Starting phenix.real_space_refine on Thu Feb 5 20:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hj3_52209/02_2026/9hj3_52209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hj3_52209/02_2026/9hj3_52209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hj3_52209/02_2026/9hj3_52209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hj3_52209/02_2026/9hj3_52209.map" model { file = "/net/cci-nas-00/data/ceres_data/9hj3_52209/02_2026/9hj3_52209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hj3_52209/02_2026/9hj3_52209.cif" } resolution = 3.46 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= 0.003 sd= 1.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 12458 2.51 5 N 3215 2.21 5 O 3783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19521 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4201 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 25, 'TRANS': 494} Chain breaks: 3 Chain: "D" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1622 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 6, 'TRANS': 186} Chain: "F" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3181 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 12, 'TRANS': 393} Chain: "H" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3522 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 18, 'TRANS': 429} Chain breaks: 2 Chain: "I" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1337 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "J" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "G" Number of atoms: 4065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4065 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 16, 'TRANS': 503} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'TDA': 1, 'Z41': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TDA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.53, per 1000 atoms: 0.23 Number of scatterers: 19521 At special positions: 0 Unit cell: (133.2, 135.42, 198.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 3783 8.00 N 3215 7.00 C 12458 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 992.4 milliseconds 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB CYS G 18 " Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 23 sheets defined 21.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.219A pdb=" N ARG A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 392 through 398 removed outlier: 3.934A pdb=" N VAL A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.722A pdb=" N GLY A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 526 through 530 removed outlier: 4.255A pdb=" N LYS A 530 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 828 through 832 Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 82 through 97 removed outlier: 3.960A pdb=" N TYR D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.740A pdb=" N ALA D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 142 removed outlier: 3.752A pdb=" N TYR D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 177 removed outlier: 4.373A pdb=" N GLU D 150 " --> pdb=" O THR D 146 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 Processing helix chain 'D' and resid 203 through 222 removed outlier: 3.605A pdb=" N TYR D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.687A pdb=" N ALA D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 33 Processing helix chain 'F' and resid 43 through 49 removed outlier: 3.548A pdb=" N ALA F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 removed outlier: 3.532A pdb=" N TYR F 70 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR F 71 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 72 " --> pdb=" O SER F 69 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 73 " --> pdb=" O TYR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 226 removed outlier: 4.363A pdb=" N LYS F 226 " --> pdb=" O ALA F 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 223 through 226' Processing helix chain 'F' and resid 300 through 303 Processing helix chain 'F' and resid 311 through 322 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'H' and resid 69 through 75 removed outlier: 3.855A pdb=" N ASP H 73 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 removed outlier: 4.210A pdb=" N VAL H 115 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 277 removed outlier: 3.638A pdb=" N GLY H 277 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 489 No H-bonds generated for 'chain 'H' and resid 487 through 489' Processing helix chain 'I' and resid 31 through 50 removed outlier: 3.644A pdb=" N ALA I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 56 Processing helix chain 'I' and resid 136 through 138 No H-bonds generated for 'chain 'I' and resid 136 through 138' Processing helix chain 'I' and resid 139 through 146 Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'J' and resid 29 through 32 Processing helix chain 'J' and resid 33 through 44 removed outlier: 3.754A pdb=" N ALA J 37 " --> pdb=" O ASP J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 126 through 131 removed outlier: 4.285A pdb=" N TYR J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR J 131 " --> pdb=" O ASN J 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 126 through 131' Processing helix chain 'J' and resid 153 through 160 Processing helix chain 'J' and resid 166 through 171 removed outlier: 3.985A pdb=" N LEU J 170 " --> pdb=" O PRO J 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU