdb=" CB CYS A 912 " ideal model delta sinusoidal sigma weight residual -86.00 -30.62 -55.38 1 1.00e+01 1.00e-02 4.15e+01 dihedral pdb=" CB CYS b 51 " pdb=" SG CYS b 51 " pdb=" SG CYS c 316 " pdb=" CB CYS c 316 " ideal model delta sinusoidal sigma weight residual -86.00 -127.97 41.97 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS a 172 " pdb=" SG CYS a 172 " pdb=" SG CYS A 826 " pdb=" CB CYS A 826 " ideal model delta sinusoidal sigma weight residual 93.00 128.55 -35.55 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 11527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2276 0.090 - 0.181: 558 0.181 - 0.271: 70 0.271 - 0.362: 4 0.362 - 0.452: 1 Chirality restraints: 2909 Sorted by residual: chirality pdb=" CB ILE A 392 " pdb=" CA ILE A 392 " pdb=" CG1 ILE A 392 " pdb=" CG2 ILE A 392 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE b 69 " pdb=" CA ILE b 69 " pdb=" CG1 ILE b 69 " pdb=" CG2 ILE b 69 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2906 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 386 " 0.006 2.00e-02 2.50e+03 5.26e-02 6.92e+01 pdb=" CG TRP A 386 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 386 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 386 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 386 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP A 386 " -0.063 2.00e-02 2.50e+03 pdb=" CE3 TRP A 386 " -0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 386 " -0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 386 " 0.070 2.00e-02 2.50e+03 pdb=" CH2 TRP A 386 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 458 " 0.041 2.00e-02 2.50e+03 4.38e-02 3.36e+01 pdb=" CG PHE A 458 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 458 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE A 458 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 458 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A 458 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 458 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 114 " 0.067 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR b 114 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR b 114 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR b 114 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR b 114 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR b 114 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR b 114 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR b 114 " 0.047 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 96 2.56 - 3.15: 15725 3.15 - 3.73: 26634 3.73 - 4.32: 38861 4.32 - 4.90: 61981 Nonbonded interactions: 143297 Sorted by model distance: nonbonded pdb=" NE2 GLN a 221 " pdb=" OE2 GLU b 443 " model vdw 1.980 3.120 nonbonded pdb=" OD1 ASP a 18 " pdb=" NH2 ARG A 908 " model vdw 2.176 3.120 nonbonded pdb=" NE2 GLN A 393 " pdb=" OD2 ASP A 430 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASN A 78 " pdb=" NZ LYS A 444 " model vdw 2.309 3.120 nonbonded pdb=" N ASP A 654 " pdb=" OD1 ASP A 654 " model vdw 2.341 3.120 ... (remaining 143292 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 Found NCS groups: ncs_group { reference = (chain 'a' and resid 2 through 488) selection = chain 'b' selection = (chain 'c' and resid 2 through 488) } 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: 16.580 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.140 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 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 : 0.018 0.834 19133 Z= 0.910 Angle : 1.611 32.533 25900 Z= 1.051 Chirality : 0.077 0.452 2909 Planarity : 0.008 0.070 3339 Dihedral : 10.824 89.224 7122 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.05 % Allowed : 0.81 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2319 helix: 0.06 (0.17), residues: 782 sheet: 0.23 (0.35), residues: 185 loop : -0.43 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.001 ARG a 184 TYR 0.067 0.007 TYR b 114 PHE 0.085 0.006 PHE A 458 TRP 0.070 0.009 TRP A 386 HIS 0.014 0.003 HIS a 182 Details of bonding type rmsd/Z covalent geometry : bond 0.01715 / 0.85 (19127) covalent geometry : angle 1.58552 / 1.04 (25888) SS BOND : bond 0.37297 / 25.74 ( 6) SS BOND : angle 13.46627 / 9.23 ( 12) hydrogen bonds : bond 0.21339 / 14.54 ( 768) hydrogen bonds : angle 7.45529 / 5.12 ( 2169) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 74 ASP cc_start: 0.7342 (m-30) cc_final: 0.6959 (m-30) REVERT: a 103 HIS cc_start: 0.5278 (m90) cc_final: 0.4704 (m-70) REVERT: a 205 LYS cc_start: 0.7564 (pttt) cc_final: 0.7238 (tptm) REVERT: a 278 GLN cc_start: 0.6956 (pp30) cc_final: 0.6537 (pt0) REVERT: a 430 GLN cc_start: 0.4482 (mm-40) cc_final: 0.3596 (mt0) REVERT: a 470 GLN cc_start: 0.7787 (tp40) cc_final: 0.6888 (tm-30) REVERT: b 103 HIS cc_start: 0.6710 (m90) cc_final: 0.6043 (m90) REVERT: b 139 ASP cc_start: 0.6032 (m-30) cc_final: 0.5488 (m-30) REVERT: b 365 GLU cc_start: 0.7285 (tp30) cc_final: 0.7084 (tp30) REVERT: b 482 VAL cc_start: 0.7268 (t) cc_final: 0.6972 (p) REVERT: c 17 VAL cc_start: 0.8341 (p) cc_final: 0.8119 (m) REVERT: c 290 TYR cc_start: 0.5704 (m-10) cc_final: 0.3915 (m-10) REVERT: c 323 PHE cc_start: 0.7876 (m-10) cc_final: 0.7569 (m-80) REVERT: c 370 ILE cc_start: 0.6941 (mt) cc_final: 0.6228 (tt) REVERT: c 400 TYR cc_start: 0.6650 (m-10) cc_final: 0.6293 (m-80) REVERT: c 444 ILE cc_start: 0.8296 (mm) cc_final: 