Starting phenix.real_space_refine on Mon May 4 11:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qof_18536/05_2026/8qof_18536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qof_18536/05_2026/8qof_18536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qof_18536/05_2026/8qof_18536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qof_18536/05_2026/8qof_18536.map" model { file = "/net/cci-nas-00/data/ceres_data/8qof_18536/05_2026/8qof_18536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qof_18536/05_2026/8qof_18536.cif" } resolution = 3.3 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 112 5.16 5 C 13310 2.51 5 N 3427 2.21 5 O 3851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20702 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3848 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain breaks: 1 Chain: "F" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3848 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain breaks: 1 Chain: "D" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 516 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 512 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain breaks: 1 Chain: "A" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1448 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "E" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1448 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "G" Number of atoms: 4395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4395 Classifications: {'peptide': 555} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 525} Chain: "C" Number of atoms: 4395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4395 Classifications: {'peptide': 555} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 525} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'WAR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'WAR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.68, per 1000 atoms: 0.23 Number of scatterers: 20702 At special positions: 0 Unit cell: (147.84, 145.992, 122.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 2 15.00 O 3851 8.00 N 3427 7.00 C 13310 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 859.0 milliseconds 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4836 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 15 sheets defined 49.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 54 through 72 removed outlier: 3.580A pdb=" N GLU B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.784A pdb=" N ALA B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.599A pdb=" N THR B 226 " --> pdb=" O PRO B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 260 through 279 Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.803A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 342 through 347 Processing helix chain 'B' and resid 368 through 379 removed outlier: 4.074A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 389 through 406 removed outlier: 4.129A pdb=" N VAL B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 4.077A pdb=" N GLN B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 458 Processing helix chain 'B' and resid 461 through 476 Processing helix chain 'B' and resid 482 through 504 removed outlier: 3.698A pdb=" N GLU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 553 Processing helix chain 'F' and resid 55 through 72 removed outlier: 3.542A pdb=" N GLU F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 92 through 100 Processing helix chain 'F' and resid 115 through 120 removed outlier: 3.742A pdb=" N ALA F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 176 Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 223 through 226 removed outlier: 3.593A pdb=" N THR F 226 " --> pdb=" O PRO F 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 223 through 226' Processing helix chain 'F' and resid 239 through 250 removed outlier: 4.181A pdb=" N ARG F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 279 removed outlier: 3.585A pdb=" N GLU F 270 " --> pdb=" O CYS F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 313 removed outlier: 3.521A pdb=" N LYS F 308 " --> pdb=" O PRO F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 3.799A pdb=" N HIS F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 342 through 347 removed outlier: 3.553A pdb=" N ILE F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 379 removed outlier: 3.598A pdb=" N HIS F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 389 through 406 removed outlier: 4.016A pdb=" N VAL F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.888A pdb=" N GLN F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 458 Processing helix chain 'F' and resid 461 through 476 Processing helix chain 'F' and resid 482 through 504 removed outlier: 3.568A pdb=" N GLU F 486 " --> pdb=" O ILE F 482 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU F 488 " --> pdb=" O PRO F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 553 Processing helix chain 'D' and resid 29 through 42 removed outlier: 3.630A