Starting phenix.real_space_refine on Sat Jul 4 11:59:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qof_18536/07_2026/8qof_18536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qof_18536/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qof_18536/07_2026/8qof_18536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qof_18536/07_2026/8qof_18536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qof_18536/07_2026/8qof_18536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qof_18536/07_2026/8qof_18536.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 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: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.44, per 1000 atoms: 0.21 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: 1.58 Conformation dependent library (CDL) restraints added in 849.4 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: 0.53 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: 3.07 Time building geometry restraints manager: 2.06 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: 28540 3.11 - 6.22: 162 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: 12673 35.71 - 71.42: 292 71.42 - 107.13: 61 107.13 - 142.84: 26 142.84 - 178.56: 3 Dihedral angle restraints: 13055 sinusoidal: 5546 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 13052 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.810 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.608 15.560 28729 Z= 0.317 Chirality : 0.047 0.888 3278 Planarity : 0.004 0.065 3607 Dihedral : 18.000 178.556 8219 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/Z covalent geometry : bond 0.00486 / 0.30 (21178) covalent geometry : angle 0.60841 / 0.32 (28729) hydrogen bonds : bond 0.21373 / 14.09 ( 886) hydrogen bonds : angle 5.83852 / 4.13 ( 2568) Misc. bond : bond 0.44555 / 29.42 ( 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 : 0.600 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: 0.1507 time to fit residues: 93.4571 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 : 0.790 ------------------------------------------------------------------------------- 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... B 295 HIS B 448 GLN F 295 HIS F 448 GLN A 65 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147739 restraints weight = 24054.104| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.25 r_work: 0.3481 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1942 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= 0.129 Angle : 0.590 9.605 28729 Z= 0.292 Chirality : 0.044 0.296 3278 Planarity : 0.004 0.046 3607 Dihedral : 14.184 140.088 3317 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.32 % Allowed : 7.44 % Favored : 91.24 % 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: 2.18 (0.16), residues: 1131 sheet: 1.14 (0.32), residues: 286 loop : -1.13 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 117 TYR 0.016 0.001 TYR C 510 PHE 0.021 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/Z covalent geometry : bond 0.00286 / 0.13 (21178) covalent geometry : angle 0.59022 / 0.29 (28729) hydrogen bonds : bond 0.05264 / 3.47 ( 886) hydrogen bonds : angle 4.25035 / 2.99 ( 2568) Misc. bond : bond 0.00240 / 0.16 ( 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 238 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 THR cc_start: 0.9029 (m) cc_final: 0.8676 (p) REVERT: B 274 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7886 (mm-40) REVERT: B 469 MET cc_start: 0.8428 (tpt) cc_final: 0.8193 (tpp) REVERT: F 226 THR cc_start: 0.8939 (m) cc_final: 0.8634 (p) REVERT: G 323 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8318 (ttpp) outliers start: 30 outliers final: 26 residues processed: 234 average time/residue: 0.1567 time to fit residues: 55.5610 Evaluate side-chains 205 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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: 7.9990 chunk 247 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 473 GLN A 200 HIS G 143 ASN G 269 HIS C 78 HIS C 143 ASN C 269 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.164319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138018 restraints weight = 24703.575| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.34 r_work: 0.3329 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21181 Z= 0.151 Angle : 0.601 9.676 28729 Z= 0.299 