J 171 " --> pdb=" O ALA J 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 166 through 171' Processing helix chain 'J' and resid 172 through 176 Processing helix chain 'J' and resid 187 through 191 Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 119 through 123 removed outlier: 3.649A pdb=" N LYS G 123 " --> pdb=" O PRO G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 187 Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 226 through 246 Processing helix chain 'G' and resid 252 through 260 removed outlier: 3.674A pdb=" N GLU G 258 " --> pdb=" O GLN G 254 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 259 " --> pdb=" O LEU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 341 removed outlier: 3.625A pdb=" N LYS G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 369 Processing helix chain 'G' and resid 406 through 408 No H-bonds generated for 'chain 'G' and resid 406 through 408' Processing helix chain 'G' and resid 409 through 414 Processing helix chain 'G' and resid 440 through 459 Processing helix chain 'G' and resid 460 through 462 No H-bonds generated for 'chain 'G' and resid 460 through 462' Processing helix chain 'G' and resid 463 through 470 Processing helix chain 'G' and resid 515 through 520 Processing helix chain 'G' and resid 521 through 525 removed outlier: 3.914A pdb=" N LYS G 525 " --> pdb=" O PRO G 522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.713A pdb=" N ASP A 322 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU A 296 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU A 368 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN A 298 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N MET A 370 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 300 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE A 372 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 302 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLU A 374 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE A 361 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 353 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 386 removed outlier: 4.297A pdb=" N ILE A 380 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE A 446 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS A 382 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU A 448 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN A 384 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 475 removed outlier: 4.298A pdb=" N SER A 591 " --> pdb=" O LYS A 626 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 626 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 621 " --> pdb=" O ASP A 640 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 710 through 718 current: chain 'A' and resid 733 through 744 removed outlier: 3.745A pdb=" N GLU A 801 " --> pdb=" O MET A 735 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 799 " --> pdb=" O ARG A 737 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TYR A 795 " --> pdb=" O TRP A 826 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TRP A 826 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG A 797 " --> pdb=" O ASN A 824 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN A 824 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLY A 799 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 822 " --> pdb=" O GLY A 799 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 801 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A 820 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG A 803 " --> pdb=" O GLY A 818 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY A 818 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 816 " --> pdb=" O PRO A 805 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 807 " --> pdb=" O ILE A 814 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 838 through 839 current: chain 'A' and resid 854 through 862 Processing sheet with id=AA4, first strand: chain 'A' and resid 757 through 759 removed outlier: 6.276A pdb=" N ASP A 758 " --> pdb=" O ILE A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 37 through 38 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 37 through 38 current: chain 'F' and resid 96 through 100 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 96 through 100 current: chain 'F' and resid 118 through 139 removed outlier: 6.616A pdb=" N LEU F 156 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN F 129 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLY F 154 " --> pdb=" O ASN F 129 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY F 131 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY F 152 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR F 133 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE F 150 " --> pdb=" O THR F 133 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER F 135 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG F 148 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER F 137 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR F 146 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER F 149 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR F 201 " --> pdb=" O MET F 190 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 228 through 237 current: chain 'F' and resid 261 through 262 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 261 through 262 current: chain 'F' and resid 289 through 298 removed outlier: 3.669A pdb=" N THR F 328 " --> pdb=" O THR