pdb=" N TYR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 58 removed outlier: 4.292A pdb=" N SER D 53 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 66 removed outlier: 3.891A pdb=" N ILE D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 removed outlier: 3.671A pdb=" N TYR H 42 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 52 No H-bonds generated for 'chain 'H' and resid 50 through 52' Processing helix chain 'H' and resid 53 through 58 removed outlier: 3.980A pdb=" N PHE H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE H 58 " --> pdb=" O PHE H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 58' Processing helix chain 'H' and resid 59 through 66 removed outlier: 3.869A pdb=" N ILE H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.641A pdb=" N ASP A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 99 removed outlier: 3.776A pdb=" N PHE A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 122 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 152 through 170 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 176 through 192 removed outlier: 3.735A pdb=" N VAL A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.656A pdb=" N ASP E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 76 removed outlier: 3.695A pdb=" N VAL E 75 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 76 " --> pdb=" O THR E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 76' Processing helix chain 'E' and resid 81 through 99 removed outlier: 4.472A pdb=" N ILE E 85 " --> pdb=" O TRP E 81 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 98 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY E 99 " --> pdb=" O TYR E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 122 Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 152 through 170 Proline residue: E 162 - end of helix Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 176 through 192 removed outlier: 3.588A pdb=" N VAL E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 28 Processing helix chain 'G' and resid 57 through 86 removed outlier: 4.132A pdb=" N SER G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 108 through 114 removed outlier: 3.698A pdb=" N ARG G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 122 removed outlier: 3.616A pdb=" N ASP G 119 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASP G 120 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 Processing helix chain 'G' and resid 200 through 215 removed outlier: 3.777A pdb=" N ILE G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 231 removed outlier: 3.707A pdb=" N ASN G 229 " --> pdb=" O GLY G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 236 removed outlier: 3.548A pdb=" N PHE G 236 " --> pdb=" O PHE G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 261 removed outlier: 3.558A pdb=" N ARG G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 286 Processing helix chain 'G' and resid 313 through 325 removed outlier: 3.635A pdb=" N LEU G 317 " --> pdb=" O ASN G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 351 Processing helix chain 'G' and resid 378 through 389 removed outlier: 3.500A pdb=" N ILE G 382 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 415 removed outlier: 3.553A pdb=" N LEU G 403 " --> pdb=" O PRO G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 444 removed outlier: 3.512A pdb=" N GLY G 444 " --> pdb=" O LEU G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 476 removed outlier: 4.171A pdb=" N ALA G 468 " --> pdb=" O SER G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 523 Processing helix chain 'G' and resid 541 through 553 Proline residue: G 550 - end of helix Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 57 through 86 removed outlier: 4.144A pdb=" N SER C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 115 through 122 removed outlier: 5.570A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.690A pdb=" N ILE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.696A pdb=" N ASN C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.504A pdb=" N ARG C 254 " --> pdb=" O HIS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.589A pdb=" N LEU C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.568A pdb=" N ILE C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.764A pdb=" N GLY C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.699A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 415 removed outlier: 3.520A pdb=" N LEU C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 444 removed outlier: 3.505A pdb=" N GLY C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 476 removed outlier: 4.146A pdb=" N ALA C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 476 " --> pdb=" O MET C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 523 Processing helix chain 'C' and resid 541 through 553 Proline residue: C 550 - end of helix Processing helix chain 'C' and resid 555 through 559 removed outlier: 4.155A pdb=" N TYR C 558 " --> pdb=" O ASP C 555 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 