Chirality : 0.045 0.299 3278 Planarity : 0.004 0.049 3607 Dihedral : 11.852 147.283 3309 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.54 % Allowed : 9.82 % Favored : 88.64 % 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: 0.83 (0.17), residues: 2545 helix: 2.19 (0.16), residues: 1131 sheet: 1.00 (0.31), residues: 302 loop : -1.40 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 112 TYR 0.020 0.001 TYR G 510 PHE 0.019 0.001 PHE C 329 TRP 0.008 0.001 TRP F 116 HIS 0.004 0.001 HIS C 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (21178) covalent geometry : angle 0.60127 / 0.30 (28729) hydrogen bonds : bond 0.05765 / 3.83 ( 886) hydrogen bonds : angle 4.05040 / 2.84 ( 2568) Misc. bond : bond 0.00210 / 0.14 ( 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 245 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7964 (mm-40) REVERT: B 469 MET cc_start: 0.8574 (tpt) cc_final: 0.8362 (tpp) REVERT: F 539 LYS cc_start: 0.8182 (tttm) cc_final: 0.7654 (mptt) REVERT: D 51 MET cc_start: 0.6465 (mmm) cc_final: 0.5900 (mmt) REVERT: A 92 ARG cc_start: 0.6972 (tmt-80) cc_final: 0.6641 (tpt170) REVERT: A 120 MET cc_start: 0.7578 (mmm) cc_final: 0.7316 (mmm) REVERT: C 158 MET cc_start: 0.8449 (ttp) cc_final: 0.8202 (ttm) outliers start: 35 outliers final: 28 residues processed: 237 average time/residue: 0.1735 time to fit residues: 60.6912 Evaluate side-chains 211 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 A residue 192 VAL 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 C residue 77 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 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: 3.9990 chunk 176 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 221 optimal weight: 0.0060 chunk 166 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 200 HIS G 78 HIS G 143 ASN C 78 HIS C 523 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138990 restraints weight = 24682.641| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.32 r_work: 0.3331 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21181 Z= 0.121 Angle : 0.550 8.818 28729 Z= 0.275 Chirality : 0.043 0.271 3278 Planarity : 0.004 0.050 3607 Dihedral : 11.224 149.265 3309 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.23 % Allowed : 11.71 % Favored : 87.06 % 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: 2.27 (0.16), residues: 1131 sheet: 0.97 (0.31), residues: 302 loop : -1.46 (0.17), residues: 1112 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 0.017 0.001 PHE C 329 TRP 0.009 0.001 TRP G 294 HIS 0.003 0.001 HIS G 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (21178) covalent geometry : angle 0.55001 / 0.27 (28729) hydrogen bonds : bond 0.04728 / 3.14 ( 886) hydrogen bonds : angle 3.90929 / 2.75 ( 2568) Misc. bond : bond 0.00159 / 0.10 ( 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 218 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 469 MET cc_start: 0.8556 (tpt) cc_final: 0.8293 (tpp) REVERT: F 539 LYS cc_start: 0.8134 (tttm) cc_final: 0.7605 (mptt) REVERT: H 51 MET cc_start: 0.6174 (mmp) cc_final: 0.5452 (mmt) REVERT: A 92 ARG cc_start: 0.6938 (tmt-80) cc_final: 0.6553 (tpt170) REVERT: C 158 MET cc_start: 0.8418 (ttp) cc_final: 0.8178 (ttm) outliers start: 28 outliers final: 24 residues processed: 215 average time/residue: 0.1724 time to fit residues: 54.8238 Evaluate side-chains 202 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 106 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 201 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 143 ASN C 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137445 restraints weight = 24642.470| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.32 r_work: 0.3322 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21181 Z= 0.131 Angle : 0.569 13.401 28729 Z= 0.282 Chirality : 0.044 0.273 3278 Planarity : 0.004 0.052 3607 Dihedral : 10.532 155.249 3309 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.76 % Allowed : 12.59 % Favored : 85.65 % 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: 0.83 (0.17), residues: 2545 helix: 2.20 (0.16), residues: 1143 sheet: 0.95 (0.31), residues: 302 loop : -1.45 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 44 TYR 0.018 0.001 TYR C 510 PHE 0.016 0.001 PHE C 329 TRP 0.007 0.001 TRP G 294 HIS 0.003 0.001 HIS C 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (21178) covalent