Starting phenix.real_space_refine on Mon Aug 10 07:26:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gcg_51229/08_2026/9gcg_51229.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gcg_51229/08_2026/9gcg_51229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gcg_51229/08_2026/9gcg_51229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gcg_51229/08_2026/9gcg_51229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gcg_51229/08_2026/9gcg_51229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gcg_51229/08_2026/9gcg_51229.map" } resolution = 3.43 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 321 5.49 5 S 170 5.16 5 C 26189 2.51 5 N 7716 2.21 5 O 8770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 333 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43167 Number of models: 1 Model: "" Number of chains: 29 Chain: "C" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3412 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 17, 'TRANS': 425} Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3403 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 11, 'TRANS': 427} Chain: "I" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3344 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3453 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "D" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3317 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain breaks: 2 Chain: "F" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3376 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5608 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 28, 'TRANS': 653} Chain breaks: 3 Chain: "H" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 785 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 13, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3277 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 29, 'TRANS': 382} Chain breaks: 2 Chain: "K" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3132 Classifications: {'DNA': 152} Link IDs: {'rna3p': 151} Chain: "L" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3100 Classifications: {'DNA': 152} Link IDs: {'rna3p': 151} Chain: "M" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "O" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "P" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "R" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "S" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 819 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "T" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27289 SG CYS H 309 15.316 62.204 142.227 1.00100.74 S ATOM 27319 SG CYS H 314 14.679 62.330 146.241 1.00 99.08 S ATOM 27444 SG CYS H 330 17.913 63.222 144.347 1.00113.02 S ATOM 27473 SG CYS H 334 16.835 59.833 144.950 1.00126.48 S Time building chain proxies: 9.52, per 1000 atoms: 0.22 Number of scatterers: 43167 At special positions: 0 Unit cell: (137.678, 191.429, 211.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 170 16.00 P 321 15.00 O 8770 8.00 N 7716 7.00 C 26189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 401 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 314 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 309 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 334 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 330 " Number of angles added : 6 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8684 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 38 sheets defined 49.4% alpha, 10.7% beta 120 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.699A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.832A pdb=" N TYR C 102 " --> pdb=" O SER C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 175 through 183 removed outlier: 4.329A pdb=" N SER C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 272 through 289 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 319 removed outlier: 4.397A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.780A pdb=" N HIS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.565A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 432 " --> pdb=" O GLU C 428 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 449 Processing helix chain 'C' and resid 450 through 454 removed outlier: 4.095A pdb=" N TYR C 454 " --> pdb=" O GLN C 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 178 through 185 removed outlier: 3.701A pdb=" N LEU E 182 " --> pdb=" O MET E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 214 removed outlier: 3.863A pdb=" N ARG E 213 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.635A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 4.159A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 removed outlier: 3.520A pdb=" N GLN E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU E 377 " --> pdb=" O ILE E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.811A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.602A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU E 445 " --> pdb=" O GLN E 441 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR E 446 " --> pdb=" O TYR E 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 199 through 207 Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'I' and resid 220 through 222 No H-bonds generated for 'chain 'I' and resid 220 through 222' Processing helix chain 'A' and resid 42 through 58 removed outlier: 4.180A pdb=" N ALA A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.599A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.831A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.606A pdb=" N ALA A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 240 through 249 removed outlier: 4.406A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.764A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.817A pdb=" N HIS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.787A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 4.049A pdb=" N GLN A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.624A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 Processing helix chain 'A' and resid 451 through 454 removed outlier: 4.125A pdb=" N TYR A 454 " --> pdb=" O GLN A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.734A pdb=" N GLU B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.109A pdb=" N MET B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 272 through 289 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.400A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.664A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.785A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 269 through 286 removed outlier: 3.636A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 4.303A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 379 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.832A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 removed outlier: 3.511A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 445 removed outlier: 3.923A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.911A pdb=" N GLN F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 109 removed outlier: 4.004A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 244 through 251 Processing helix chain 'F' and resid 257 through 263 removed outlier: 4.259A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.644A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 4.323A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.515A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 446 removed outlier: 3.559A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR F 446 " --> pdb=" O TYR F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 450 Processing helix chain 'G' and resid 519 through 536 Processing helix chain 'G' and resid 548 through 559 removed outlier: 3.567A pdb=" N LEU G 556 " --> pdb=" O GLN G 552 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS G 559 " --> pdb=" O ALA G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 575 through 577 No H-bonds generated for 'chain 'G' and resid 575 through 577' Processing helix chain 'G' and resid 578 through 590 removed outlier: 3.764A pdb=" N TRP G 582 " --> pdb=" O THR G 578 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS G 583 " --> pdb=" O LEU G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 612 removed outlier: 3.792A pdb=" N ARG G 610 " --> pdb=" O LYS G 606 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE G 611 " --> pdb=" O VAL G 607 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 635 Processing helix chain 'G' and resid 637 through 642 Processing helix chain 'G' and resid 653 through 658 Processing helix chain 'G' and resid 662 through 669 Processing helix chain 'G' and resid 687 through 699 Processing helix chain 'G' and resid 707 through 712 removed outlier: 3.547A pdb=" N GLU G 711 " --> pdb=" O GLU G 707 " (cutoff:3.500A) Processing helix chain 'G' and resid 730 through 740 removed outlier: 4.234A pdb=" N ARG G 734 " --> pdb=" O ASN G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 747 through 752 removed outlier: 4.070A pdb=" N VAL G 751 " --> pdb=" O ILE G 747 " (cutoff:3.500A) Processing helix chain 'G' and resid 768 through 780 Processing helix chain 'G' and resid 809 through 818 Processing helix chain 'G' and resid 819 through 822 Processing helix chain 'G' and resid 841 through 848 Processing helix chain 'G' and resid 849 through 854 Processing helix chain 'G' and resid 854 through 864 removed outlier: 4.208A pdb=" N TRP G 860 " --> pdb=" O SER G 856 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 861 " --> pdb=" O ARG G 857 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 862 " --> pdb=" O ASP G 858 " (cutoff:3.500A) Processing helix chain 'G' and resid 868 through 878 removed outlier: 3.513A pdb=" N HIS G 878 " --> pdb=" O ARG G 874 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 893 Processing helix chain 'G' and resid 897 through 907 Processing helix chain 'G' and resid 908 through 933 removed outlier: 3.649A pdb=" N ARG G 912 " --> pdb=" O GLY G 908 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR G 924 " --> pdb=" O LEU G 920 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG G 925 " --> pdb=" O LYS G 921 " (cutoff:3.500A) Processing helix chain 'G' and resid 958 through 965 Processing helix chain 'G' and resid 967 through 972 removed outlier: 3.687A pdb=" N VAL G 972 " --> pdb=" O LYS G 969 " (cutoff:3.500A) Processing helix chain 'G' and resid 1007 through 1011 removed outlier: 3.884A pdb=" N LEU G1010 " --> pdb=" O PRO G1007 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS G1011 " --> pdb=" O SER G1008 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1007 through 1011' Processing helix chain 'G' and resid 1028 through 1041 Processing helix chain 'G' and resid 1043 through 1053 Processing helix chain 'G' and resid 1054 through 1062 Processing helix chain 'G' and resid 1063 through 1067 Processing helix chain 'G' and resid 1075 through 1079 Processing helix chain 'G' and resid 1094 through 1099 Processing helix chain 'G' and resid 1100 through 1117 removed outlier: 3.700A pdb=" N VAL G1108 " --> pdb=" O TYR G1104 " (cutoff:3.500A) Processing helix chain 'G' and resid 1126 through 1140 removed outlier: 3.557A pdb=" N LEU G1132 " --> pdb=" O ARG G1128 " (cutoff:3.500A) Processing helix chain 'G' and resid 1152 through 1164 removed outlier: 3.681A pdb=" N ARG G1157 " --> pdb=" O ILE G1153 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP G1158 " --> pdb=" O SER G1154 " (cutoff:3.500A) Processing helix chain 'G' and resid 1175 through 1180 Processing helix chain 'G' and resid 1201 through 1209 Processing helix chain 'G' and resid 1230 through 1248 removed outlier: 3.752A pdb=" N ILE G1234 " --> pdb=" O ILE G1230 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU G1243 " --> pdb=" O LYS G1239 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE G1244 " --> pdb=" O GLU G1240 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 233 Processing helix chain 'H' and resid 331 through 342 Processing helix chain 'J' and resid 106 through 121 removed outlier: 3.728A pdb=" N LEU J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR J 115 " --> pdb=" O LEU J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 157 removed outlier: 4.548A pdb=" N CYS J 155 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 175 Processing helix chain 'J' and resid 214 through 230 Processing helix chain 'J' and resid 231 through 237 removed outlier: 3.888A pdb=" N LEU J 234 " --> pdb=" O PRO J 231 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA J 235 " --> pdb=" O GLY J 232 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE J 237 " --> pdb=" O LEU J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 249 removed outlier: 3.976A pdb=" N GLU J 244 " --> pdb=" O SER J 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE J 245 " --> pdb=" O ARG J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 263 removed outlier: 3.851A pdb=" N HIS J 261 " --> pdb=" O VAL J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 273 removed outlier: 4.032A pdb=" N ASN J 271 " --> pdb=" O ASP J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 451 Processing helix chain 'J' and resid 452 through 456 removed outlier: 3.878A pdb=" N ILE J 455 " --> pdb=" O PRO J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 461 Processing helix chain 'J' and resid 466 through 477 removed outlier: 3.950A pdb=" N GLU J 470 " --> pdb=" O ALA J 466 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 472 " --> pdb=" O ILE J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 488 removed outlier: 3.657A pdb=" N GLU J 485 " --> pdb=" O LYS J 481 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 500 Processing helix chain 'J' and resid 502 through 513 removed outlier: 3.698A pdb=" N GLU J 513 " --> pdb=" O LYS J 509 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 544 Processing helix chain 'J' and resid 555 through 559 Processing helix chain 'M' and resid 45 through 55 removed outlier: 3.908A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.602A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.590A pdb=" N VAL M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.572A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA N 76 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 4.022A pdb=" N GLN N 93 " --> pdb=" O ALA N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 22 removed outlier: 3.603A pdb=" N ARG O 20 " --> pdb=" O SER O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 33 removed outlier: 3.919A pdb=" N ARG O 32 " --> pdb=" O GLY O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 37 Processing helix chain 'O' and resid 44 through 52 removed outlier: 4.094A pdb=" N ALA O 48 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA O 49 " --> pdb=" O GLY O 45 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL O 50 " --> pdb=" O ALA O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 69 Processing helix chain 'O' and resid 70 through 74 Processing helix chain 'P' and resid 37 through 49 removed outlier: 3.952A pdb=" N TYR P 42 " --> pdb=" O SER P 38 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN P 47 " --> pdb=" O LYS P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 85 removed outlier: 3.720A pdb=" N GLY P 60 " --> pdb=" O SER P 56 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG P 79 " --> pdb=" O GLY P 75 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU P 80 " --> pdb=" O GLU P 76 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 101 Processing helix chain 'P' and resid 103 through 123 removed outlier: 3.976A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER P 112 " --> pdb=" O LYS P 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 55 removed outlier: 3.520A pdb=" N ARG Q 52 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 77 removed outlier: 3.896A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 114 removed outlier: 3.520A pdb=" N ALA Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Q 98 " --> pdb=" O GLU Q 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY Q 102 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU Q 109 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS Q 110 " --> pdb=" O ASP Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.729A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG Q 129 " --> pdb=" O GLN Q 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 30 through 42 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.536A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY R 56 " --> pdb=" O GLU R 52 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA R 76 " --> pdb=" O TYR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 35 Processing helix chain 'S' and resid 45 through 62 removed outlier: 3.767A pdb=" N ALA S 49 " --> pdb=" O GLY S 45 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR S 51 " --> pdb=" O THR S 47 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA S 54 " --> pdb=" O VAL S 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE S 55 " --> pdb=" O TYR S 51 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 71 Processing helix chain 'S' and resid 80 through 88 removed outlier: 3.785A pdb=" N LEU S 84 " --> pdb=" O THR S 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU S 86 " --> pdb=" O ARG S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'T' and resid 37 through 49 removed outlier: 3.613A pdb=" N TYR T 42 " --> pdb=" O SER T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 84 removed outlier: 4.007A pdb=" N ILE T 61 " --> pdb=" O LYS T 57 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET T 62 " --> pdb=" O ALA T 58 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 102 removed outlier: 4.053A pdb=" N ALA T 97 " --> pdb=" O GLU T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.788A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR T 119 " --> pdb=" O THR T 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.573A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU C 299 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA C 330 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL C 301 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 142 removed outlier: 6.420A pdb=" N GLY C 160 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU C 138 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE C 158 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N HIS C 156 " --> pdb=" O PRO C 140 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU C 142 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 154 " --> pdb=" O GLU C 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 172 current: chain 'C' and resid 200 through 205 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 200 through 205 current: chain 'E' and resid 158 through 164 removed outlier: 4.368A pdb=" N GLY E 159 " --> pdb=" O LEU E 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 174 current: chain 'E' and resid 201 through 207 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 201 through 207 current: chain 'G' and resid 996 through 1005 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 996 through 1005 current: chain 'H' and resid 283 through 286 Processing sheet with id=AA4, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.331A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AA8, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.551A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 120 through 141 removed outlier: 5.773A pdb=" N VAL A 135 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A 162 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 137 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 156 " --> pdb=" O CYS A 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 172 current: chain 'A' and resid 199 through 206 removed outlier: 5.309A pdb=" N VAL A 221 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG A 205 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 385 through 386 removed outlier: 7.638A pdb=" N ASN A 385 " --> pdb=" O ILE A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.595A