559 " --> pdb=" O ASP C 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 555 through 559' Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 124 removed outlier: 7.032A pdb=" N ILE B 135 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N THR B 145 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG B 137 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS B 143 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU B 506 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B 148 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.550A pdb=" N ILE B 349 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE B 318 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 288 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP B 320 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR B 290 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N GLU B 291 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N ASP B 235 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 232 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE B 256 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 234 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.547A pdb=" N THR B 508 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 123 through 124 removed outlier: 7.071A pdb=" N ILE F 135 " --> pdb=" O THR F 145 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR F 145 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ARG F 137 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS F 143 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU F 506 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE F 148 " --> pdb=" O LEU F 506 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 207 through 211 removed outlier: 3.585A pdb=" N ILE F 349 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE F 318 " --> pdb=" O LYS F 286 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE F 288 " --> pdb=" O PHE F 318 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP F 320 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR F 290 " --> pdb=" O ASP F 320 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL F 231 " --> pdb=" O PHE F 287 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL F 289 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL F 233 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N GLU F 291 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASP F 235 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 434 through 436 removed outlier: 3.534A pdb=" N THR F 508 " --> pdb=" O LYS F 526 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA8, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'G' and resid 126 through 127 removed outlier: 3.775A pdb=" N ARG G 135 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP G 138 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA G 153 " --> pdb=" O ASP G 138 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE G 140 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER G 151 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS G 142 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR G 149 " --> pdb=" O HIS G 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 218 through 222 removed outlier: 3.612A pdb=" N ASP G 218 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY G 373 " --> pdb=" O PHE G 222 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE G 359 " --> pdb=" O LEU G 328 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU G 242 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS G 300 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE G 244 " --> pdb=" O CYS G 300 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLU G 302 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ASP G 246 " --> pdb=" O GLU G 302 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL G 243 " --> pdb=" O ARG G 265 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE G 267 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER G 245 " --> pdb=" O PHE G 267 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 455 through 459 removed outlier: 4.264A pdb=" N VAL G 481 " --> pdb=" O ARG G 496 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.740A pdb=" N ARG C 135 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA C 153 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE C 140 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER C 151 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N HIS C 142 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR C 149 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.549A pdb=" N ASP C 218 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY C 373 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 362 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 297 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N PHE C 329 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE C 299 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASP C 331 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA C 301 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU C 242 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N CYS C 300 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE C 244 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N GLU C 302 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ASP C 246 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 243 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N PHE C 267 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER C 245 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 304 through 305 removed outlier: 3.809A pdb=" N THR C 310 " --> pdb=" O PHE C 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 455 through 459 removed outlier: 3.579A pdb=" N ARG C 494 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6550 1.34 - 1.46: 4454 1.46 - 1.58: 9994 1.58 - 1.70: 6 1.70 - 1.81: 174 Bond restraints: 21178 Sorted by residual: bond pdb=" N PRO F 75 " pdb=" CD PRO F 75 " ideal model delta sigma weight residual 1.473 1.801 -0.328 1.40e-02 5.10e+03 5.47e+02 bond pdb=" N PRO B 75 " pdb=" CD PRO B 75 " ideal model delta sigma weight residual 1.473 1.800 -0.327 1.40e-02 5.10e+03 5.45e+02 bond pdb=" C15 WAR E 301 " pdb=" O49 WAR E 301 " ideal model delta sigma weight residual 1.448 1.341 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C15 WAR A 301 " pdb=" O49 WAR A 301 " ideal model delta sigma weight residual 1.448 1.345 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C16 WAR E 301 " pdb=" O17 WAR E 301 " ideal model delta sigma weight residual 1.436 1.336 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 21173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 28530 3.11 - 6.22: 172 6.22 - 9.34: 22 9.34 - 12.45: 4 12.45 - 15.56: 1 Bond angle restraints: 28729 Sorted by residual: angle pdb=" N PRO F 75 " pdb=" CA PRO F 75 " pdb=" CB PRO F 75 " ideal model delta sigma weight residual 102.35 109.31 -6.96 7.10e-01 1.98e+00 9.61e+01 angle pdb=" N PRO B 75 " pdb=" CA PRO B 75 " pdb=" CB PRO B 75 " ideal model delta sigma weight residual 102.35 109.23 -6.88 7.10e-01 1.98e+00 9.38e+01 angle pdb=" N VAL F 191 " pdb=" CA VAL F 191 " pdb=" C VAL F 191 " ideal model delta sigma weight residual 113.71 106.26 7.45 9.50e-01 1.11e+00 6.15e+01 angle pdb=" CA PRO B 75 " pdb=" N PRO B 75 " pdb=" CD PRO B 75 " ideal model delta sigma weight residual 112.00 102.17 9.83 1.40e+00 5.10e-01 4.93e+01 angle pdb=" CA PRO F 75 " pdb=" N PRO F 75 " pdb=" CD PRO F 75 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 ... (remaining 28724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 12674 35.71 - 71.42: 287 71.42 - 107.13: 59 107.13 - 142.84: 26 142.84 - 178.56: 3 Dihedral angle restraints: 13049 sinusoidal: 5540 harmonic: 7509 Sorted by residual: dihedral pdb=" C20 WAR E 301 " pdb=" C18 WAR E 301 " pdb=" N19 WAR E 301 " pdb=" C47 WAR E 301 " ideal model delta sinusoidal sigma weight residual 200.59 22.03 178.56 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C22 WAR E 301 " pdb=" C20 WAR E 301 " pdb=" C21 WAR E 301 " pdb=" O46 WAR E 301 " ideal model delta sinusoidal sigma weight residual -98.65 71.26 -169.91 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C01 WAR E 301 " pdb=" C02 WAR E 301 " pdb=" C03 WAR E 301 " pdb=" C04 WAR E 301 " ideal model delta sinusoidal sigma weight residual -73.05 73.16 -146.21 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 13046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 3264 0.178 - 0.355: 12 0.355 - 0.533: 0 0.533 - 0.710: 1 0.710 - 0.888: 1 Chirality restraints: 3278 Sorted by residual: chirality pdb=" C18 WAR E 301 " pdb=" C16 WAR E 301 " pdb=" C47 WAR E 301 " pdb=" N19 WAR E 301 " both_signs ideal model delta sigma weight residual False 2.63 1.75 0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" C15 WAR E 301 " pdb=" C14 WAR E 301 " pdb=" C16 WAR E 301 " pdb=" O49 WAR E 301 " both_signs ideal model delta sigma weight residual False 2.69 2.15 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" C51 Q7G G 602 " pdb=" C41 Q7G G 602 " pdb=" C61 Q7G G 602 " pdb=" O51 Q7G G 602 " both_signs ideal model delta sigma weight residual False -2.21 -2.52 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3275 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G C 602 " -0.016 2.00e-02 2.50e+03 6.54e-02 5.34e+01 pdb=" C13 Q7G C 602 " -0.015 2.00e-02 2.50e+03 pdb=" C14 Q7G C 602 " -0.106 2.00e-02 2.50e+03 pdb=" C15 Q7G C 602 " 0.079 2.00e-02 2.50e+03 pdb=" C16 Q7G C 602 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G G 602 " -0.016 2.00e-02 2.50e+03 5.91e-02 4.36e+01 pdb=" C13 Q7G G 602 " -0.007 2.00e-02 2.50e+03 pdb=" C14 Q7G G 602 " -0.098 2.00e-02 2.50e+03 pdb=" C15 Q7G G 602 " 0.071 2.00e-02 2.50e+03 pdb=" C16 Q7G G 602 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 181 " -0.034 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO B 182 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " -0.029 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 8 2.26 - 2.92: 8041 2.92 - 3.58: 27527 3.58 - 4.24: 41653 