0.8069 (pt) REVERT: c 447 ASP cc_start: 0.6201 (m-30) cc_final: 0.5832 (p0) REVERT: c 449 ASN cc_start: 0.7964 (m-40) cc_final: 0.6986 (p0) REVERT: A 46 THR cc_start: 0.6856 (p) cc_final: 0.6580 (t) REVERT: A 134 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8095 (mtmm) REVERT: A 253 MET cc_start: 0.5327 (mmm) cc_final: 0.5017 (mmm) REVERT: A 519 PHE cc_start: 0.7669 (t80) cc_final: 0.7275 (t80) REVERT: A 646 LYS cc_start: 0.2500 (tttt) cc_final: 0.2234 (mmmt) REVERT: A 649 GLU cc_start: 0.5517 (mt-10) cc_final: 0.5090 (tp30) REVERT: A 728 PHE cc_start: 0.6284 (m-80) cc_final: 0.5072 (t80) REVERT: A 752 TYR cc_start: 0.7661 (m-10) cc_final: 0.7452 (m-80) REVERT: A 755 MET cc_start: 0.7768 (mmm) cc_final: 0.7532 (mmt) REVERT: A 852 LYS cc_start: 0.7560 (ptmt) cc_final: 0.7352 (pttp) REVERT: A 882 SER cc_start: 0.7249 (m) cc_final: 0.6770 (t) outliers start: 1 outliers final: 1 residues processed: 522 average time/residue: 0.1572 time to fit residues: 121.4154 Evaluate side-chains 235 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.1980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 200 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 11 GLN a 174 ASN a 182 HIS a 291 GLN a 321 ASN a 326 HIS b 175 GLN b 257 ASN c 36 GLN c 326 HIS A 91 GLN A 187 ASN A 560 GLN A 562 ASN A 854 ASN A 887 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.154221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134718 restraints weight = 38272.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135548 restraints weight = 40121.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136533 restraints weight = 29714.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136500 restraints weight = 22007.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136614 restraints weight = 21480.422| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19133 Z= 0.167 Angle : 0.662 8.519 25900 Z= 0.368 Chirality : 0.045 0.189 2909 Planarity : 0.005 0.044 3339 Dihedral : 5.370 35.593 2519 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.16 % Allowed : 7.86 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.17), residues: 2319 helix: 1.36 (0.18), residues: 816 sheet: 0.31 (0.31), residues: 236 loop : -0.69 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 38 TYR 0.018 0.002 TYR b 114 PHE 0.031 0.002 PHE b 117 TRP 0.011 0.001 TRP b 127 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (19127) covalent geometry : angle 0.66174 / 0.37 (25888) SS BOND : bond 0.00394 / 0.20 ( 6) SS BOND : angle 1.57924 / 1.04 ( 12) hydrogen bonds : bond 0.06040 / 4.06 ( 768) hydrogen bonds : angle 5.28758 / 3.68 ( 2169) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 278 GLN cc_start: 0.6892 (pp30) cc_final: 0.6649 (mt0) REVERT: a 430 GLN cc_start: 0.4754 (mm-40) cc_final: 0.4401 (pt0) REVERT: b 103 HIS cc_start: 0.6609 (m90) cc_final: 0.5963 (m-70) REVERT: b 155 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7424 (tp) REVERT: c 100 ASP cc_start: 0.7513 (m-30) cc_final: 0.7037 (p0) REVERT: c 130 VAL cc_start: 0.6498 (p) cc_final: 0.5577 (p) REVERT: c 221 GLN cc_start: 0.6582 (tt0) cc_final: 0.5780 (tm-30) REVERT: c 290 TYR cc_start: 0.6076 (m-10) cc_final: 0.3371 (m-10) REVERT: c 400 TYR cc_start: 0.6645 (m-10) cc_final: 0.6420 (m-80) REVERT: c 449 ASN cc_start: 0.7779 (m-40) cc_final: 0.6691 (p0) REVERT: A 32 TYR cc_start: 0.7036 (m-10) cc_final: 0.6623 (m-80) REVERT: A 46 THR cc_start: 0.6789 (p) cc_final: 0.6483 (t) REVERT: A 134 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7962 (mtpt) REVERT: A 253 MET cc_start: 0.5260 (mmm) cc_final: 0.4578 (mmm) REVERT: A 641 TYR cc_start: 0.7092 (m-10) cc_final: 0.6702 (m-10) REVERT: A 725 LYS cc_start: 0.7272 (tmmt) cc_final: 0.6672 (ttpt) REVERT: A 883 MET cc_start: 0.7793 (mmm) cc_final: 0.7509 (mmp) outliers start: 45 outliers final: 21 residues processed: 302 average time/residue: 0.1286 time to fit residues: 61.7035 Evaluate side-chains 201 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 GLU Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain a residue 332 VAL Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 155 LEU Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 422 SER Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain c residue 348 SER Chi-restraints excluded: chain c residue 354 THR Chi-restraints excluded: chain c residue 356 VAL Chi-restraints excluded: chain c residue 467 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 902 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 197 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 211 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 291 GLN a 321 ASN a 326 HIS a 375 HIS b 125 ASN b 375 HIS A 560 GLN A 608 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.148947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130081 restraints weight = 38974.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129762 restraints weight = 47130.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130920 restraints weight = 41236.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131206 restraints weight = 29791.