geometry : angle 0.56933 / 0.28 (28729) hydrogen bonds : bond 0.05075 / 3.38 ( 886) hydrogen bonds : angle 3.89793 / 2.74 ( 2568) Misc. bond : bond 0.00164 / 0.11 ( 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 228 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7361 (mt0) REVERT: B 469 MET cc_start: 0.8558 (tpt) cc_final: 0.8282 (tpp) REVERT: F 539 LYS cc_start: 0.8110 (tttm) cc_final: 0.7630 (mptt) REVERT: D 51 MET cc_start: 0.6033 (mmp) cc_final: 0.5211 (mmt) REVERT: A 66 MET cc_start: 0.6655 (ptt) cc_final: 0.6394 (ptt) REVERT: A 92 ARG cc_start: 0.7012 (tmt-80) cc_final: 0.6612 (tpt170) REVERT: C 158 MET cc_start: 0.8394 (ttp) cc_final: 0.8132 (ttm) outliers start: 40 outliers final: 32 residues processed: 222 average time/residue: 0.1686 time to fit residues: 56.1299 Evaluate side-chains 211 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 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 D residue 53 SER Chi-restraints excluded: chain H residue 53 SER 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 342 THR 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 129 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 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: 0.0970 chunk 230 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 375 GLN G 78 HIS G 142 HIS C 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140230 restraints weight = 24552.107| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.31 r_work: 0.3311 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21181 Z= 0.101 Angle : 0.525 11.756 28729 Z= 0.260 Chirality : 0.042 0.272 3278 Planarity : 0.004 0.049 3607 Dihedral : 9.654 158.229 3309 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.58 % Allowed : 13.25 % Favored : 85.17 % 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: 0.96 (0.17), residues: 2545 helix: 2.32 (0.16), residues: 1143 sheet: 1.01 (0.31), residues: 306 loop : -1.40 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.014 0.001 TYR G 510 PHE 0.015 0.001 PHE C 329 TRP 0.007 0.001 TRP C 294 HIS 0.003 0.001 HIS F 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (21178) covalent geometry : angle 0.52516 / 0.26 (28729) hydrogen bonds : bond 0.04100 / 2.73 ( 886) hydrogen bonds : angle 3.77816 / 2.66 ( 2568) Misc. bond : bond 0.00105 / 0.07 ( 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 229 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7395 (mt0) REVERT: F 539 LYS cc_start: 0.8092 (tttm) cc_final: 0.7635 (mptt) REVERT: D 48 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: D 51 MET cc_start: 0.6040 (mmp) cc_final: 0.5547 (mmt) REVERT: H 51 MET cc_start: 0.6506 (mmm) cc_final: 0.5592 (mmt) REVERT: A 66 MET cc_start: 0.6611 (ptt) cc_final: 0.6321 (ptt) REVERT: A 92 ARG cc_start: 0.6963 (tmt-80) cc_final: 0.6645 (tpt170) REVERT: E 64 GLN cc_start: 0.7330 (mm-40) cc_final: 0.7025 (mm110) REVERT: G 517 GLU cc_start: 0.8378 (tp30) cc_final: 0.7880 (tp30) REVERT: C 517 GLU cc_start: 0.8274 (tp30) cc_final: 0.7708 (tp30) outliers start: 36 outliers final: 27 residues processed: 224 average time/residue: 0.1641 time to fit residues: 55.3392 Evaluate side-chains 210 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 48 PHE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 53 optimal weight: 0.0770 chunk 172 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 152 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 473 GLN C 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.167404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141644 restraints weight = 24585.265| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.33 r_work: 0.3350 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21181 Z= 0.093 Angle : 0.512 13.283 28729 Z= 0.251 Chirality : 0.042 0.268 3278 Planarity : 0.004 0.049 3607 Dihedral : 9.206 161.887 3309 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.28 % Allowed : 13.69 % Favored : 85.04 % 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: 1.09 (0.17), residues: 2545 helix: 2.40 (0.16), residues: 1148 sheet: 1.16 (0.31), residues: 304 loop : -1.35 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 45 TYR 0.014 0.001 TYR B 460 PHE 0.014 0.001 PHE C 329 TRP 0.007 0.001 TRP C 294 HIS 0.004 0.000 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (21178) covalent geometry : angle 