4.24 - 4.90: 76459 Nonbonded interactions: 153688 Sorted by model distance: nonbonded pdb=" OD1 ASN E 71 " pdb=" O46 WAR E 301 " model vdw 1.595 3.040 nonbonded pdb=" O MET G 83 " pdb=" O61 Q7G G 602 " model vdw 2.019 3.040 nonbonded pdb=" OE2 GLU F 60 " pdb=" ND2 ASN A 170 " model vdw 2.132 3.120 nonbonded pdb=" O LEU G 460 " pdb=" OG SER G 493 " model vdw 2.134 3.040 nonbonded pdb=" OE2 GLU B 60 " pdb=" ND2 ASN E 170 " model vdw 2.161 3.120 ... (remaining 153683 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 4 through 21 or resid 28 through 68)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.110 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.749 21181 Z= 0.607 Angle : 0.612 15.560 28729 Z= 0.318 Chirality : 0.047 0.888 3278 Planarity : 0.004 0.065 3607 Dihedral : 17.936 178.556 8213 Min Nonbonded Distance : 1.595 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.13 % Allowed : 0.18 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.82 (0.17), residues: 2545 helix: 2.12 (0.16), residues: 1084 sheet: 1.24 (0.31), residues: 298 loop : -1.24 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 344 TYR 0.014 0.001 TYR G 510 PHE 0.018 0.001 PHE C 236 TRP 0.007 0.001 TRP H 40 HIS 0.003 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00486 (21178) covalent geometry : angle 0.61172 (28729) hydrogen bonds : bond 0.21373 ( 886) hydrogen bonds : angle 5.83852 ( 2568) Misc. bond : bond 0.44555 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 406 time to evaluate : 0.861 Fit side-chains REVERT: B 226 THR cc_start: 0.8866 (m) cc_final: 0.8561 (p) REVERT: B 274 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7420 (mt0) REVERT: B 469 MET cc_start: 0.8234 (tpt) cc_final: 0.8017 (tpp) REVERT: F 78 LYS cc_start: 0.7127 (tmtt) cc_final: 0.6923 (tptp) REVERT: F 226 THR cc_start: 0.8809 (m) cc_final: 0.8588 (p) REVERT: E 168 ILE cc_start: 0.8134 (mm) cc_final: 0.7788 (mp) REVERT: G 366 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7600 (mmtm) REVERT: C 366 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7013 (mttp) outliers start: 3 outliers final: 0 residues processed: 409 average time/residue: 0.1592 time to fit residues: 98.5452 Evaluate side-chains 205 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 366 LYS Chi-restraints excluded: chain C residue 366 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 HIS B 448 GLN F 295 HIS F 448 GLN E 65 GLN G 90 HIS G 143 ASN C 67 ASN C 78 HIS C 142 HIS C 143 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.174096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147834 restraints weight = 24057.679| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.26 r_work: 0.3484 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21181 Z= 0.127 Angle : 0.593 9.462 28729 Z= 0.294 Chirality : 0.044 0.286 3278 Planarity : 0.004 0.046 3607 Dihedral : 14.125 141.088 3311 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.32 % Allowed : 7.57 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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 (0.17), residues: 2545 helix: 2.20 (0.16), residues: 1131 sheet: 1.14 (0.32), residues: 286 loop : -1.14 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.015 0.001 TYR G 510 PHE 0.023 0.001 PHE D 57 TRP 0.007 0.001 TRP C 294 HIS 0.004 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00285 (21178) covalent geometry : angle 0.59332 (28729) hydrogen bonds : bond 0.05024 ( 886) hydrogen bonds : angle 4.22740 ( 2568) Misc. bond : bond 0.00157 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 THR cc_start: 0.9031 (m) cc_final: 0.8687 (p) REVERT: B 274 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7884 (mm-40) REVERT: B 469 MET cc_start: 0.8418 (tpt) cc_final: 0.8178 (tpp) REVERT: F 226 THR cc_start: 0.8939 (m) cc_final: 0.8648 (p) REVERT: G 323 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8358 (ttpp) outliers start: 30 outliers final: 26 residues processed: 235 average time/residue: 0.1616 time to fit residues: 57.4040 Evaluate side-chains 206 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 134 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 473 GLN A 65 GLN A 200 HIS G 78 HIS G 143 ASN G 269 HIS C 78 HIS C 143 ASN C 269 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.168599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142775 restraints weight = 24632.732| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.28 r_work: 0.3377 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21181 Z= 0.114 Angle : 0.548 10.181 28729 Z= 0.271 Chirality : 0.043 0.281 3278 Planarity : 0.004 0.044 3607 Dihedral : 11.844 143.812 3303 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.19 % Allowed : 9.51 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.99 (0.17), residues: 2545 helix: 2.32 (0.16), residues: 1127 sheet: 1.09 (0.33), residues: 286 loop : -1.27 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.015 0.001 TYR G 510 PHE 0.018 0.001 PHE C 329 TRP 0.007 0.001 TRP C 294 HIS 0.002 0.001 