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131443 restraints weight = 27989.753| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19133 Z= 0.161 Angle : 0.615 7.538 25900 Z= 0.341 Chirality : 0.045 0.174 2909 Planarity : 0.004 0.046 3339 Dihedral : 5.187 35.071 2519 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.54 % Allowed : 10.16 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.17), residues: 2319 helix: 1.49 (0.19), residues: 824 sheet: -0.04 (0.31), residues: 230 loop : -1.06 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 38 TYR 0.025 0.002 TYR a 101 PHE 0.028 0.002 PHE b 117 TRP 0.012 0.002 TRP c 294 HIS 0.009 0.001 HIS c 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (19127) covalent geometry : angle 0.61433 / 0.34 (25888) SS BOND : bond 0.00345 / 0.21 ( 6) SS BOND : angle 1.12143 / 0.80 ( 12) hydrogen bonds : bond 0.05948 / 4.02 ( 768) hydrogen bonds : angle 4.99228 / 3.45 ( 2169) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: a 82 ARG cc_start: 0.6663 (mtm110) cc_final: 0.6338 (mtt90) REVERT: a 83 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5692 (mt-10) REVERT: a 101 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: a 278 GLN cc_start: 0.6924 (pp30) cc_final: 0.6586 (mt0) REVERT: b 103 HIS cc_start: 0.6772 (m90) cc_final: 0.6454 (m-70) REVERT: c 100 ASP cc_start: 0.7641 (m-30) cc_final: 0.7406 (p0) REVERT: c 221 GLN cc_start: 0.6285 (tt0) cc_final: 0.5503 (tm-30) REVERT: c 238 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.6325 (t0) REVERT: c 323 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: c 458 GLN cc_start: 0.4608 (tp-100) cc_final: 0.4359 (tp-100) REVERT: A 31 ARG cc_start: 0.5615 (ptt180) cc_final: 0.4987 (mtp180) REVERT: A 32 TYR cc_start: 0.6946 (m-10) cc_final: 0.6330 (m-80) REVERT: A 46 THR cc_start: 0.6691 (p) cc_final: 0.6343 (t) REVERT: A 158 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 253 MET cc_start: 0.5130 (mmm) cc_final: 0.4792 (mmm) REVERT: A 498 ARG cc_start: 0.7226 (mtp85) cc_final: 0.6934 (mtp85) REVERT: A 522 LYS cc_start: 0.7165 (ptmt) cc_final: 0.6899 (ttpp) REVERT: A 725 LYS cc_start: 0.7433 (tmmt) cc_final: 0.6662 (ttpt) outliers start: 53 outliers final: 36 residues processed: 250 average time/residue: 0.1353 time to fit residues: 53.3493 Evaluate side-chains 208 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 83 GLU Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 101 TYR Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 109 ASP Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 175 GLN Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain a residue 400 TYR Chi-restraints excluded: chain a residue 487 ILE Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 190 VAL Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 446 THR Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 301 THR Chi-restraints excluded: chain c residue 317 LEU Chi-restraints excluded: chain c residue 323 PHE Chi-restraints excluded: chain c residue 335 SER Chi-restraints excluded: chain c residue 348 SER Chi-restraints excluded: chain c residue 354 THR Chi-restraints excluded: chain c residue 367 LEU Chi-restraints excluded: chain c residue 416 SER Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 752 TYR Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 902 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 94 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN a 326 HIS a 343 HIS a 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127706 restraints weight = 39277.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127123 restraints weight = 46824.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128366 restraints weight = 40585.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128580 restraints weight = 29678.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128640 restraints weight = 28636.902| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19133 Z= 0.163 Angle : 0.600 9.206 25900 Z= 0.329 Chirality : 0.045 0.156 2909 Planarity : 0.004 0.050 3339 Dihedral : 5.222 35.066 2519 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.36 % Allowed : 10.98 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.17), residues: 2319 helix: 1.56 (0.19), residues: 815 sheet: -0.13 (0.31), residues: 227 loop : -1.36 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 38 TYR 0.019 0.002 TYR a 114 PHE 0.027 0.002 PHE b 117 TRP 0.013 0.002 TRP b 127 HIS 0.007 0.001 HIS c 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (19127) covalent geometry : angle 0.59943 / 0.33 (25888) SS BOND : bond 0.00332 / 0.18 ( 6) SS BOND : angle 1.18650 / 0.91 ( 12) hydrogen bonds : bond 0.05661 / 3.79 ( 768) hydrogen bonds : angle 4.88557 / 3.37 ( 2169) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 196 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 175 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6144 (mt0) REVERT: b 187 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7925 (mp) REVERT: c 61 THR cc_start: 0.7140 (p) cc_final: 0.6557 (t) REVERT: c 221 GLN cc_start: 0.6107 (tt0) cc_final: 0.5415 (tm-30) REVERT: c 245 MET cc_start: 0.6448 (tpp) cc_final: 0.5755 (ttm) REVERT: c 323 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: c 463 GLU cc_start: 0.6883 (mp0) cc_final: 0.6620 (mp0) REVERT: A 14 MET cc_start: -0.0121 (tmm) cc_final: -0.0443 (tmm) REVERT: A 31 ARG cc_start: 0.5405 (ptt180) cc_final: 0.4923 (mtm110) REVERT: A 32 TYR cc_start: 0.6984 (m-10) cc_final: 0.6351 (m-80) REVERT: A 130 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (tt) REVERT: A 253 MET cc_start: 0.5227 (mmm) cc_final: 0.4878 (mmm) REVERT: A 261 PHE cc_start: 0.6072 (t80) cc_final: 0.5847 (t80) REVERT: A 521 MET cc_start: 0.8532 (tpp) cc_final: 0.7756 (tpp) REVERT: A 523 PHE cc_start: 0.7220 (m-10) cc_final: 0.6944 (m-10) REVERT: A 541 LEU cc_start: 0.8094 (tp) cc_final: 0.7833 (tp) outliers start: 70 outliers final: 49 residues processed: 250 average time/residue: 0.1345 time to fit residues: 53.3867 Evaluate side-chains 221 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 109 ASP Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 158 GLU Chi-restraints excluded: chain a residue 175 GLN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain a residue 400 TYR Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 458 GLN Chi-restraints excluded: chain a residue 482 VAL Chi-restraints excluded: chain a residue 487 ILE Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 117 PHE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 190 VAL Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 422 SER Chi-restraints excluded: chain b residue 446 THR Chi-restraints excluded: chain c residue 210 THR Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain c residue 265 VAL Chi-restraints excluded: chain c residue 301 THR Chi-restraints excluded: chain c residue 317 LEU Chi-restraints excluded: chain c residue 323 PHE Chi-restraints excluded: chain c residue 354 THR Chi-restraints excluded: chain c residue 356 VAL Chi-restraints excluded: chain c residue 367 LEU Chi-restraints excluded: chain c residue 416 SER Chi-restraints excluded: chain c residue 467 ILE Chi-restraints excluded: chain c residue 471 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 903 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 94 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 219 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 chunk 156 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN a 326 HIS A 69 ASN ** A 149 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 = 0.3913 r_free = 0.3913 target = 0.147156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128029 restraints weight = 38997.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127442 restraints weight = 46321.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128594 restraints weight = 40388.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128947 restraints weight = 29726.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129242 restraints weight = 27288.566| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19133 Z= 0.133 Angle : 0.546 6.978 25900 Z= 0.302 Chirality : 0.043 0.152 2909 Planarity : 0.004 0.051 3339 Dihedral : 5.015 34.577 2519 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.16 % Allowed : 12.66 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2319 helix: 1.72 (0.19), residues: 810 sheet: -0.02 (0.33), residues: 209 loop : -1.40 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.021 0.002 TYR a 101 PHE 0.026 0.002 PHE c 480 TRP 0.012 0.001 TRP b 127 HIS 0.006 0.001 HIS c 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (19127) covalent geometry : angle 0.54502 / 0.30 (25888) SS BOND : bond 0.00839 / 0.42 ( 6) SS BOND : angle 1.24798 / 0.90 ( 12) hydrogen bonds : bond 0.05200 / 3.50 ( 768) hydrogen bonds : angle 4.73011 / 3.25 ( 2169) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 184 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: a 101 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: a 139 ASP cc_start: 0.7198 (t0) cc_final: 0.6942 (t0) REVERT: b 103 HIS cc_start: 0.6468 (m90) cc_final: 0.6266 (m170) REVERT: c 221 GLN cc_start: 0.6149 (tt0) cc_final: 0.5324 (tm-30) REVERT: c 238 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6467 (t0) REVERT: c 245 MET cc_start: 0.6440 (tpp) cc_final: 0.5824 (ttm) REVERT: c 323 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: c 463 GLU cc_start: 0.6835 (mp0) cc_final: 0.6617 (mp0) REVERT: A 31 ARG cc_start: 0.5445 (ptt180) cc_final: 0.4802 (mtp180) REVERT: A 32 TYR cc_start: 0.6991 (m-10) cc_final: 0.6338 (m-80) REVERT: A 130 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7887 (tt) REVERT: A 261 PHE cc_start: 0.6103 (t80) cc_final: 0.5854 (t80) REVERT: A 521 MET cc_start: 0.8617 (tpp) cc_final: 0.7774 (tpp) outliers start: 66 outliers final: 47 residues processed: 229 average time/residue: 0.1277 time to fit residues: 47.0427 Evaluate side-chains 221 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 101 TYR Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 109 ASP Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 158 GLU Chi-restraints excluded: chain a residue 175 GLN Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain a residue 400 TYR Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 482 VAL Chi-restraints excluded: chain a residue 487 ILE Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 117 PHE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 155 LEU Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 190 VAL Chi-restraints excluded: chain b residue 230 THR Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 422 SER Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 210 THR Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 265 VAL Chi-restraints excluded: chain c residue 301 THR Chi-restraints excluded: chain c residue 323 PHE Chi-restraints excluded: chain c residue 335 SER Chi-restraints excluded: chain c residue 354 THR Chi-restraints excluded: chain c residue 367 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 902 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 134 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 61 optimal weight: 0.0070 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN a 326 HIS b 477 ASN A 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.148017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128841 restraints weight = 38741.