pdb=" N ILE B 3 " --> pdb=" O LEU G 762 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR G 764 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU B 5 " --> pdb=" O TYR G 764 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU G1121 " --> pdb=" O ILE G1192 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET G1145 " --> pdb=" O LEU G1173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.377A pdb=" N CYS B 94 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP B 302 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET B 96 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 120 through 143 removed outlier: 8.624A pdb=" N GLY B 133 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR B 163 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 135 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 161 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU B 137 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE B 159 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B 139 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL B 157 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N CYS B 141 " --> pdb=" O SER B 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 172 current: chain 'B' and resid 199 through 206 removed outlier: 5.896A pdb=" N VAL B 221 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG B 205 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.481A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 146 removed outlier: 6.352A pdb=" N THR D 162 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 174 current: chain 'D' and resid 202 through 208 removed outlier: 5.519A pdb=" N VAL D 225 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG D 207 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AC2, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.415A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 235 through 243 Processing sheet with id=AC5, first strand: chain 'F' and resid 224 through 225 removed outlier: 6.406A pdb=" N VAL F 225 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG F 207 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 192 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP F 191 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL F 142 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS F 164 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU F 144 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AC7, first strand: chain 'G' and resid 539 through 540 removed outlier: 6.720A pdb=" N GLY G 539 " --> pdb=" O LEU G 678 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET G 649 " --> pdb=" O LEU G 677 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU G 596 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N SER G 630 " --> pdb=" O LEU G 596 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N TYR G 598 " --> pdb=" O SER G 630 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 831 through 833 removed outlier: 6.872A pdb=" N PHE G 831 " --> pdb=" O THR G1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 838 through 839 removed outlier: 5.995A pdb=" N TYR G 838 " --> pdb=" O TYR G1025 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'J' and resid 61 through 62 Processing sheet with id=AD2, first strand: chain 'J' and resid 65 through 66 Processing sheet with id=AD3, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AD4, first strand: chain 'J' and resid 183 through 188 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 202 through 203 current: chain 'J' and resid 523 through 525 Processing sheet with id=AD5, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.616A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AD7, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AD8, first strand: chain 'O' and resid 100 through 102 Processing sheet with id=AD9, first strand: chain 'Q' and resid 83 through 84 removed outlier: 7.063A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AE2, first strand: chain 'S' and resid 77 through 78 1519 hydrogen bonds defined for protein. 4290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 301 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 13.32 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7145 1.32 - 1.45: 12586 1.45 - 1.58: 23866 1.58 - 1.70: 648 1.70 - 1.83: 281 Bond restraints: 44526 Sorted by residual: bond pdb=" CG HIS O 83 " pdb=" CD2 HIS O 83 " ideal model delta sigma weight residual 1.354 1.280 0.074 1.10e-02 8.26e+03 4.49e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.363 0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" CB ILE D 86 " pdb=" CG1 ILE D 86 " ideal model delta sigma weight residual 1.530 1.407 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.367 0.123 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.369 0.121 2.00e-02 2.50e+03 3.65e+01 ... (remaining 44521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 58604 4.18 - 8.37: 2679 8.37 - 12.55: 130 12.55 - 16.73: 8 16.73 - 20.91: 1 Bond angle restraints: 61422 Sorted by residual: angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 115.92 20.91 1.00e+00 1.00e+00 4.37e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 127.78 12.09 1.00e+00 1.00e+00 1.46e+02 angle pdb=" C5' ATP A 501 " pdb=" O5' ATP A 501 " pdb=" PA ATP A 501 " ideal model delta sigma weight residual 121.27 109.89 11.38 1.00e+00 1.00e+00 1.29e+02 angle pdb=" N LEU O 64 " pdb=" CA LEU O 64 " pdb=" CB LEU O 64 " ideal model delta sigma weight residual 110.49 125.37 -14.88 1.69e+00 3.50e-01 7.75e+01 angle pdb=" CA ASP F 214 " pdb=" CB ASP F 214 " pdb=" CG ASP F 214 " ideal model delta sigma weight residual 112.60 120.41 -7.81 1.00e+00 1.00e+00 6.10e+01 ... (remaining 61417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 24516 34.72 - 69.44: 1748 69.44 - 104.16: 98 104.16 - 138.88: 10 138.88 - 173.60: 4 Dihedral angle restraints: 26376 sinusoidal: 12910 harmonic: 13466 Sorted by residual: dihedral pdb=" O1B ADP J 701 " pdb=" O3A ADP J 701 " pdb=" PB ADP J 701 " pdb=" PA ADP J 701 " ideal model delta sinusoidal sigma weight residual -60.00 88.59 -148.59 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" CA ILE O 55 " pdb=" C ILE O 55 " pdb=" N LEU O 56 " pdb=" CA LEU O 56 " ideal model delta harmonic sigma weight residual 180.00 146.73 33.27 0 5.00e+00 4.00e-02 4.43e+01 dihedral pdb=" CA ASN I 138 " pdb=" C ASN I 138 " pdb=" N ARG I 139 " pdb=" CA ARG I 139 " ideal model delta harmonic sigma weight residual -180.00 -147.30 -32.70 0 5.00e+00 4.00e-02 4.28e+01 ... (remaining 26373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 5377 0.127 - 0.254: 1175 0.254 - 0.381: 147 0.381 - 0.509: 95 0.509 - 0.636: 187 Chirality restraints: 6981 Sorted by residual: chirality pdb=" P DT L -81 " pdb=" OP1 DT L -81 " pdb=" OP2 DT L -81 " pdb=" O5' DT L -81 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA GLU B 342 " pdb=" N GLU B 342 " pdb=" C GLU B 342 " pdb=" CB GLU B 342 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.79e+00 chirality pdb=" P DT K 53 " pdb=" OP1 DT K 53 " pdb=" OP2 DT K 53 " pdb=" O5' DT K 53 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.70e+00 ... (remaining 6978 not shown) Planarity restraints: 6772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 664 " -0.726 9.50e-02 1.11e+02 3.25e-01 6.45e+01 pdb=" NE ARG G 664 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG G 664 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG G 664 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 664 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 314 " 0.637 9.50e-02 1.11e+02 2.87e-01 5.77e+01 pdb=" NE ARG D 314 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG D 314 " -0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG D 314 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 314 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 51 " 0.104 2.00e-02 2.50e+03 5.35e-02 5.73e+01 pdb=" CG TYR O 51 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR O 51 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR O 51 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR O 51 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR O 51 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR O 51 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR O 51 " 0.047 2.00e-02 2.50e+03 ... (remaining 6769 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 59 2.52 - 3.11: 30884 3.11 - 3.71: 66871 3.71 - 4.30: 97425 4.30 - 4.90: 152035 Nonbonded interactions: 347274 Sorted by model distance: nonbonded pdb=" NH2 ARG H 216 " pdb=" OP2 DC L 14 " model vdw 1.921 3.120 nonbonded pdb=" OE1 GLU Q 50 " pdb=" NH1 ARG R 39 " model vdw 2.117 3.120 nonbonded pdb=" OP1 DA L 39 " pdb=" CE LYS O 35 " model vdw 2.221 3.440 nonbonded pdb=" OH TYR S 51 " pdb=" CG PHE T 70 " model vdw 2.240 3.260 nonbonded pdb=" NH2 ARG S 20 " pdb=" O SER T 123 " model vdw 2.261 3.120 ... (remaining 347269 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 12 through 141 or resid 152 through 454)) selection = (chain 'B' and (resid 12 through 141 or resid 152 through 454)) selection = (chain 'C' and (resid 12 through 141 or resid 152 through 454)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) selection = (chain 'F' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) } ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 43 through 133) } ncs_group { reference = (chain 'N' and resid 24 through 102) selection = chain 'R' } ncs_group { reference = (chain 'O' and (resid 13 through 107 or resid 109 through 118)) selection = (chain 'S' and (resid 13 through 107 or resid 109 through 118)) } ncs_group { reference = (chain 'P' and resid 32 through 123) selection = chain 'T' } 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.280 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 52.410 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.012 0.127 44530 Z= 0.749 Angle : 1.931 20.914 61428 Z= 1.179 Chirality : 0.146 0.636 6981 Planarity : 0.021 0.325 6772 Dihedral : 20.539 173.601 17692 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.25 % Favored : 95.25 % Rotamer: Outliers : 1.56 % Allowed : 5.55 % Favored : 92.89 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.19 (0.11), residues: 4615 helix: -1.94 (0.09), residues: 2109 sheet: 0.29 (0.19), residues: 620 loop : -1.25 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.006 ARG R 67 TYR 0.104 0.013 TYR O 51 PHE 0.054 0.011 PHE B 329 TRP 0.050 0.012 TRP G 646 HIS 0.027 0.005 HIS F 245 Details of bonding type rmsd/Z covalent geometry : bond 0.01220 / 0.75 (44526) covalent geometry : angle 1.92906 / 1.18 (61422) hydrogen bonds : bond 0.22403 / 15.34 ( 1820) hydrogen bonds : angle 8.82171 / 6.21 ( 4884) metal coordination : bond 0.02575 / 1.27 ( 4) metal coordination : angle 9.41479 / 4.