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00255 (21178) covalent geometry : angle 0.54807 (28729) hydrogen bonds : bond 0.04646 ( 886) hydrogen bonds : angle 3.97171 ( 2568) Misc. bond : bond 0.00168 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7846 (mm-40) REVERT: B 469 MET cc_start: 0.8524 (tpt) cc_final: 0.8270 (tpp) REVERT: A 92 ARG cc_start: 0.6903 (tmt-80) cc_final: 0.6626 (tpt170) REVERT: A 120 MET cc_start: 0.7689 (mmm) cc_final: 0.7422 (mmm) outliers start: 27 outliers final: 21 residues processed: 228 average time/residue: 0.1786 time to fit residues: 59.8337 Evaluate side-chains 199 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 546 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 55 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 221 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 200 HIS C 78 HIS C 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.166495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140524 restraints weight = 24705.532| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.33 r_work: 0.3325 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21181 Z= 0.120 Angle : 0.547 8.698 28729 Z= 0.272 Chirality : 0.043 0.270 3278 Planarity : 0.004 0.050 3607 Dihedral : 11.132 148.570 3303 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.50 % Allowed : 10.56 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.94 (0.17), residues: 2545 helix: 2.32 (0.16), residues: 1131 sheet: 1.06 (0.31), residues: 302 loop : -1.40 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 44 TYR 0.017 0.001 TYR G 510 PHE 0.017 0.001 PHE C 329 TRP 0.008 0.001 TRP G 294 HIS 0.003 0.001 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00278 (21178) covalent geometry : angle 0.54722 (28729) hydrogen bonds : bond 0.04676 ( 886) hydrogen bonds : angle 3.88556 ( 2568) Misc. bond : bond 0.00152 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 469 MET cc_start: 0.8517 (tpt) cc_final: 0.8247 (tpp) REVERT: F 539 LYS cc_start: 0.8152 (tttm) cc_final: 0.7600 (mptt) REVERT: H 51 MET cc_start: 0.6157 (mmp) cc_final: 0.5347 (mmt) REVERT: A 92 ARG cc_start: 0.6906 (tmt-80) cc_final: 0.6542 (tpt170) outliers start: 34 outliers final: 28 residues processed: 220 average time/residue: 0.1758 time to fit residues: 56.9601 Evaluate side-chains 206 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 495 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 546 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 201 optimal weight: 0.0070 chunk 153 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136854 restraints weight = 24675.467| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.31 r_work: 0.3313 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21181 Z= 0.150 Angle : 0.589 12.669 28729 Z= 0.294 Chirality : 0.044 0.258 3278 Planarity : 0.004 0.053 3607 Dihedral : 10.687 152.851 3303 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.94 % Allowed : 11.53 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2545 helix: 2.28 (0.16), residues: 1131 sheet: 0.90 (0.31), residues: 304 loop : -1.46 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.020 0.001 TYR G 510 PHE 0.017 0.001 PHE C 329 TRP 0.007 0.001 TRP A 142 HIS 0.003 0.001 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00360 (21178) covalent geometry : angle 0.58916 (28729) hydrogen bonds : bond 0.05417 ( 886) hydrogen bonds : angle 3.93305 ( 2568) Misc. bond : bond 0.00179 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7377 (mt0) REVERT: B 469 MET cc_start: 0.8563 (tpt) cc_final: 0.8302 (tpp) REVERT: F 539 LYS cc_start: 0.8122 (tttm) cc_final: 0.7636 (mptt) REVERT: D 51 MET cc_start: 0.6223 (mmp) cc_final: 0.5544 (mmt) REVERT: A 92 ARG cc_start: 0.7027 (tmt-80) cc_final: 0.6628 (tpt170) outliers start: 44 outliers final: 35 residues processed: 218 average time/residue: 0.1632 time to fit residues: 54.2800 Evaluate side-chains 205 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 552 CYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 495 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 546 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 184 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 189 optimal weight: 0.0270 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.164687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138685 restraints weight = 24572.122| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.33 r_work: 0.3306 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21181 Z= 0.116 Angle : 0.552 11.744 28729 Z= 0.272 Chirality : 0.043 0.272 3278 Planarity : 0.004 0.053 3607 Dihedral : 9.741 156.425 3303 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.50 % Allowed : 12.76 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.89 (0.17), residues: 2545 helix: 2.23 (0.16), residues: 1155 sheet: 0.99 (0.31), residues: 302 loop : -1.44 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 44 TYR 0.016 0.001 TYR G 510 PHE 0.015 0.001 PHE C 329 TRP 0.007 0.001 TRP G 294 HIS 0.003 0.001 HIS F 498 Details of bonding