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128401 restraints weight = 43968.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129179 restraints weight = 37742.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129689 restraints weight = 29763.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129741 restraints weight = 26864.845| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19133 Z= 0.115 Angle : 0.524 7.034 25900 Z= 0.288 Chirality : 0.042 0.165 2909 Planarity : 0.004 0.052 3339 Dihedral : 4.784 34.392 2519 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 3.21 % Allowed : 13.14 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2319 helix: 1.76 (0.19), residues: 823 sheet: -0.11 (0.33), residues: 222 loop : -1.41 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.020 0.001 TYR a 101 PHE 0.027 0.001 PHE c 480 TRP 0.014 0.001 TRP A 386 HIS 0.008 0.001 HIS a 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (19127) covalent geometry : angle 0.52368 / 0.29 (25888) SS BOND : bond 0.00458 / 0.23 ( 6) SS BOND : angle 0.97408 / 0.71 ( 12) hydrogen bonds : bond 0.04769 / 3.21 ( 768) hydrogen bonds : angle 4.60322 / 3.16 ( 2169) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: a 101 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: a 431 LYS cc_start: 0.5602 (mmtt) cc_final: 0.5032 (mmtt) REVERT: c 142 ILE cc_start: 0.7876 (mt) cc_final: 0.7641 (mm) REVERT: c 221 GLN cc_start: 0.6050 (tt0) cc_final: 0.5308 (tm-30) REVERT: c 238 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6500 (t0) REVERT: c 245 MET cc_start: 0.6320 (tpp) cc_final: 0.5825 (ttm) REVERT: c 323 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: c 425 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7482 (p) REVERT: c 463 GLU cc_start: 0.7118 (mp0) cc_final: 0.6907 (mp0) REVERT: A 32 TYR cc_start: 0.7005 (m-10) cc_final: 0.6574 (m-80) REVERT: A 130 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7878 (tt) REVERT: A 261 PHE cc_start: 0.6050 (t80) cc_final: 0.5766 (t80) REVERT: A 458 PHE cc_start: 0.4174 (OUTLIER) cc_final: 0.1566 (p90) REVERT: A 521 MET cc_start: 0.8572 (tpp) cc_final: 0.8072 (tpp) REVERT: A 541 LEU cc_start: 0.8022 (tp) cc_final: 0.7677 (tp) REVERT: A 733 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6959 (mt-10) outliers start: 67 outliers final: 46 residues processed: 240 average time/residue: 0.1306 time to fit residues: 49.9808 Evaluate side-chains 230 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 101 TYR Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 158 GLU Chi-restraints excluded: chain a residue 175 GLN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 326 HIS Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain a residue 400 TYR Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 482 VAL Chi-restraints excluded: chain a residue 487 ILE Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 117 PHE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 190 VAL Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 422 SER Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 159 THR Chi-restraints excluded: chain c residue 210 THR Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 301 THR Chi-restraints excluded: chain c residue 317 LEU Chi-restraints excluded: chain c residue 323 PHE Chi-restraints excluded: chain c residue 367 LEU Chi-restraints excluded: chain c residue 425 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 923 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 220 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 218 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 226 optimal weight: 0.5980 chunk 188 optimal weight: 0.0070 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 25 GLN a 108 ASN a 291 GLN a 326 HIS b 103 HIS A 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.150312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130997 restraints weight = 38821.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130595 restraints weight = 41139.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131654 restraints weight = 36033.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131904 restraints weight = 27569.