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 752 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 GLU cc_start: 0.9548 (pm20) cc_final: 0.9287 (tp30) REVERT: E 112 GLU cc_start: 0.9333 (tm-30) cc_final: 0.8953 (tm-30) REVERT: E 178 MET cc_start: 0.8885 (tmm) cc_final: 0.8281 (tmm) REVERT: E 299 ASP cc_start: 0.9402 (t0) cc_final: 0.9134 (t0) REVERT: I 159 ASN cc_start: 0.9583 (m-40) cc_final: 0.9186 (p0) REVERT: A 90 LYS cc_start: 0.9104 (mppt) cc_final: 0.8713 (tttm) REVERT: B 113 MET cc_start: 0.9203 (mmm) cc_final: 0.8925 (tpp) REVERT: B 249 ARG cc_start: 0.9380 (mtp-110) cc_final: 0.9064 (mtt-85) REVERT: D 229 ASP cc_start: 0.9346 (m-30) cc_final: 0.9139 (t70) REVERT: D 231 GLU cc_start: 0.8705 (pm20) cc_final: 0.8490 (pm20) REVERT: D 349 ASP cc_start: 0.9282 (t0) cc_final: 0.8935 (t0) REVERT: D 447 GLN cc_start: 0.9361 (tt0) cc_final: 0.9159 (tp-100) REVERT: F 178 MET cc_start: 0.9468 (tpt) cc_final: 0.9111 (tpp) REVERT: G 737 MET cc_start: 0.9660 (mmm) cc_final: 0.9385 (ptt) REVERT: G 1145 MET cc_start: 0.8446 (ttm) cc_final: 0.8167 (ttp) REVERT: G 1159 MET cc_start: 0.8780 (mmm) cc_final: 0.8332 (mmp) REVERT: G 1168 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8840 (t0) REVERT: H 272 MET cc_start: 0.8607 (mmm) cc_final: 0.8374 (mmt) REVERT: J 51 GLN cc_start: 0.7570 (mt0) cc_final: 0.7267 (tt0) REVERT: J 178 ASN cc_start: 0.8833 (m-40) cc_final: 0.8248 (p0) REVERT: J 440 HIS cc_start: 0.8795 (t-90) cc_final: 0.8552 (t-170) REVERT: J 547 ASP cc_start: 0.9384 (m-30) cc_final: 0.9132 (t0) REVERT: Q 130 ILE cc_start: 0.8704 (mt) cc_final: 0.8502 (tt) REVERT: S 47 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8127 (m) REVERT: S 73 ASP cc_start: 0.8434 (m-30) cc_final: 0.8233 (m-30) outliers start: 62 outliers final: 23 residues processed: 798 average time/residue: 0.3178 time to fit residues: 394.4666 Evaluate side-chains 465 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 440 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 662 SER Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1168 ASP Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 HIS I 146 GLN I 192 GLN A 20 HIS A 34 GLN A 247 ASN A 373 GLN B 34 GLN D 344 HIS F 27 HIS G 580 ASN G 903 ASN ** H 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 ASN J 227 GLN J 272 ASN ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 112 HIS ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 85 GLN ** R 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.105747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.066277 restraints weight = 108556.015| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.66 r_work: 0.2978 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 44530 Z= 0.200 Angle : 0.855 14.602 61428 Z= 0.451 Chirality : 0.054 0.418 6981 Planarity : 0.005 0.076 6772 Dihedral : 23.993 175.992 8572 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.88 % Favored : 96.92 % Rotamer: Outliers : 2.49 % Allowed : 10.68 % Favored : 86.84 % 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: -1.11 (0.12), residues: 4615 helix: -0.50 (0.11), residues: 2110 sheet: 0.15 (0.19), residues: 681 loop : -1.22 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 43 TYR 0.025 0.002 TYR O 51 PHE 0.028 0.002 PHE G 853 TRP 0.019 0.002 TRP G 665 HIS 0.012 0.002 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (44526) covalent geometry : angle 0.85474 / 0.45 (61422) hydrogen bonds : bond 0.07241 / 4.79 ( 1820) hydrogen bonds : angle 4.95331 / 3.50 ( 4884) metal coordination : bond 0.00760 / 0.36 ( 4) metal coordination : angle 3.07041 / 1.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 514 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7878 (tm-30) REVERT: E 178 MET cc_start: 0.8731 (tmm) cc_final: 0.8045 (tmm) REVERT: I 159 ASN cc_start: 0.9097 (m-40) cc_final: 0.8702 (p0) REVERT: I 221 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8894 (mtm180) REVERT: D 313 ASN cc_start: 0.8958 (t0) cc_final: 0.8034 (t0) REVERT: D 349 ASP cc_start: 0.8768 (t0) cc_final: 0.8333 (t0) REVERT: D 442 TYR cc_start: 0.8858 (m-10) cc_final: 0.8610 (m-80) REVERT: F 178 MET cc_start: 0.9209 (tpt) cc_final: 0.8756 (tpp) REVERT: F 231 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: G 526 MET cc_start: 0.8204 (tmm) cc_final: 0.7989 (tmm) REVERT: G 603 HIS cc_start: 0.9256 (m-70) cc_final: 0.9049 (t-170) REVERT: G 688 MET cc_start: 0.9070 (mmm) cc_final: 0.8839 (ppp) REVERT: G 699 MET cc_start: 0.8541 (mmm) cc_final: 0.8283 (mmt) REVERT: G 735 LEU cc_start: 0.9222 (mt) cc_final: 0.8648 (pp) REVERT: G 737 MET cc_start: 0.9272 (mmm) cc_final: 0.8978 (ptt) REVERT: G 810 MET cc_start: 0.8550 (mmm) cc_final: 0.8299 (tpt) REVERT: G 962 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9045 (tt) REVERT: G 1247 MET cc_start: 0.7540 (ptm) cc_final: 0.7067 (ppp) REVERT: H 218 GLU cc_start: 0.8880 (tp30) cc_final: 0.8580 (mm-30) REVERT: H 272 MET cc_start: 0.8211 (mmm) cc_final: 0.7663 (mmm) REVERT: J 503 MET cc_start: 0.9065 (tpt) cc_final: 0.8279 (tpt) REVERT: J 547 ASP cc_start: 0.8382 (m-30) cc_final: 0.8120 (p0) REVERT: M 93 GLN cc_start: 0.9425 (tt0) cc_final: 0.8604 (tt0) REVERT: N 63 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8448 (mt-10) REVERT: N 75 HIS cc_start: 0.8571 (t70) cc_final: 0.8341 (t70) REVERT: N 95 ARG cc_start: 0.8475 (mmt-90) cc_final: 0.7837 (mmm-85) REVERT: O 25 PHE cc_start: 0.9019 (m-10) cc_final: 0.8731 (m-80) REVERT: O 37 ARG cc_start: 0.8844 (mtp85) cc_final: 0.8519 (mmt-90) REVERT: P 43 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8713 (mttt) REVERT: P 89 ILE cc_start: 0.7395 (mm) cc_final: 0.6805 (mp) REVERT: S 37 ARG cc_start: 0.7280 (mmp-170) cc_final: 0.6996 (tpp-160) REVERT: S 69 ASN cc_start: 0.8667 (m-40) cc_final: 0.8418 (t0) REVERT: S 72 LYS cc_start: 0.9061 (mtmm) cc_final: 0.8779 (mtmm) REVERT: S 86 LEU cc_start: 0.9122 (mm) cc_final: 0.8888 (mm) REVERT: T 92 ARG cc_start: 0.8815 (ptm-80) cc_final: 0.8578 (ptm-80) REVERT: T 105 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8880 (pp20) outliers start: 99 outliers final: 41 residues processed: 573 average time/residue: 0.3113 time to fit residues: 284.1983 Evaluate side-chains 467 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 423 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 414 ARG Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 638 VAL Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 962 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 555 LYS Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 109 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 257 optimal weight: 3.9990 chunk 455 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 424 optimal weight: 9.9990 chunk 383 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 415 optimal weight: 50.0000 chunk 242 optimal weight: 0.7980 chunk 342 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 HIS ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN B 156 HIS F 245 HIS ** J 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 112 HIS ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 41 HIS ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.099418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058752 restraints weight = 110704.455| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.75 r_work: 0.2762 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 44530 Z= 0.288 Angle : 0.815 15.465 61428 Z= 0.429 Chirality : 0.051 0.375 6981 Planarity : 0.005 0.063 6772 Dihedral : 23.782 178.526 8549 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 3.39 % Allowed : 12.38 % Favored : 84.23 % 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: -1.00 (0.12), residues: 4615 helix: -0.19 (0.11), residues: 2102 sheet: -0.05 (0.19), residues: 670 loop : -1.34 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 32 TYR 0.061 0.002 TYR N 88 PHE 0.023 0.002 PHE T 70 TRP 0.021 0.002 TRP G 612 HIS 0.009 0.002 HIS O 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 (44526) covalent geometry : angle 0.81373 / 0.43 (61422) hydrogen bonds : bond 0.06999 / 4.74 ( 1820) hydrogen bonds : angle 4.80370 / 3.39 ( 4884) metal coordination : bond 0.01154 / 0.53 ( 4) metal coordination : angle 4.56965 / 2.