type rmsd covalent geometry : bond 0.00266 (21178) covalent geometry : angle 0.55180 (28729) hydrogen bonds : bond 0.04520 ( 886) hydrogen bonds : angle 3.82309 ( 2568) Misc. bond : bond 0.00120 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7355 (mt0) REVERT: B 469 MET cc_start: 0.8539 (tpt) cc_final: 0.8213 (tpp) REVERT: F 539 LYS cc_start: 0.8119 (tttm) cc_final: 0.7595 (mptt) REVERT: D 51 MET cc_start: 0.6143 (mmp) cc_final: 0.5504 (mmt) REVERT: H 51 MET cc_start: 0.5847 (mmp) cc_final: 0.5447 (mmt) REVERT: E 64 GLN cc_start: 0.7298 (mm-40) cc_final: 0.6991 (mm110) REVERT: G 517 GLU cc_start: 0.8416 (tp30) cc_final: 0.7886 (tp30) outliers start: 34 outliers final: 29 residues processed: 210 average time/residue: 0.1523 time to fit residues: 49.5709 Evaluate side-chains 205 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 552 CYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 452 ASP Chi-restraints excluded: chain G residue 495 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 504 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 53 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 118 optimal weight: 0.0670 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS G 142 HIS C 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141593 restraints weight = 24595.869| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.32 r_work: 0.3353 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21181 Z= 0.094 Angle : 0.515 11.271 28729 Z= 0.253 Chirality : 0.042 0.273 3278 Planarity : 0.004 0.056 3607 Dihedral : 9.194 160.974 3303 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.23 % Allowed : 13.20 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.06 (0.17), residues: 2545 helix: 2.38 (0.16), residues: 1150 sheet: 1.07 (0.31), residues: 306 loop : -1.34 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 45 TYR 0.015 0.001 TYR B 460 PHE 0.015 0.001 PHE C 329 TRP 0.008 0.001 TRP C 294 HIS 0.003 0.000 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00205 (21178) covalent geometry : angle 0.51469 (28729) hydrogen bonds : bond 0.03683 ( 886) hydrogen bonds : angle 3.72072 ( 2568) Misc. bond : bond 0.00081 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7429 (mt0) REVERT: F 539 LYS cc_start: 0.8041 (tttm) cc_final: 0.7611 (mptt) REVERT: D 51 MET cc_start: 0.6079 (mmp) cc_final: 0.5512 (mmt) REVERT: H 51 MET cc_start: 0.5766 (mmp) cc_final: 0.5178 (mmt) REVERT: E 64 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6899 (mm110) outliers start: 28 outliers final: 24 residues processed: 213 average time/residue: 0.1543 time to fit residues: 50.5035 Evaluate side-chains 201 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 552 CYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 495 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 546 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 144 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 186 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 53 optimal weight: 0.0170 chunk 194 optimal weight: 1.9990 chunk 211 optimal weight: 0.0020 chunk 77 optimal weight: 0.7980 overall best weight: 0.6228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 473 GLN G 78 HIS C 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140567 restraints weight = 24551.590| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.32 r_work: 0.3327 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21181 Z= 0.100 Angle : 0.527 10.994 28729 Z= 0.258 Chirality : 0.042 0.273 3278 Planarity : 0.004 0.101 3607 Dihedral : 9.027 162.238 3303 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.19 % Allowed : 13.29 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.10 (0.17), residues: 2545 helix: 2.40 (0.16), residues: 1150 sheet: 1.10 (0.31), residues: 306 loop : -1.31 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 117 TYR 0.013 0.001 TYR G 510 PHE 0.014 0.001 PHE C 329 TRP 0.007 0.001 TRP C 294 HIS 0.003 0.000 HIS F 498 Details of bonding type rmsd covalent geometry : bond 0.00220 (21178) covalent geometry : angle 0.52737 (28729) hydrogen bonds : bond 0.03854 ( 886) hydrogen bonds : angle 3.72191 ( 2568) Misc. bond : bond 0.00092 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7375 (mt0) REVERT: F 539 LYS cc_start: 0.8083 (tttm) cc_final: 0.7614 (mptt) REVERT: D 40 TRP cc_start: 0.7963 (t-100) cc_final: 0.6778 (t-100) REVERT: D 51 MET cc_start: 0.6129 (mmp) cc_final: 0.5594 (mmt) REVERT: H 51 MET cc_start: 0.5766 (mmp) cc_final: 0.5199 (mmt) REVERT: A 212 ARG cc_start: 0.7421 (tmm160) cc_final: 0.7216 (tmm-80) REVERT: E 64 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6958 (mm110) REVERT: G 517 GLU cc_start: 0.8450 (tp30) cc_final: 0.8235 (tt0) outliers start: 27 outliers final: 25 residues processed: 204 average time/residue: 0.1639 time to fit residues: 51.0716 Evaluate side-chains 201 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 495 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 546 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS C 