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132000 restraints weight = 25162.132| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19133 Z= 0.110 Angle : 0.517 7.029 25900 Z= 0.283 Chirality : 0.042 0.217 2909 Planarity : 0.004 0.051 3339 Dihedral : 4.640 34.268 2519 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 2.92 % Allowed : 13.66 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2319 helix: 1.79 (0.19), residues: 825 sheet: -0.03 (0.33), residues: 223 loop : -1.38 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.020 0.001 TYR a 101 PHE 0.026 0.001 PHE c 480 TRP 0.017 0.001 TRP A 386 HIS 0.008 0.001 HIS a 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (19127) covalent geometry : angle 0.51640 / 0.28 (25888) SS BOND : bond 0.00400 / 0.21 ( 6) SS BOND : angle 0.83867 / 0.63 ( 12) hydrogen bonds : bond 0.04534 / 3.06 ( 768) hydrogen bonds : angle 4.54957 / 3.13 ( 2169) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 101 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: a 326 HIS cc_start: 0.7010 (OUTLIER) cc_final: 0.6632 (t70) REVERT: b 175 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.5864 (mt0) REVERT: c 142 ILE cc_start: 0.7699 (mt) cc_final: 0.7477 (mm) REVERT: c 221 GLN cc_start: 0.5975 (tt0) cc_final: 0.5214 (tm-30) REVERT: c 238 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6700 (t0) REVERT: c 245 MET cc_start: 0.6187 (tpp) cc_final: 0.5839 (ttm) REVERT: c 323 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: c 425 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7436 (p) REVERT: c 444 ILE cc_start: 0.8995 (mm) cc_final: 0.8364 (pt) REVERT: c 463 GLU cc_start: 0.7150 (mp0) cc_final: 0.6933 (mp0) REVERT: A 31 ARG cc_start: 0.7002 (ptm160) cc_final: 0.5936 (mtp180) REVERT: A 32 TYR cc_start: 0.6957 (m-10) cc_final: 0.6344 (m-80) REVERT: A 74 ASP cc_start: 0.5794 (OUTLIER) cc_final: 0.5409 (t0) REVERT: A 261 PHE cc_start: 0.6025 (t80) cc_final: 0.5763 (t80) REVERT: A 458 PHE cc_start: 0.4054 (OUTLIER) cc_final: 0.1475 (p90) REVERT: A 521 MET cc_start: 0.8598 (tpp) cc_final: 0.8115 (tpp) outliers start: 61 outliers final: 43 residues processed: 225 average time/residue: 0.1235 time to fit residues: 44.6832 Evaluate side-chains 223 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 101 TYR Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 158 GLU Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 326 HIS Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain a residue 400 TYR Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 482 VAL Chi-restraints excluded: chain a residue 487 ILE Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 155 LEU Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 190 VAL Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 159 THR Chi-restraints excluded: chain c residue 210 THR Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 301 THR Chi-restraints excluded: chain c residue 317 LEU Chi-restraints excluded: chain c residue 323 PHE Chi-restraints excluded: chain c residue 335 SER Chi-restraints excluded: chain c residue 354 THR Chi-restraints excluded: chain c residue 367 LEU Chi-restraints excluded: chain c residue 425 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 923 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 7 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN a 326 HIS b 103 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127019 restraints weight = 39183.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126043 restraints weight = 45035.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126863 restraints weight = 41327.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127487 restraints weight = 31528.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127471 restraints weight = 28865.354| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19133 Z= 0.145 Angle : 0.566 9.203 25900 Z= 0.309 Chirality : 0.043 0.161 2909 Planarity : 0.004 0.053 3339 Dihedral : 4.832 34.208 2519 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 2.92 % Allowed : 14.09 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2319 helix: 1.70 (0.19), residues: 824 sheet: -0.14 (0.32), residues: 221 loop : -1.49 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 38 TYR 0.021 0.002 TYR a 101 PHE 0.026 0.002 PHE c 480 TRP 0.012 0.002 TRP A 386 HIS 0.016 0.001 HIS a 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (19127) covalent geometry : angle 0.56573 / 0.31 (25888) SS BOND : bond 0.00442 / 0.23 ( 6) SS BOND : angle 1.03724 / 0.76 ( 12) hydrogen bonds : bond 0.05207 / 3.50 ( 768) hydrogen bonds : angle 4.66857 / 3.21 ( 2169) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 101 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: a 142 ILE cc_start: 0.7626 (mp) cc_final: 0.7418 (mt) REVERT: a 438 THR cc_start: 0.6845 (p) cc_final: 0.6643 (p) REVERT: b 175 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.5953 (mt0) REVERT: c 221 GLN cc_start: 0.5916 (tt0) cc_final: 0.5142 (tm-30) REVERT: c 238 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6548 (t0) REVERT: c 245 MET cc_start: 0.6306 (tpp) cc_final: 0.5923 (ttm) REVERT: c 323 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: c 425 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7391 (p) REVERT: c 444 ILE cc_start: 0.9043 (mm) cc_final: 0.8418 (pt) REVERT: c 463 GLU cc_start: 0.7145 (mp0) cc_final: 0.6943 (mp0) REVERT: A 32 TYR cc_start: 0.6768 (m-10) cc_final: 0.6563 (m-80) REVERT: A 74 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5619 (t0) REVERT: A 261 PHE cc_start: 0.5849 (t80) cc_final: 0.5622 (t80) REVERT: A 458 PHE cc_start: 0.4339 (OUTLIER) cc_final: 0.1613 (p90) REVERT: A 521 MET cc_start: 0.8596 (tpp) cc_final: 0.8083 (tpp) REVERT: A 541 LEU cc_start: 0.8210 (tp) cc_final: 0.7935 (tp) outliers start: 61 outliers final: 49 residues processed: 219 average time/residue: 0.1248 time to fit residues: 44.0874 Evaluate side-chains 226 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 101 TYR Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 109 