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 448 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 GLU cc_start: 0.8657 (tm-30) cc_final: 0.7871 (tm-30) REVERT: E 178 MET cc_start: 0.8792 (tmm) cc_final: 0.7863 (tmm) REVERT: E 258 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8891 (tp) REVERT: E 282 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8810 (tt0) REVERT: I 159 ASN cc_start: 0.9233 (m-40) cc_final: 0.8749 (p0) REVERT: I 221 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8880 (mtm180) REVERT: A 370 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: B 156 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.6048 (m170) REVERT: D 135 THR cc_start: 0.8967 (m) cc_final: 0.8510 (p) REVERT: D 168 MET cc_start: 0.8371 (ptp) cc_final: 0.8125 (ptp) REVERT: D 178 MET cc_start: 0.8772 (tpp) cc_final: 0.8549 (tpt) REVERT: D 313 ASN cc_start: 0.8966 (t0) cc_final: 0.8129 (t0) REVERT: D 349 ASP cc_start: 0.8914 (t0) cc_final: 0.8420 (t0) REVERT: F 178 MET cc_start: 0.9085 (tpt) cc_final: 0.8339 (tpp) REVERT: F 231 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: F 303 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8580 (ptp) REVERT: G 526 MET cc_start: 0.8242 (tmm) cc_final: 0.7954 (tmm) REVERT: G 603 HIS cc_start: 0.9367 (m-70) cc_final: 0.9058 (t-170) REVERT: G 699 MET cc_start: 0.8364 (mmm) cc_final: 0.8060 (mmt) REVERT: G 737 MET cc_start: 0.9348 (mmm) cc_final: 0.9041 (ptt) REVERT: G 810 MET cc_start: 0.8541 (mmm) cc_final: 0.8305 (tpt) REVERT: G 1168 ASP cc_start: 0.8730 (m-30) cc_final: 0.8496 (t0) REVERT: G 1247 MET cc_start: 0.7754 (ptm) cc_final: 0.7154 (ppp) REVERT: H 215 LYS cc_start: 0.6254 (tttt) cc_final: 0.5955 (tptt) REVERT: H 272 MET cc_start: 0.8158 (mmm) cc_final: 0.7815 (mmt) REVERT: H 320 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7002 (p90) REVERT: J 503 MET cc_start: 0.8902 (tpt) cc_final: 0.8367 (tpt) REVERT: J 547 ASP cc_start: 0.8603 (m-30) cc_final: 0.8160 (p0) REVERT: M 93 GLN cc_start: 0.9362 (tt0) cc_final: 0.8683 (tt0) REVERT: N 59 LYS cc_start: 0.8596 (tppt) cc_final: 0.8173 (tppt) REVERT: N 63 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8551 (mt-10) REVERT: N 95 ARG cc_start: 0.8488 (mmt-90) cc_final: 0.7607 (mmm-85) REVERT: O 32 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8299 (ttp80) REVERT: P 43 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8597 (mtmm) REVERT: R 77 LYS cc_start: 0.9325 (mmtm) cc_final: 0.9122 (mmtm) REVERT: R 78 ARG cc_start: 0.8945 (ptp-170) cc_final: 0.8024 (ptp-170) REVERT: S 37 ARG cc_start: 0.7323 (mmp-170) cc_final: 0.7005 (mmp-170) REVERT: S 69 ASN cc_start: 0.8727 (m-40) cc_final: 0.8478 (t0) REVERT: S 72 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8563 (mtmm) REVERT: T 47 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8928 (mt0) REVERT: T 92 ARG cc_start: 0.8821 (ptm-80) cc_final: 0.8335 (ptm-80) REVERT: T 105 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8891 (pp20) outliers start: 135 outliers final: 70 residues processed: 536 average time/residue: 0.2802 time to fit residues: 239.4586 Evaluate side-chains 478 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 401 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 555 LYS Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 82 HIS Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain T residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 284 optimal weight: 0.0010 chunk 93 optimal weight: 5.9990 chunk 418 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 473 optimal weight: 8.9990 chunk 373 optimal weight: 7.9990 chunk 351 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 413 optimal weight: 40.0000 chunk 127 optimal weight: 2.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 236 GLN ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 GLN A 34 GLN A 373 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 961 ASN J 130 HIS ** J 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 544 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS O 69 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.100145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.059318 restraints weight = 110503.419| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.77 r_work: 0.2782 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 44530 Z= 0.212 Angle : 0.740 14.663 61428 Z= 0.390 Chirality : 0.049 0.394 6981 Planarity : 0.005 0.070 6772 Dihedral : 23.654 177.911 8548 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.34 % Rotamer: Outliers : 3.37 % Allowed : 13.77 % Favored : 82.87 % 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: -0.78 (0.12), residues: 4615 helix: 0.08 (0.11), residues: 2098 sheet: -0.15 (0.19), residues: 677 loop : -1.26 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 235 TYR 0.036 0.002 TYR E 215 PHE 0.024 0.002 PHE G 853 TRP 0.018 0.001 TRP G 612 HIS 0.029 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (44526) covalent geometry : angle 0.73871 / 0.39 (61422) hydrogen bonds : bond 0.05799 / 3.87 ( 1820) hydrogen bonds : angle 4.48408 / 3.16 ( 4884) metal coordination : bond 0.00834 / 0.39 ( 4) metal coordination : angle 3.53332 / 1.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 441 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7813 (tm-30) REVERT: E 178 MET cc_start: 0.8845 (tmm) cc_final: 0.7883 (tmm) REVERT: E 216 ASP cc_start: 0.6691 (OUTLIER) cc_final: 0.5517 (m-30) REVERT: E 282 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8843 (tt0) REVERT: I 159 ASN cc_start: 0.9229 (m-40) cc_final: 0.8785 (p0) REVERT: I 221 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8887 (mtm180) REVERT: A 34 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8839 (tm-30) REVERT: A 370 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: B 81 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8996 (mm) REVERT: B 108 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8382 (mtpt) REVERT: D 349 ASP cc_start: 0.8898 (t0) cc_final: 0.8451 (t0) REVERT: F 178 MET cc_start: 0.9100 (tpt) cc_final: 0.8523 (tpp) REVERT: F 231 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8218 (tm-30) REVERT: F 303 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8523 (ptp) REVERT: G 526 MET cc_start: 0.8277 (tmm) cc_final: 0.7945 (tmm) REVERT: G 603 HIS cc_start: 0.9359 (m-70) cc_final: 0.9050 (t-170) REVERT: G 680 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7498 (t) REVERT: G 699 MET cc_start: 0.8285 (mmm) cc_final: 0.7782 (mmt) REVERT: G 737 MET cc_start: 0.9338 (mmm) cc_final: 0.9035 (ptt) REVERT: G 810 MET cc_start: 0.8463 (mmm) cc_final: 0.8254 (tpt) REVERT: G 962 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9130 (tt) REVERT: G 1247 MET cc_start: 0.7843 (ptm) cc_final: 0.7187 (ppp) REVERT: H 215 LYS cc_start: 0.6287 (tttt) cc_final: 0.5930 (tptt) REVERT: H 272 MET cc_start: 0.8167 (mmm) cc_final: 0.7820 (mmt) REVERT: H 320 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.6995 (p90) REVERT: J 503 MET cc_start: 0.8900 (tpt) cc_final: 0.8515 (tpt) REVERT: J 547 ASP cc_start: 0.8626 (m-30) cc_final: 0.8252 (p0) REVERT: M 94 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9014 (tp30) REVERT: N 59 LYS cc_start: 0.8612 (tppt) cc_final: 0.7794 (tppt) REVERT: N 63 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8435 (mt-10) REVERT: N 95 ARG cc_start: 0.8596 (mmt-90) cc_final: 0.7638 (mmm-85) REVERT: O 32 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8417 (ttp80) REVERT: O 37 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8211 (mpt-90) REVERT: P 116 LYS cc_start: 0.8136 (pptt) cc_final: 0.7553 (pttt) REVERT: Q 100 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8257 (mm) REVERT: Q 108 ASN cc_start: 0.7765 (t0) cc_final: 0.7529 (t0) REVERT: R 40 ARG cc_start: 0.7016 (mtt180) cc_final: 0.5944 (ptp-170) REVERT: R 77 LYS cc_start: 0.9282 (mmtm) cc_final: 0.9071 (mmtm) REVERT: R 78 ARG cc_start: 0.9036 (ptp-170) cc_final: 0.8100 (ptp-170) REVERT: S 37 ARG cc_start: 0.7184 (mmp-170) cc_final: 0.6858 (mmp-170) REVERT: S 72 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8661 (mtmm) REVERT: T 35 GLU cc_start: 0.8830 (tt0) cc_final: 0.8192 (tp30) REVERT: T 47 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8932 (mt0) REVERT: T 105 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9078 (mt-10) outliers start: 134 outliers final: 80 residues processed: 527 average time/residue: 0.2662 time to fit residues: 226.3333 Evaluate side-chains 498 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 405 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 962 LEU Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain G residue 1141 LYS Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 69 ASN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain T residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 214 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 171 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN A 373 GLN J 440 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN N 27 GLN O 69 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.101045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.060148 restraints weight = 110592.744| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.80 r_work: 0.2804 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 44530 Z= 0.158 Angle : 0.694 14.292 61428 Z= 0.364 Chirality : 0.047 0.398 6981 Planarity : 0.004 0.058 6772 Dihedral : 23.479 176.397 8548 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.47 % Favored : 96.38 % Rotamer: Outliers : 3.04 % Allowed : 15.02 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4615 helix: 0.26 (0.11), residues: 2115 sheet: -0.04 (0.20), residues: 655 loop : -1.18 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 78 TYR 0.024 0.001 TYR E 215 PHE 0.024 0.001 PHE G 853 TRP 0.018 0.001 TRP G 612 HIS 0.018 0.001 HIS J 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (44526) covalent geometry : angle 0.69305 / 0.36 (61422) hydrogen bonds : bond 0.05285 / 3.53 ( 1820) hydrogen bonds : angle 4.25060 / 2.99 ( 4884) metal coordination : bond 0.00741 / 0.34 ( 4) metal coordination : angle 3.11820 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 458 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 GLU cc_start: 0.8604 (tm-30) cc_final: 0.7816 (tm-30) REVERT: E 178 MET cc_start: 0.8878 (tmm) cc_final: 0.7941 (tmm) REVERT: E 216 ASP cc_start: 0.6649 (OUTLIER) cc_final: 0.5488 (m-30) REVERT: E 246 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: E 282 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8834 (tt0) REVERT: I 159 ASN cc_start: 0.9194 (m-40) cc_final: 0.8797 (p0) REVERT: I 221 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8915 (mtm180) REVERT: A 370 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 371 MET cc_start: 0.8448 (mmt) cc_final: 0.8204 (mmt) REVERT: B 81 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9004 (mm) REVERT: B 108 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8326 (mtpt) REVERT: B 453 LYS cc_start: 0.9502 (mttt) cc_final: 0.9294 (mtmt) REVERT: D 62 MET cc_start: 0.8693 (ttm) cc_final: 0.8407 (ttm) REVERT: D 136 