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140384 restraints weight = 24520.472| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.32 r_work: 0.3333 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21181 Z= 0.108 Angle : 0.537 10.421 28729 Z= 0.264 Chirality : 0.042 0.271 3278 Planarity : 0.004 0.093 3607 Dihedral : 8.880 163.475 3303 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.32 % Allowed : 13.56 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.13 (0.17), residues: 2545 helix: 2.44 (0.16), residues: 1142 sheet: 1.09 (0.31), residues: 306 loop : -1.28 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.016 0.001 TYR G 510 PHE 0.014 0.001 PHE C 329 TRP 0.006 0.001 TRP C 294 HIS 0.003 0.000 HIS F 498 Details of bonding type rmsd covalent geometry : bond 0.00244 (21178) covalent geometry : angle 0.53677 (28729) hydrogen bonds : bond 0.04146 ( 886) hydrogen bonds : angle 3.73831 ( 2568) Misc. bond : bond 0.00105 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7405 (mt0) REVERT: F 539 LYS cc_start: 0.8075 (tttm) cc_final: 0.7620 (mptt) REVERT: D 40 TRP cc_start: 0.7920 (t-100) cc_final: 0.6738 (t-100) REVERT: D 51 MET cc_start: 0.5987 (mmp) cc_final: 0.5177 (mmt) REVERT: H 51 MET cc_start: 0.5768 (mmp) cc_final: 0.5396 (mmt) REVERT: A 212 ARG cc_start: 0.7380 (tmm160) cc_final: 0.7170 (tmm-80) REVERT: E 64 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7146 (mm110) REVERT: G 517 GLU cc_start: 0.8403 (tp30) cc_final: 0.8180 (tt0) REVERT: C 271 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7425 (m-30) outliers start: 30 outliers final: 26 residues processed: 203 average time/residue: 0.1557 time to fit residues: 48.9291 Evaluate side-chains 198 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 495 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 546 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 27 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 162 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 213 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 248 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS F 189 GLN C 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.167987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143025 restraints weight = 24710.189| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.29 r_work: 0.3405 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21181 Z= 0.099 Angle : 0.530 10.620 28729 Z= 0.259 Chirality : 0.042 0.269 3278 Planarity : 0.004 0.091 3607 Dihedral : 8.727 162.946 3303 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.19 % Allowed : 13.91 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.22 (0.17), residues: 2545 helix: 2.49 (0.16), residues: 1136 sheet: 1.12 (0.31), residues: 306 loop : -1.18 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 45 TYR 0.013 0.001 TYR G 510 PHE 0.014 0.001 PHE C 329 TRP 0.007 0.001 TRP C 294 HIS 0.003 0.000 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00221 (21178) covalent geometry : angle 0.53020 (28729) hydrogen bonds : bond 0.03827 ( 886) hydrogen bonds : angle 3.70565 ( 2568) Misc. bond : bond 0.00088 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7394 (mt0) REVERT: F 539 LYS cc_start: 0.8067 (tttm) cc_final: 0.7632 (mptt) REVERT: D 40 TRP cc_start: 0.7918 (t-100) cc_final: 0.6765 (t-100) REVERT: D 51 MET cc_start: 0.5925 (mmp) cc_final: 0.5457 (mmt) REVERT: H 51 MET cc_start: 0.5729 (mmp) cc_final: 0.5356 (mmt) REVERT: E 64 GLN cc_start: 0.7251 (mm-40) cc_final: 0.7019 (mm110) REVERT: C 271 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7377 (m-30) outliers start: 27 outliers final: 26 residues processed: 200 average time/residue: 0.1599 time to fit residues: 49.1073 Evaluate side-chains 201 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 495 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 546 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 47 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.164654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139115 restraints weight = 24775.835| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.31 r_work: 0.3356 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21181 Z= 0.133 Angle : 0.576 10.703 28729 Z= 0.285 Chirality : 0.043 0.279 3278 Planarity : 0.004 0.091 3607 Dihedral : 8.787 161.757 3303 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.28 % Allowed : 13.82 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.05 (0.17), residues: 2545 helix: 2.42 (0.16), residues: 1124 sheet: 1.02 (0.32), residues: 302 loop : -1.29 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.020 0.001 TYR G 510 PHE 0.015 0.001 PHE F 256 TRP 0.007 0.001 TRP A 142 HIS 0.005 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00316 (21178) covalent geometry : angle 0.57587 (28729) hydrogen bonds : bond 0.04943 ( 886) hydrogen bonds : angle 3.81801 ( 2568) Misc. bond : bond 0.00133 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3986.83 seconds wall clock time: 69 minutes 21.36 seconds (4161.36 seconds total)