ASP Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 158 GLU Chi-restraints excluded: chain a residue 175 GLN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 326 HIS Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain a residue 400 TYR Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 482 VAL Chi-restraints excluded: chain a residue 487 ILE Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 155 LEU Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 190 VAL Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 422 SER Chi-restraints excluded: chain c residue 159 THR Chi-restraints excluded: chain c residue 210 THR Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 301 THR Chi-restraints excluded: chain c residue 317 LEU Chi-restraints excluded: chain c residue 323 PHE Chi-restraints excluded: chain c residue 335 SER Chi-restraints excluded: chain c residue 354 THR Chi-restraints excluded: chain c residue 367 LEU Chi-restraints excluded: chain c residue 425 THR Chi-restraints excluded: chain c residue 472 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 923 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 107 optimal weight: 1.9990 chunk 180 optimal weight: 0.0170 chunk 191 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 129 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 162 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN ** a 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126871 restraints weight = 38933.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126520 restraints weight = 42336.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127476 restraints weight = 36590.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127864 restraints weight = 28466.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128005 restraints weight = 25744.534| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19133 Z= 0.121 Angle : 0.539 10.624 25900 Z= 0.294 Chirality : 0.042 0.156 2909 Planarity : 0.004 0.055 3339 Dihedral : 4.725 34.454 2519 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 3.02 % Allowed : 14.43 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2319 helix: 1.77 (0.19), residues: 823 sheet: -0.07 (0.33), residues: 223 loop : -1.51 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.020 0.001 TYR a 101 PHE 0.027 0.001 PHE c 480 TRP 0.012 0.001 TRP A 386 HIS 0.009 0.001 HIS a 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (19127) covalent geometry : angle 0.53861 / 0.29 (25888) SS BOND : bond 0.00527 / 0.32 ( 6) SS BOND : angle 0.91832 / 0.70 ( 12) hydrogen bonds : bond 0.04831 / 3.25 ( 768) hydrogen bonds : angle 4.61643 / 3.17 ( 2169) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 101 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: b 175 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.5897 (mt0) REVERT: c 221 GLN cc_start: 0.5902 (tt0) cc_final: 0.5147 (tm-30) REVERT: c 238 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6579 (t0) REVERT: c 245 MET cc_start: 0.6218 (tpp) cc_final: 0.5867 (ttm) REVERT: c 323 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: c 444 ILE cc_start: 0.9037 (mm) cc_final: 0.8408 (pt) REVERT: A 32 TYR cc_start: 0.6768 (m-10) cc_final: 0.6552 (m-80) REVERT: A 74 ASP cc_start: 0.5829 (OUTLIER) cc_final: 0.5504 (t0) REVERT: A 261 PHE cc_start: 0.5720 (t80) cc_final: 0.5455 (t80) REVERT: A 372 ASP cc_start: 0.4329 (m-30) cc_final: 0.3818 (p0) REVERT: A 458 PHE cc_start: 0.4228 (OUTLIER) cc_final: 0.1764 (p90) REVERT: A 521 MET cc_start: 0.8571 (tpp) cc_final: 0.8103 (tpp) REVERT: A 541 LEU cc_start: 0.8171 (tp) cc_final: 0.7890 (tp) outliers start: 63 outliers final: 48 residues processed: 227 average time/residue: 0.1231 time to fit residues: 45.1284 Evaluate side-chains 227 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 101 TYR Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 109 ASP Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 158 GLU Chi-restraints excluded: chain a residue 175 GLN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain a residue 400 TYR Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 482 VAL Chi-restraints excluded: chain a residue 487 ILE Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 155 LEU Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 190 VAL Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain c residue 159 THR Chi-restraints excluded: chain c residue 210 THR Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 301 THR Chi-restraints excluded: chain c residue 317 LEU Chi-restraints excluded: chain c residue 323 PHE Chi-restraints excluded: chain c residue 335 SER Chi-restraints excluded: chain c residue 354 THR Chi-restraints excluded: chain c residue 356 VAL Chi-restraints excluded: chain c residue 367 LEU Chi-restraints excluded: chain c residue 472 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 923 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 159 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 207 optimal weight: 0.0040 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 222 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN a 326 HIS b 103 HIS c 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126491 restraints weight = 38966.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126287 restraints weight = 42220.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127652 restraints weight = 35576.