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8487 (mm-30) REVERT: D 211 ARG cc_start: 0.8848 (mmm160) cc_final: 0.8217 (mmm160) REVERT: D 349 ASP cc_start: 0.8854 (t0) cc_final: 0.8516 (t70) REVERT: F 178 MET cc_start: 0.9110 (tpt) cc_final: 0.8567 (tpp) REVERT: F 231 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: F 303 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8433 (ptp) REVERT: F 379 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8685 (t0) REVERT: G 526 MET cc_start: 0.8314 (tmm) cc_final: 0.7960 (tmm) REVERT: G 603 HIS cc_start: 0.9354 (m-70) cc_final: 0.9055 (t-170) REVERT: G 680 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7555 (t) REVERT: G 737 MET cc_start: 0.9316 (mmm) cc_final: 0.9037 (ptt) REVERT: G 810 MET cc_start: 0.8463 (mmm) cc_final: 0.8260 (tpt) REVERT: G 1159 MET cc_start: 0.8661 (mmp) cc_final: 0.8431 (mmp) REVERT: G 1247 MET cc_start: 0.7759 (ptm) cc_final: 0.7133 (ppp) REVERT: H 215 LYS cc_start: 0.6357 (tttt) cc_final: 0.5533 (ptmt) REVERT: H 272 MET cc_start: 0.8173 (mmm) cc_final: 0.7444 (mmm) REVERT: H 320 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.6993 (p90) REVERT: H 341 MET cc_start: 0.8309 (ttp) cc_final: 0.7790 (tmm) REVERT: J 547 ASP cc_start: 0.8600 (m-30) cc_final: 0.8218 (p0) REVERT: M 93 GLN cc_start: 0.9431 (tt0) cc_final: 0.8547 (tp40) REVERT: M 94 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9170 (tp30) REVERT: N 59 LYS cc_start: 0.8636 (tppt) cc_final: 0.8319 (tppt) REVERT: N 63 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8627 (mt-10) REVERT: N 95 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.7851 (mmm-85) REVERT: O 32 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8241 (ttp80) REVERT: P 43 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8584 (mttp) REVERT: P 96 THR cc_start: 0.8787 (m) cc_final: 0.8112 (m) REVERT: Q 100 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8191 (mm) REVERT: Q 108 ASN cc_start: 0.7860 (t0) cc_final: 0.7625 (t0) REVERT: R 40 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6779 (mtt-85) REVERT: R 78 ARG cc_start: 0.9010 (ptp-170) cc_final: 0.8130 (ptp-170) REVERT: S 37 ARG cc_start: 0.6931 (mmp-170) cc_final: 0.6675 (mmp-170) REVERT: S 82 ARG cc_start: 0.9026 (ttm110) cc_final: 0.8825 (ttm110) outliers start: 121 outliers final: 68 residues processed: 537 average time/residue: 0.2748 time to fit residues: 237.7899 Evaluate side-chains 497 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 417 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 274 HIS Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 469 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 370 optimal weight: 0.7980 chunk 383 optimal weight: 5.9990 chunk 458 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 427 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 396 optimal weight: 50.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 685 GLN ** J 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.098741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.058082 restraints weight = 109433.805| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.70 r_work: 0.2750 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 44530 Z= 0.300 Angle : 0.776 15.327 61428 Z= 0.404 Chirality : 0.049 0.409 6981 Planarity : 0.005 0.171 6772 Dihedral : 23.460 177.002 8548 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.20 % Favored : 95.64 % Rotamer: Outliers : 3.32 % Allowed : 15.70 % Favored : 80.98 % 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: -0.80 (0.12), residues: 4615 helix: 0.16 (0.11), residues: 2126 sheet: -0.31 (0.20), residues: 667 loop : -1.36 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 69 TYR 0.024 0.002 TYR T 40 PHE 0.021 0.002 PHE N 61 TRP 0.019 0.002 TRP G 612 HIS 0.017 0.002 HIS J 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.30 (44526) covalent geometry : angle 0.77457 / 0.40 (61422) hydrogen bonds : bond 0.06011 / 4.05 ( 1820) hydrogen bonds : angle 4.57010 / 3.21 ( 4884) metal coordination : bond 0.01270 / 0.58 ( 4) metal coordination : angle 4.60652 / 2.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 412 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.8859 (tpt) cc_final: 0.8598 (tpp) REVERT: E 112 GLU cc_start: 0.8680 (tm-30) cc_final: 0.7854 (tm-30) REVERT: E 178 MET cc_start: 0.8909 (tmm) cc_final: 0.7823 (tmm) REVERT: E 216 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.5099 (m-30) REVERT: E 246 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: E 282 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8860 (tt0) REVERT: E 299 ASP cc_start: 0.8968 (t0) cc_final: 0.8663 (t0) REVERT: I 159 ASN cc_start: 0.9223 (m-40) cc_final: 0.8792 (p0) REVERT: I 221 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8814 (mtm180) REVERT: A 370 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: B 81 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9081 (mm) REVERT: B 108 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8395 (mtpt) REVERT: B 113 MET cc_start: 0.9031 (tpt) cc_final: 0.8809 (tpp) REVERT: D 211 ARG cc_start: 0.8907 (mmm160) cc_final: 0.8306 (mmm160) REVERT: D 313 ASN cc_start: 0.8823 (t0) cc_final: 0.7558 (t0) REVERT: D 349 ASP cc_start: 0.8888 (t0) cc_final: 0.8456 (t0) REVERT: F 178 MET cc_start: 0.9114 (tpt) cc_final: 0.8651 (tpp) REVERT: F 303 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8504 (ptp) REVERT: G 526 MET cc_start: 0.8371 (tmm) cc_final: 0.7979 (tmm) REVERT: G 603 HIS cc_start: 0.9361 (m-70) cc_final: 0.9058 (t-170) REVERT: G 680 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7760 (t) REVERT: G 699 MET cc_start: 0.7799 (mmt) cc_final: 0.7571 (mmt) REVERT: G 737 MET cc_start: 0.9317 (mmm) cc_final: 0.9055 (ptt) REVERT: G 1247 MET cc_start: 0.7831 (ptm) cc_final: 0.7299 (ppp) REVERT: H 215 LYS cc_start: 0.6326 (tttt) cc_final: 0.5488 (pttt) REVERT: H 272 MET cc_start: 0.8231 (mmm) cc_final: 0.7888 (mmt) REVERT: H 320 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7121 (p90) REVERT: H 341 MET cc_start: 0.8292 (ttp) cc_final: 0.7732 (tmm) REVERT: J 547 ASP cc_start: 0.8595 (m-30) cc_final: 0.8355 (p0) REVERT: M 50 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8461 (tt0) REVERT: M 94 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9086 (tp30) REVERT: N 59 LYS cc_start: 0.8625 (tppt) cc_final: 0.8281 (tppt) REVERT: N 63 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8632 (mt-10) REVERT: N 95 ARG cc_start: 0.8683 (mmt-90) cc_final: 0.7965 (mmm-85) REVERT: Q 105 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8612 (tm-30) REVERT: R 40 ARG cc_start: 0.7098 (mtt180) cc_final: 0.6853 (mtt-85) REVERT: R 78 ARG cc_start: 0.8996 (ptp-170) cc_final: 0.8188 (ptp-170) REVERT: S 37 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6811 (mmp-170) REVERT: S 82 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8343 (ttm110) REVERT: S 85 GLN cc_start: 0.8671 (mt0) cc_final: 0.8130 (mp10) REVERT: S 89 ARG cc_start: 0.8617 (tmm160) cc_final: 0.8167 (tmm160) REVERT: T 45 LEU cc_start: 0.8711 (tp) cc_final: 0.8384 (tt) REVERT: T 105 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8883 (pp20) outliers start: 132 outliers final: 90 residues processed: 504 average time/residue: 0.2930 time to fit residues: 237.0689 Evaluate side-chains 492 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 392 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 426 ILE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 648 TYR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 555 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 108 optimal weight: 0.7980 chunk 311 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 340 optimal weight: 7.9990 chunk 456 optimal weight: 0.9980 chunk 262 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 445 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 387 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 832 HIS J 440 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.100944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060303 restraints weight = 107613.955| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.72 r_work: 0.2804 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44530 Z= 0.150 Angle : 0.684 14.017 61428 Z= 0.358 Chirality : 0.046 0.410 6981 Planarity : 0.004 0.066 6772 Dihedral : 23.350 178.784 8547 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.32 % Favored : 96.53 % Rotamer: Outliers : 2.69 % Allowed : 16.73 % Favored : 80.58 % 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: -0.51 (0.12), residues: 4615 helix: 0.38 (0.11), residues: 2127 sheet: -0.14 (0.20), residues: 660 loop : -1.19 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG O 32 TYR 0.023 0.001 TYR Q 99 PHE 0.025 0.001 PHE G 853 TRP 0.017 0.001 TRP G 612 HIS 0.019 0.001 HIS J 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (44526) covalent geometry : angle 0.68376 / 0.36 (61422) hydrogen bonds : bond 0.04983 / 3.31 ( 1820) hydrogen bonds : angle 4.20369 / 2.95 ( 4884) metal coordination : bond 0.00719 / 0.34 ( 4) metal coordination : angle 3.16917 / 1.