F 359 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 370 through 379 current: chain 'F' and resid 408 through 414 Processing sheet with id=AA6, first strand: chain 'F' and resid 240 through 242 removed outlier: 4.603A pdb=" N PHE F 271 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP F 268 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL F 308 " --> pdb=" O ASP F 268 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 306 " --> pdb=" O THR F 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 363 through 364 removed outlier: 3.537A pdb=" N LYS F 367 " --> pdb=" O ILE F 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 41 through 42 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 56 removed outlier: 4.048A pdb=" N ASN H 64 " --> pdb=" O ASN H 142 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL H 125 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS H 94 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 101 " --> pdb=" O MET H 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 153 through 154 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 153 through 154 current: chain 'H' and resid 469 through 473 removed outlier: 4.065A pdb=" N LYS H 479 " --> pdb=" O GLY H 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 172 through 177 Processing sheet with id=AB3, first strand: chain 'H' and resid 222 through 229 removed outlier: 6.054A pdb=" N SER H 226 " --> pdb=" O LEU H 237 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU H 237 " --> pdb=" O SER H 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 265 through 272 removed outlier: 8.060A pdb=" N THR H 266 " --> pdb=" O GLU H 291 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU H 291 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU H 268 " --> pdb=" O ILE H 289 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE H 289 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR H 270 " --> pdb=" O ALA H 287 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR H 315 " --> pdb=" O PHE H 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 324 through 332 removed outlier: 5.787A pdb=" N ASN H 325 " --> pdb=" O ASN H 345 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN H 345 " --> pdb=" O ASN H 325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 382 through 389 removed outlier: 5.706A pdb=" N ASP H 383 " --> pdb=" O LYS H 398 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS H 398 " --> pdb=" O ASP H 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 68 through 73 current: chain 'I' and resid 106 through 109 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 106 through 109 current: chain 'I' and resid 180 through 189 Processing sheet with id=AB8, first strand: chain 'J' and resid 48 through 51 removed outlier: 7.951A pdb=" N GLU J 68 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE J 80 " --> pdb=" O GLU J 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 77 through 82 current: chain 'J' and resid 112 through 116 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 112 through 116 current: chain 'J' and resid 146 through 151 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 146 through 151 current: chain 'J' and resid 202 through 211 Processing sheet with id=AB9, first strand: chain 'G' and resid 38 through 52 removed outlier: 3.929A pdb=" N THR G 47 " --> pdb=" O THR G 359 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 354 through 359 current: chain 'G' and resid 423 through 427 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 423 through 427 current: chain 'G' and resid 498 through 503 Processing sheet with id=AC1, first strand: chain 'G' and resid 63 through 70 removed outlier: 7.426A pdb=" N TYR G 64 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE G 80 " --> pdb=" O TYR G 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 74 through 82 current: chain 'G' and resid 189 through 200 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 189 through 200 current: chain 'G' and resid 310 through 318 Processing sheet with id=AC2, first strand: chain 'G' and resid 97 through 100 removed outlier: 3.607A pdb=" N SER G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 126 through 130 removed outlier: 3.691A pdb=" N GLY G 136 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP G 130 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 345 through 347 Processing sheet with id=AC5, first strand: chain 'G' and resid 380 through 382 577 hydrogen bonds defined for protein. 1533 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: 3.47 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 3284 1.31 - 1.45: 5653 1.45 - 1.59: 10908 1.59 - 1.73: 3 1.73 - 1.87: 116 Bond restraints: 19964 Sorted by residual: bond pdb=" C CYS G 18 " pdb=" N ASP G 19 " ideal model delta sigma weight residual 1.329 1.404 -0.075 1.43e-02 4.89e+03 2.77e+01 bond pdb=" CG1 ILE I 173 " pdb=" CD1 ILE I 173 " ideal model delta sigma weight residual 1.513 1.336 0.177 3.90e-02 6.57e+02 2.06e+01 bond pdb=" CB VAL H 224 " pdb=" CG2 VAL H 224 " ideal model delta sigma weight residual 1.521 1.393 0.128 3.30e-02 9.18e+02 1.51e+01 bond pdb=" N ASP G 19 " pdb=" CA ASP G 19 " ideal model delta sigma weight residual 1.454 1.504 -0.049 1.27e-02 6.20e+03 1.50e+01 bond pdb=" CA ASP G 19 " pdb=" CB ASP G 19 " ideal model delta sigma weight residual 1.530 1.586 -0.057 1.55e-02 4.16e+03 1.34e+01 ... (remaining 19959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.22: 