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127645 restraints weight = 26386.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127784 restraints weight = 25996.187| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19133 Z= 0.133 Angle : 0.557 11.346 25900 Z= 0.303 Chirality : 0.043 0.159 2909 Planarity : 0.004 0.055 3339 Dihedral : 4.761 34.292 2519 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 2.88 % Allowed : 14.62 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2319 helix: 1.73 (0.19), residues: 823 sheet: -0.16 (0.33), residues: 221 loop : -1.56 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 498 TYR 0.022 0.002 TYR b 101 PHE 0.026 0.001 PHE c 480 TRP 0.016 0.001 TRP A 386 HIS 0.005 0.001 HIS c 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (19127) covalent geometry : angle 0.55678 / 0.30 (25888) SS BOND : bond 0.00407 / 0.20 ( 6) SS BOND : angle 1.03514 / 0.81 ( 12) hydrogen bonds : bond 0.04978 / 3.35 ( 768) hydrogen bonds : angle 4.64882 / 3.19 ( 2169) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: a 101 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: a 326 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6833 (t70) REVERT: a 431 LYS cc_start: 0.6269 (mmtt) cc_final: 0.5852 (mmtt) REVERT: b 175 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.5920 (mt0) REVERT: c 144 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6958 (mt0) REVERT: c 221 GLN cc_start: 0.5869 (tt0) cc_final: 0.5329 (tm-30) REVERT: c 238 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6579 (t0) REVERT: c 245 MET cc_start: 0.6218 (tpp) cc_final: 0.5891 (ttm) REVERT: c 323 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: c 444 ILE cc_start: 0.9064 (mm) cc_final: 0.8443 (pt) REVERT: A 32 TYR cc_start: 0.6755 (m-10) cc_final: 0.6541 (m-80) REVERT: A 74 ASP cc_start: 0.5913 (OUTLIER) cc_final: 0.5144 (t0) REVERT: A 261 PHE cc_start: 0.5726 (t80) cc_final: 0.5483 (t80) REVERT: A 372 ASP cc_start: 0.4339 (m-30) cc_final: 0.3817 (p0) REVERT: A 458 PHE cc_start: 0.4431 (OUTLIER) cc_final: 0.2043 (p90) REVERT: A 521 MET cc_start: 0.8614 (tpp) cc_final: 0.8106 (tpp) REVERT: A 541 LEU cc_start: 0.8206 (tp) cc_final: 0.7933 (tp) outliers start: 60 outliers final: 48 residues processed: 216 average time/residue: 0.1269 time to fit residues: 44.2190 Evaluate side-chains 225 residues out of total 2089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 101 TYR Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 109 ASP Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 158 GLU Chi-restraints excluded: chain a residue 175 GLN Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 326 HIS Chi-restraints excluded: chain a residue 384 THR Chi-restraints excluded: chain a residue 400 TYR Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 482 VAL Chi-restraints excluded: chain a residue 487 ILE Chi-restraints excluded: chain b residue 22 THR Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 155 LEU Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 190 VAL Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain b residue 407 LEU Chi-restraints excluded: chain b residue 422 SER Chi-restraints excluded: chain c residue 159 THR Chi-restraints excluded: chain c residue 210 THR Chi-restraints excluded: chain c residue 225 LEU Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 301 THR Chi-restraints excluded: chain c residue 317 LEU Chi-restraints excluded: chain c residue 323 PHE Chi-restraints excluded: chain c residue 335 SER Chi-restraints excluded: chain c residue 354 THR Chi-restraints excluded: chain c residue 356 VAL Chi-restraints excluded: chain c residue 367 LEU Chi-restraints excluded: chain c residue 472 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 923 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 77 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 219 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 ASN a 326 HIS b 103 HIS A 380 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124982 restraints weight = 39366.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124513 restraints weight = 42210.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125928 restraints weight = 36936.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126028 restraints weight = 27400.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126189 restraints weight = 25325.255| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19133 Z= 0.164 Angle : 0.597 10.853 25900 Z= 0.325 Chirality : 0.044 0.203 2909 Planarity : 0.004 0.057 3339 Dihedral : 4.941 34.136 2519 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 2.83 % Allowed : 14.67 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2319 helix: 1.60 (0.18), residues: 824 sheet: -0.24 (0.33), residues: 221 loop : -1.62 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 498 TYR 0.024 0.002 TYR b 101 PHE 0.026 0.002 PHE c 480 TRP 0.016 0.002 TRP A 386 HIS 0.010 0.001 HIS a 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (19127) covalent geometry : angle 0.59621 / 0.32 (25888) SS BOND : bond 0.00435 / 0.22 ( 6) SS BOND : angle 1.15110 / 0.88 ( 12) hydrogen bonds : bond 0.05404 / 3.64 ( 768) hydrogen bonds : angle 4.73732 / 3.25 ( 2169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3347.85 seconds wall clock time: 58 minutes 34.78 seconds (3514.78 seconds total)