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 436 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.8772 (tpt) cc_final: 0.8488 (tpp) REVERT: E 112 GLU cc_start: 0.8608 (tm-30) cc_final: 0.7811 (tm-30) REVERT: E 178 MET cc_start: 0.8856 (tmm) cc_final: 0.7807 (tmm) REVERT: E 216 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.5555 (m-30) REVERT: E 246 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: E 282 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8845 (tt0) REVERT: I 137 LYS cc_start: 0.8127 (mppt) cc_final: 0.7911 (mptt) REVERT: I 159 ASN cc_start: 0.9216 (m-40) cc_final: 0.8803 (p0) REVERT: I 221 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8749 (mtm180) REVERT: A 370 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: B 81 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8970 (mm) REVERT: B 108 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8222 (mtpt) REVERT: D 136 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8411 (mm-30) REVERT: D 196 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8528 (t0) REVERT: D 211 ARG cc_start: 0.8869 (mmm160) cc_final: 0.8247 (mmm160) REVERT: F 178 MET cc_start: 0.9059 (tpt) cc_final: 0.8614 (tpp) REVERT: F 188 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: F 379 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8690 (t0) REVERT: G 526 MET cc_start: 0.8388 (tmm) cc_final: 0.7972 (tmm) REVERT: G 603 HIS cc_start: 0.9339 (m-70) cc_final: 0.9041 (t-170) REVERT: G 680 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7687 (t) REVERT: G 699 MET cc_start: 0.7808 (mmt) cc_final: 0.7536 (mmt) REVERT: G 737 MET cc_start: 0.9314 (mmm) cc_final: 0.9054 (ptt) REVERT: G 1247 MET cc_start: 0.7757 (ptm) cc_final: 0.7239 (ppp) REVERT: H 215 LYS cc_start: 0.6344 (tttt) cc_final: 0.5603 (pttt) REVERT: H 272 MET cc_start: 0.8185 (mmm) cc_final: 0.7508 (mmm) REVERT: H 320 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7084 (p90) REVERT: H 341 MET cc_start: 0.8241 (ttp) cc_final: 0.7716 (tmm) REVERT: J 547 ASP cc_start: 0.8574 (m-30) cc_final: 0.8275 (p0) REVERT: M 50 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8433 (tt0) REVERT: M 93 GLN cc_start: 0.9378 (tt0) cc_final: 0.8499 (tp40) REVERT: M 94 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8999 (tp30) REVERT: N 63 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8647 (mt-10) REVERT: N 95 ARG cc_start: 0.8643 (mmt-90) cc_final: 0.8034 (mmm-85) REVERT: O 32 ARG cc_start: 0.8747 (tmm160) cc_final: 0.8321 (ptt90) REVERT: Q 105 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8593 (tm-30) REVERT: R 40 ARG cc_start: 0.6949 (mtt180) cc_final: 0.6479 (mtt180) REVERT: R 55 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7594 (mpt-90) REVERT: R 78 ARG cc_start: 0.9114 (ptp-170) cc_final: 0.8186 (ptp-170) REVERT: S 37 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6517 (mmp-170) REVERT: S 75 LYS cc_start: 0.9051 (tptp) cc_final: 0.8500 (tptt) REVERT: S 82 ARG cc_start: 0.9015 (ttm110) cc_final: 0.8496 (mtt90) REVERT: S 85 GLN cc_start: 0.8784 (mt0) cc_final: 0.8205 (mp10) REVERT: T 105 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8867 (pp20) outliers start: 107 outliers final: 64 residues processed: 505 average time/residue: 0.2785 time to fit residues: 226.1175 Evaluate side-chains 486 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 410 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 687 THR Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 274 HIS Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 95 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 208 optimal weight: 0.0870 chunk 338 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 354 optimal weight: 0.7980 chunk 129 optimal weight: 0.0570 chunk 185 optimal weight: 1.9990 chunk 31 optimal weight: 0.0000 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 HIS E 302 HIS ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN B 156 HIS B 408 GLN G 989 HIS J 440 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061574 restraints weight = 107247.162| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.87 r_work: 0.2806 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 44530 Z= 0.126 Angle : 0.668 13.037 61428 Z= 0.347 Chirality : 0.045 0.380 6981 Planarity : 0.004 0.059 6772 Dihedral : 23.150 176.363 8546 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.66 % Rotamer: Outliers : 1.98 % Allowed : 17.81 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 4615 helix: 0.57 (0.11), residues: 2116 sheet: 0.01 (0.20), residues: 663 loop : -1.08 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 86 TYR 0.020 0.001 TYR Q 99 PHE 0.023 0.001 PHE N 61 TRP 0.017 0.001 TRP G 612 HIS 0.021 0.001 HIS J 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (44526) covalent geometry : angle 0.66793 / 0.35 (61422) hydrogen bonds : bond 0.04511 / 2.96 ( 1820) hydrogen bonds : angle 3.97896 / 2.79 ( 4884) metal coordination : bond 0.00620 / 0.29 ( 4) metal coordination : angle 2.55563 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 460 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.8623 (tpt) cc_final: 0.8409 (tpt) REVERT: E 112 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7733 (tm-30) REVERT: E 178 MET cc_start: 0.8853 (tmm) cc_final: 0.7808 (tmm) REVERT: E 216 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.4478 (m-30) REVERT: E 282 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8912 (tt0) REVERT: E 352 ASP cc_start: 0.8982 (t70) cc_final: 0.8579 (t0) REVERT: I 137 LYS cc_start: 0.8097 (mppt) cc_final: 0.7853 (mptt) REVERT: I 138 ASN cc_start: 0.8502 (m110) cc_final: 0.8274 (m-40) REVERT: I 159 ASN cc_start: 0.9260 (m-40) cc_final: 0.8818 (p0) REVERT: I 160 ASP cc_start: 0.8909 (m-30) cc_final: 0.8704 (m-30) REVERT: I 221 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8054 (mtm180) REVERT: A 353 ASP cc_start: 0.8464 (m-30) cc_final: 0.8179 (p0) REVERT: A 370 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: B 249 ARG cc_start: 0.8541 (mtp-110) cc_final: 0.8166 (mmt90) REVERT: D 211 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8210 (mmm160) REVERT: D 349 ASP cc_start: 0.8796 (t0) cc_final: 0.8522 (t0) REVERT: F 178 MET cc_start: 0.8997 (tpt) cc_final: 0.8509 (tpp) REVERT: F 188 GLN cc_start: 0.8700 (mt0) cc_final: 0.8427 (pt0) REVERT: G 526 MET cc_start: 0.8428 (tmm) cc_final: 0.8036 (tmm) REVERT: G 603 HIS cc_start: 0.9375 (m-70) cc_final: 0.9036 (t-170) REVERT: G 680 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7396 (t) REVERT: G 699 MET cc_start: 0.7617 (mmt) cc_final: 0.7342 (mmt) REVERT: G 737 MET cc_start: 0.9304 (mmm) cc_final: 0.9045 (ptt) REVERT: G 1247 MET cc_start: 0.7776 (ptm) cc_final: 0.7247 (ppp) REVERT: H 215 LYS cc_start: 0.6459 (tttt) cc_final: 0.5639 (ptmt) REVERT: H 224 ARG cc_start: 0.8627 (mmp-170) cc_final: 0.7924 (tpp-160) REVERT: H 272 MET cc_start: 0.8096 (mmm) cc_final: 0.7378 (mmm) REVERT: H 320 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.6899 (p90) REVERT: H 341 MET cc_start: 0.8142 (ttp) cc_final: 0.7581 (tmm) REVERT: J 114 ASP cc_start: 0.9046 (m-30) cc_final: 0.8712 (m-30) REVERT: J 547 ASP cc_start: 0.8540 (m-30) cc_final: 0.8197 (p0) REVERT: M 50 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8430 (tt0) REVERT: M 93 GLN cc_start: 0.9311 (tt0) cc_final: 0.8447 (tp40) REVERT: M 94 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9132 (tp30) REVERT: N 95 ARG cc_start: 0.8628 (mmt-90) cc_final: 0.7900 (mmm-85) REVERT: O 32 ARG cc_start: 0.8726 (tmm160) cc_final: 0.8292 (ptt90) REVERT: O 112 HIS cc_start: 0.8086 (m170) cc_final: 0.7782 (m-70) REVERT: Q 120 MET cc_start: 0.8821 (tpp) cc_final: 0.8106 (mtp) REVERT: R 55 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7578 (mpt-90) REVERT: R 78 ARG cc_start: 0.9032 (ptp-170) cc_final: 0.8356 (ptp-170) REVERT: S 37 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.6220 (mmp-170) REVERT: S 72 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8850 (pttm) REVERT: S 75 LYS cc_start: 0.9054 (tptp) cc_final: 0.8728 (tptt) REVERT: S 82 ARG cc_start: 0.9022 (ttm110) cc_final: 0.8795 (mtp180) REVERT: S 85 GLN cc_start: 0.8731 (mt0) cc_final: 0.8194 (mp10) REVERT: T 105 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8850 (pp20) outliers start: 79 outliers final: 53 residues processed: 505 average time/residue: 0.2989 time to fit residues: 241.3471 Evaluate side-chains 468 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 408 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 58 TYR Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 360 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 425 optimal weight: 0.0670 chunk 293 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 361 optimal weight: 0.9990 chunk 402 optimal weight: 30.0000 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 241 HIS ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS B 408 GLN ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN R 93 GLN T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061486 restraints weight = 106452.336| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.86 r_work: 0.2807 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44530 Z= 0.128 Angle : 0.667 12.682 61428 Z= 0.346 Chirality : 0.044 0.369 6981 Planarity : 0.004 0.071 6772 Dihedral : 23.030 172.982 8544 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.12 % Favored : 96.75 % Rotamer: Outliers : 1.96 % Allowed : 17.91 % Favored : 80.13 % 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: -0.18 (0.12), residues: 4615 helix: 0.63 (0.11), residues: 2119 sheet: 0.10 (0.20), residues: 670 loop : -1.03 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 372 TYR 0.019 0.001 TYR Q 99 PHE 0.024 0.001 PHE N 61 TRP 0.018 0.001 TRP G 612 HIS 0.006 0.001 HIS T 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (44526) covalent geometry : angle 0.66642 / 0.35 (61422) hydrogen bonds : bond 0.04434 / 2.91 ( 1820) hydrogen bonds : angle 3.92890 / 2.76 ( 4884) metal coordination : bond 0.00468 / 0.23 ( 4) metal coordination : angle 2.63280 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 427 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ILE cc_start: 0.8888 (mm) cc_final: 0.8634 (tt) REVERT: E 112 GLU cc_start: 0.8600 (tm-30) cc_final: 0.7762 (tm-30) REVERT: E 178 MET cc_start: 0.8853 (tmm) cc_final: 0.7890 (tmm) REVERT: E 216 ASP cc_start: 0.6205 (OUTLIER) cc_final: 0.5086 (m-30) REVERT: E 282 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8900 (tt0) REVERT: E 352 ASP cc_start: 0.8963 (t70) cc_final: 0.8553 (t0) REVERT: I 137 LYS cc_start: 0.8129 (mppt) cc_final: 0.7650 (mppt) REVERT: I 138 ASN cc_start: 0.8472 (m110) cc_final: 0.8262 (m-40) REVERT: I 159 ASN cc_start: 0.9266 (m-40) cc_final: 0.8821 (p0) REVERT: I 160 ASP cc_start: 0.8902 (m-30) cc_final: 0.8692 (m-30) REVERT: I 221 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8667 (mtm180) REVERT: A 197 SER cc_start: 0.9577 (m) cc_final: 0.9349 (p) REVERT: A 353 ASP cc_start: 0.8484 (m-30) cc_final: 0.8208 (p0) REVERT: A 370 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: B 249 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8186 (mmt90) REVERT: B 260 MET cc_start: 0.8729 (ttp) cc_final: 0.8349 (tmm) REVERT: F 178 MET cc_start: 0.9016 (tpt) cc_final: 0.8499 (tpp) REVERT: F 188 GLN cc_start: 0.8725 (mt0) cc_final: 0.8461 (pt0) REVERT: G 526 MET cc_start: 0.8433 (tmm) cc_final: 0.8024 (tmm) REVERT: G 603 HIS cc_start: 0.9345 (m-70) cc_final: 0.9039 (t-170) REVERT: G 680 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7338 (t) REVERT: G 737 MET cc_start: 0.9281 (mmm) cc_final: 0.9034 (ptt) REVERT: G 920 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9203 (tt) REVERT: G 1247 MET cc_start: 0.7755 (ptm) cc_final: 0.7236 (ppp) REVERT: H 215 LYS cc_start: 0.6472 (tttt) cc_final: 0.5655 (ptmt) REVERT: H 224 ARG cc_start: 0.8576 (mmp-170) cc_final: 0.7889 (tpp-160) REVERT: H 272 MET cc_start: 0.8080 (mmm) cc_final: 0.7375 (mmm) REVERT: H 320 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.6915 (p90) REVERT: H 341 MET cc_start: 0.8174 (ttp) cc_final: 0.7617 (tmm) REVERT: J 114 ASP cc_start: 0.9037 (m-30) cc_final: 0.8671 (m-30) REVERT: J 242 MET cc_start: 0.8017 (mmm) cc_final: 0.7753 (mmm) REVERT: J 547 ASP cc_start: 0.8528 (m-30) cc_final: 0.8188 (p0) REVERT: M 50 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8408 (tt0) REVERT: M 93 GLN cc_start: 0.9338 (tt0) cc_final: 0.8592 (tp40) REVERT: M 94 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9011 (tp30) REVERT: N 95 ARG cc_start: 0.8662 (mmt-90) cc_final: 0.7940 (mmm-85) REVERT: O 32 ARG cc_start: 0.8750 (tmm160) cc_final: 0.8297 (ptt90) REVERT: P 54 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7130 (mt) REVERT: Q 108 ASN cc_start: 0.8058 (t0) cc_final: 0.7779 (t0) REVERT: R 40 ARG cc_start: 0.6992 (mtp85) cc_final: 0.5916 (ptp-170) REVERT: R 46 ILE cc_start: 0.8049 (mm) cc_final: 0.7676 (pt) REVERT: R 78 ARG cc_start: 0.9121 (ptp-170) cc_final: 0.8157 (ptp-170) REVERT: S 37 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5947 (mmp-170) REVERT: S 75 LYS cc_start: 0.9061 (tptp) cc_final: 0.8476 (tptt) REVERT: S 82 ARG cc_start: 0.9050 (ttm110) cc_final: 0.8723 (mtp180) REVERT: S 85 GLN cc_start: 0.8735 (mt0) cc_final: 0.8203 (mp10) REVERT: T 105 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8849 (pp20) outliers start: 78 outliers final: 59 residues processed: 475 average time/residue: 0.2718 time to fit residues: 207.1785 Evaluate side-chains 472 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 405 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 687 THR Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 58 TYR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 232 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 462 optimal weight: 9.9990 chunk 454 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 HIS ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 85 GLN R 93 GLN T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061259 restraints weight = 107421.588| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.90 r_work: 0.2807 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 44530 Z= 0.131 Angle : 0.664 12.745 61428 Z= 0.344 Chirality : 0.044 0.370 6981 Planarity : 0.004 0.075 6772 Dihedral : 22.903 171.925 8544 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 2.01 % Allowed : 17.96 % Favored : 80.03 % 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 (0.12), residues: 4615 helix: 0.68 (0.11), residues: 2116 sheet: 0.13 (0.20), residues: 661 loop : -0.99 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 78 TYR 0.027 0.001 TYR P 40 PHE 0.026 0.001 PHE N 61 TRP 0.018 0.001 TRP G 612 HIS 0.006 0.001 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (44526) covalent geometry : angle 0.66341 / 0.34 (61422) hydrogen bonds : bond 0.04381 / 2.88 ( 1820) hydrogen bonds : angle 3.89531 / 2.74 ( 4884) metal coordination : bond 0.00533 / 0.26 ( 4) metal coordination : angle 2.73554 / 1.51 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9230 Ramachandran restraints generated. 4615 Oldfield, 0 Emsley, 4615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 427 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 GLU cc_start: 0.8599 (tm-30) cc_final: 0.7742 (tm-30) REVERT: E 178 MET cc_start: 0.8821 (tmm) cc_final: 0.7848 (tmm) REVERT: E 216 ASP cc_start: 0.6097 (OUTLIER) cc_final: 0.4990 (m-30) REVERT: E 282 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8895 (tt0) REVERT: E 352 ASP cc_start: 0.9000 (t70) cc_final: 0.8633 (t0) REVERT: I 137 LYS cc_start: 0.8151 (mppt) cc_final: 0.7659 (mppt) REVERT: I 138 ASN cc_start: 0.8483 (m110) cc_final: 0.8271 (m-40) REVERT: I 159 ASN cc_start: 0.9254 (m-40) cc_final: 0.8728 (p0) REVERT: I 160 ASP cc_start: 0.8914 (m-30) cc_final: 0.8712 (m-30) REVERT: I 221 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8557 (mtm-85) REVERT: A 197 SER cc_start: 0.9581 (m) cc_final: 0.9352 (p) REVERT: A 216 GLU cc_start: 0.8787 (tp30) cc_final: 0.8469 (tp30) REVERT: A 353 ASP cc_start: 0.8481 (m-30) cc_final: 0.8219 (p0) REVERT: A 370 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: B 249 ARG cc_start: 0.8563 (mtp-110) cc_final: 0.8179 (mmt90) REVERT: B 260 MET cc_start: 0.8662 (ttp) cc_final: 0.8272 (tmm) REVERT: B 264 MET cc_start: 0.8532 (mmm) cc_final: 0.8107 (mmp) REVERT: D 211 ARG cc_start: 0.8854 (mmm160) cc_final: 0.8202 (mmm160) REVERT: F 178 MET cc_start: 0.9022 (tpt) cc_final: 0.8493 (tpp) REVERT: F 188 GLN cc_start: 0.8737 (mt0) cc_final: 0.8482 (pt0) REVERT: G 526 MET cc_start: 0.8442 (tmm) cc_final: 0.8043 (tmm) REVERT: G 603 HIS cc_start: 0.9354 (m-70) cc_final: 0.9044 (t-170) REVERT: G 680 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7285 (t) REVERT: G 737 MET cc_start: 0.9289 (mmm) cc_final: 0.9020 (ptt) REVERT: G 920 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9216 (tt) REVERT: G 1016 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7762 (mtm180) REVERT: G 1247 MET cc_start: 0.7648 (ptm) cc_final: 0.7132 (ppp) REVERT: H 215 LYS cc_start: 0.6466 (tttt) cc_final: 0.5674 (ptmt) REVERT: H 224 ARG cc_start: 0.8586 (mmp-170) cc_final: 0.7900 (tpp-160) REVERT: H 272 MET cc_start: 0.8103 (mmm) cc_final: 0.7325 (mmm) REVERT: H 320 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.6879 (p90) REVERT: H 341 MET cc_start: 0.7975 (ttp) cc_final: 0.7465 (tmm) REVERT: J 114 ASP cc_start: 0.9043 (m-30) cc_final: 0.8668 (m-30) REVERT: J 547 ASP cc_start: 0.8559 (m-30) cc_final: 0.8137 (p0) REVERT: J 565 LEU cc_start: 0.8447 (tp) cc_final: 0.8218 (mt) REVERT: M 50 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8457 (tt0) REVERT: M 93 GLN cc_start: 0.9305 (tt0) cc_final: 0.8525 (tp40) REVERT: M 94 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9023 (tp30) REVERT: N 95 ARG cc_start: 0.8638 (mmt-90) cc_final: 0.7947 (mmm-85) REVERT: O 32 ARG cc_start: 0.8712 (tmm160) cc_final: 0.8245 (ptt90) REVERT: P 43 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8533 (ptpp) REVERT: Q 108 ASN cc_start: 0.8027 (t0) cc_final: 0.7788 (t0) REVERT: R 40 ARG cc_start: 0.6974 (mtp85) cc_final: 0.5785 (ptp-170) REVERT: R 46 ILE cc_start: 0.8032 (mm) cc_final: 0.7644 (pt) REVERT: R 78 ARG cc_start: 0.8906 (ptp-170) cc_final: 0.8211 (ptp-170) REVERT: S 37 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5822 (mmp-170) REVERT: S 75 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8595 (tptt) REVERT: S 82 ARG cc_start: 0.9048 (ttm110) cc_final: 0.8731 (mtp180) REVERT: S 85 GLN cc_start: 0.8647 (mt0) cc_final: 0.8269 (mp10) REVERT: T 105 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8839 (pp20) outliers start: 80 outliers final: 62 residues processed: 476 average time/residue: 0.2863 time to fit residues: 218.7767 Evaluate side-chains 476 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 406 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 688 MET Chi-restraints excluded: chain G residue 742 PHE Chi-restraints excluded: chain G residue 920 LEU Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1078 SER Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 320 TYR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain O residue 33 HIS Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 49 HIS Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 37 ARG Chi-restraints excluded: chain S residue 58 TYR Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 71 optimal weight: 0.1980 chunk 134 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 185 optimal weight: 0.0070 chunk 96 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 447 optimal weight: 20.0000 chunk 469 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 444 optimal weight: 7.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 GLN R 93 GLN T 82 HIS ** T 84 ASN ** 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 = 0.3828 r_free = 0.3828 target = 0.102996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061849 restraints weight = 107808.046| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.90 r_work: 0.2820 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 44530 Z= 0.125 Angle : 0.670 16.277 61428 Z= 0.345 Chirality : 0.044 0.372 6981 Planarity : 0.004 0.061 6772 Dihedral : 22.812 171.784 8544 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 1.86 % Allowed : 18.21 % Favored : 79.93 % 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: -0.09 (0.12), residues: 4615 helix: 0.70 (0.11), residues: 2121 sheet: 0.22 (0.20), residues: 666 loop : -0.99 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 86 TYR 0.018 0.001 TYR Q 99 PHE 0.026 0.001 PHE N 61 TRP 0.018 0.001 TRP G 612 HIS 0.025 0.001 HIS P 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (44526) covalent geometry : angle 0.66977 / 0.34 (61422) hydrogen bonds : bond 0.04283 / 2.80 ( 1820) hydrogen bonds : angle 3.86213 / 2.72 ( 4884) metal coordination : bond 0.00488 / 0.24 ( 4) metal coordination : angle 2.68082 / 1.50 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11590.78 seconds wall clock time: 199 minutes 2.44 seconds (11942.44 seconds total)