0.51226 / 0.25 (28729) hydrogen bonds : bond 0.03630 / 2.41 ( 886) hydrogen bonds : angle 3.70996 / 2.61 ( 2568) Misc. bond : bond 0.00086 / 0.06 ( 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 223 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7398 (mt0) REVERT: F 539 LYS cc_start: 0.8069 (tttm) cc_final: 0.7598 (mptt) REVERT: D 40 TRP cc_start: 0.7932 (t-100) cc_final: 0.6777 (t-100) REVERT: H 51 MET cc_start: 0.6478 (mmm) cc_final: 0.5683 (mmt) REVERT: A 66 MET cc_start: 0.6629 (ptt) cc_final: 0.6353 (ptt) REVERT: A 92 ARG cc_start: 0.6924 (tmt-80) cc_final: 0.6618 (tpt170) REVERT: E 64 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6919 (mm110) outliers start: 29 outliers final: 26 residues processed: 217 average time/residue: 0.1684 time to fit residues: 54.9655 Evaluate side-chains 211 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 D 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 144 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 250 optimal weight: 0.0000 chunk 53 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 77 optimal weight: 0.0070 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3898 r_free = 0.3898 target = 0.167725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142142 restraints weight = 24597.051| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.31 r_work: 0.3359 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21181 Z= 0.095 Angle : 0.522 13.309 28729 Z= 0.255 Chirality : 0.042 0.262 3278 Planarity : 0.004 0.098 3607 Dihedral : 8.953 163.274 3309 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.36 % Allowed : 13.78 % Favored : 84.86 % 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: 1.16 (0.17), residues: 2545 helix: 2.44 (0.16), residues: 1147 sheet: 1.20 (0.31), residues: 304 loop : -1.28 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.013 0.001 TYR G 68 PHE 0.013 0.001 PHE C 329 TRP 0.006 0.001 TRP C 294 HIS 0.003 0.000 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (21178) covalent geometry : angle 0.52209 / 0.25 (28729) hydrogen bonds : bond 0.03670 / 2.43 ( 886) hydrogen bonds : angle 3.69376 / 2.60 ( 2568) Misc. bond : bond 0.00091 / 0.06 ( 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 222 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7372 (mt0) REVERT: F 539 LYS cc_start: 0.8033 (tttm) cc_final: 0.7600 (mptt) REVERT: D 40 TRP cc_start: 0.7925 (t-100) cc_final: 0.6726 (t-100) REVERT: H 51 MET cc_start: 0.6468 (mmm) cc_final: 0.5694 (mmt) REVERT: A 66 MET cc_start: 0.6641 (ptt) cc_final: 0.6354 (ptt) REVERT: A 92 ARG cc_start: 0.6908 (tmt-80) cc_final: 0.6640 (tpt170) REVERT: G 517 GLU cc_start: 0.8402 (tp30) cc_final: 0.8199 (tt0) outliers start: 31 outliers final: 27 residues processed: 217 average time/residue: 0.1607 time to fit residues: 52.7633 Evaluate side-chains 207 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 331 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 88 LEU 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 F residue 450 THR Chi-restraints excluded: chain D 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: 4.9990 chunk 43 optimal weight: 0.0670 chunk 244 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 162 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 498 HIS E 64 GLN G 78 HIS C 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.168671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143198 restraints weight = 24544.863| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.29 r_work: 0.3401 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3356 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= 0.097 Angle : 0.523 13.502 28729 Z= 0.255 Chirality : 0.042 0.262 3278 Planarity : 0.004 0.091 3607 Dihedral : 8.787 163.023 3309 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.28 % Allowed : 14.04 % Favored : 84.68 % 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: 1.16 (0.17), residues: 2545 helix: 2.46 (0.16), residues: 1140 sheet: 1.19 (0.31), residues: 304 loop : -1.27 (0.17), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.013 0.001 TYR G 510 PHE 0.013 0.001 PHE C 329 TRP 0.006 0.001 TRP C 294 HIS 0.004 0.000 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (21178) covalent geometry : angle 0.52336 / 0.26 (28729) hydrogen bonds : bond 0.03725 / 2.48 ( 886) hydrogen bonds : angle 3.68367 / 2.59 ( 2568) Misc. bond : bond 0.00096 / 0.06 ( 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 216 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7383 (mt0) REVERT: F 539 LYS cc_start: 0.8072 (tttm) cc_final: 0.7651 (mptt) REVERT: D 40 TRP cc_start: 0.7940 (t-100) cc_final: 0.6769 (t-100) REVERT: D 51 MET cc_start: 0.5923 (mmp) cc_final: 0.5483 (mmp) REVERT: H 51 MET cc_start: 0.6438 (mmm) cc_final: 0.5717 (mmt) REVERT: A 66 MET cc_start: 0.6671 (ptt) cc_final: 0.6397 (ptt) REVERT: A 92 ARG cc_start: 0.6914 (tmt-80) cc_final: 0.6641 (tpt170) REVERT: C 271 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7367 (m-30) outliers start: 29 outliers final: 26 residues processed: 210 average time/residue: 0.1581 time to fit residues: 50.2440 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 : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 331 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 88 LEU 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 F residue 450 THR Chi-restraints excluded: chain D 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 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: 0.0970 chunk 93 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 189 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 = 0.3912 r_free = 0.3912 target = 0.168367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143407 restraints weight = 24740.898| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.31 r_work: 0.3409 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3402 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= 0.100 Angle : 0.533 13.151 28729 Z= 0.260 Chirality : 0.042 0.267 3278 Planarity : 0.004 0.088 3607 Dihedral : 8.611 161.787 3309 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.28 % Allowed : 14.22 % Favored : 84.51 % 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: 1.17 (0.17), residues: 2545 helix: 2.46 (0.16), residues: 1141 sheet: 1.14 (0.31), residues: 306 loop : -1.25 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.014 0.001 TYR C 510 PHE 0.013 0.001 PHE C 329 TRP 0.006 0.001 TRP C 294 HIS 0.006 0.000 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (21178) covalent geometry : angle 0.53282 / 0.26 (28729) hydrogen bonds : bond 0.03793 / 2.51 ( 886) hydrogen bonds : angle 3.69106 / 2.59 ( 2568) Misc. bond : bond 0.00097 / 0.06 ( 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 213 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 274 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7395 (mt0) REVERT: F 539 LYS cc_start: 0.8022 (tttm) cc_final: 0.7668 (mptt) REVERT: D 40 TRP cc_start: 0.7879 (t-100) cc_final: 0.6668 (t-100) REVERT: D 51 MET cc_start: 0.6032 (mmp) cc_final: 0.5402 (mmp) REVERT: H 51 MET cc_start: 0.6363 (mmm) cc_final: 0.5648 (mmt) REVERT: A 92 ARG cc_start: 0.6954 (tmt-80) cc_final: 0.6688 (tpt170) REVERT: G 308 GLU cc_start: 0.8231 (mp0) cc_final: 0.7896 (mp0) outliers start: 29 outliers final: 29 residues processed: 207 average time/residue: 0.1575 time to fit residues: 48.8332 Evaluate side-chains 211 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 331 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 88 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 47 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 226 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138104 restraints weight = 24826.006| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.33 r_work: 0.3328 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21181 Z= 0.141 Angle : 0.589 13.023 28729 Z= 0.291 Chirality : 0.044 0.302 3278 Planarity : 0.004 0.088 3607 Dihedral : 8.789 160.036 3309 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.45 % Allowed : 14.04 % Favored : 84.51 % 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: 0.98 (0.17), residues: 2545 helix: 2.34 (0.16), residues: 1133 sheet: 1.00 (0.31), residues: 302 loop : -1.35 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.021 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/Z covalent geometry : bond 0.00339 / 0.14 (21178) covalent geometry : angle 0.58928 / 0.29 (28729) hydrogen bonds : bond 0.05139 / 3.43 ( 886) hydrogen bonds : angle 3.84160 / 2.69 ( 2568) Misc. bond : bond 0.00156 / 0.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4048.06 seconds wall clock time: 70 minutes 26.64 seconds (4226.64 seconds total)