26947 5.22 - 10.44: 83 10.44 - 15.66: 6 15.66 - 20.88: 2 20.88 - 26.09: 1 Bond angle restraints: 27039 Sorted by residual: angle pdb=" C CYS G 18 " pdb=" CA CYS G 18 " pdb=" CB CYS G 18 " ideal model delta sigma weight residual 110.10 136.19 -26.09 1.90e+00 2.77e-01 1.89e+02 angle pdb=" CG MET A 700 " pdb=" SD MET A 700 " pdb=" CE MET A 700 " ideal model delta sigma weight residual 100.90 84.18 16.72 2.20e+00 2.07e-01 5.78e+01 angle pdb=" CA CYS G 18 " pdb=" C CYS G 18 " pdb=" N ASP G 19 " ideal model delta sigma weight residual 116.20 130.36 -14.16 2.00e+00 2.50e-01 5.02e+01 angle pdb=" CA CYS G 18 " pdb=" C CYS G 18 " pdb=" O CYS G 18 " ideal model delta sigma weight residual 120.80 111.18 9.62 1.70e+00 3.46e-01 3.20e+01 angle pdb=" N SER F 415 " pdb=" CA SER F 415 " pdb=" C SER F 415 " ideal model delta sigma weight residual 107.28 117.10 -9.82 1.75e+00 3.27e-01 3.15e+01 ... (remaining 27034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 10889 18.04 - 36.08: 766 36.08 - 54.12: 98 54.12 - 72.16: 39 72.16 - 90.19: 11 Dihedral angle restraints: 11803 sinusoidal: 4711 harmonic: 7092 Sorted by residual: dihedral pdb=" CD ARG F 188 " pdb=" NE ARG F 188 " pdb=" CZ ARG F 188 " pdb=" NH1 ARG F 188 " ideal model delta sinusoidal sigma weight residual 0.00 -55.23 55.23 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CA VAL I 95 " pdb=" C VAL I 95 " pdb=" N TYR I 96 " pdb=" CA TYR I 96 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN G 434 " pdb=" C GLN G 434 " pdb=" N TYR G 435 " pdb=" CA TYR G 435 " ideal model delta harmonic sigma weight residual 180.00 154.20 25.80 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 11800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.850: 2913 0.850 - 1.700: 0 1.700 - 2.550: 0 2.550 - 3.400: 0 3.400 - 4.250: 1 Chirality restraints: 2914 Sorted by residual: chirality pdb=" CA CYS G 18 " pdb=" N CYS G 18 " pdb=" C CYS G 18 " pdb=" CB CYS G 18 " both_signs ideal model delta sigma weight residual False 2.51 -1.74 4.25 2.00e-01 2.50e+01 4.52e+02 chirality pdb=" CA TRP A 607 " pdb=" N TRP A 607 " pdb=" C TRP A 607 " pdb=" CB TRP A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE F 337 " pdb=" CA ILE F 337 " pdb=" CG1 ILE F 337 " pdb=" CG2 ILE F 337 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2911 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 188 " 0.837 9.50e-02 1.11e+02 3.75e-01 8.64e+01 pdb=" NE ARG F 188 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG F 188 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 188 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 188 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 607 " -0.037 2.00e-02 2.50e+03 3.68e-02 3.38e+01 pdb=" CG TRP A 607 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP A 607 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP A 607 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 607 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 607 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 607 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 607 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 607 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 607 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 413 " 0.346 9.50e-02 1.11e+02 1.55e-01 1.48e+01 pdb=" NE ARG F 413 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG F 413 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG F 413 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 413 " 0.011 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 285 2.67 - 3.22: 18524 3.22 - 3.78: 27877 3.78 - 4.34: 40475 4.34 - 4.90: 66845 Nonbonded interactions: 154006 Sorted by model distance: nonbonded pdb=" O GLY F 36 " pdb=" OH TYR F 361 " model vdw 2.106 3.040 nonbonded pdb=" NH1 ARG A 839 " pdb=" OD1 ASN F 24 " model vdw 2.119 3.120 nonbonded pdb=" ND2 ASN I 86 " pdb=" O MET I 149 " model vdw 2.131 3.120 nonbonded pdb=" ND2 ASN I 101 " pdb=" OE2 GLU I 105 " model vdw 2.140 3.120 nonbonded pdb=" OG1 THR F 231 " pdb=" OG1 THR F 282 " model vdw 2.168 3.040 ... (remaining 154001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.770 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.006 0.177 19966 Z= 0.268 Angle : 0.939 26.094 27039 Z= 0.491 Chirality : 0.096 4.250 2914 Planarity : 0.010 0.375 3486 Dihedral : 13.038 90.195 7303 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.45 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2420 helix: -0.79 (0.25), residues: 403 sheet: -0.07 (0.18), residues: 772 loop : -1.56 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 659 TYR 0.046 0.002 TYR I 163 PHE 0.045 0.003 PHE I 107 TRP 0.097 0.004 TRP A 607 HIS 0.006 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00564 (19964) covalent geometry : angle 0.93937 (27039) hydrogen bonds : bond 0.17352 ( 577) hydrogen bonds : angle 7.43658 ( 1533) Misc. bond : bond 0.07730 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 ASP cc_start: 0.7457 (m-30) cc_final: 0.7237 (m-30) REVERT: A 423 MET cc_start: 0.7690 (ttp) cc_final: 0.7472 (ttp) REVERT: A 854 MET cc_start: 0.6749 (mmt) cc_final: 0.6365 (mmp) REVERT: F 373 TYR cc_start: 0.6942 (m-80) cc_final: 0.6641 (m-80) REVERT: H 240 ASN cc_start: 0.8278 (t0) cc_final: 0.7801 (t0) REVERT: H 274 ASP cc_start: 0.7963 (t0) cc_final: 0.7745 (t0) REVERT: H 323 ILE cc_start: 0.8621 (mm) cc_final: 0.8413 (pt) REVERT: H 400 THR cc_start: 0.7738 (p) cc_final: 0.7397 (t) REVERT: J 78 MET cc_start: 0.8861 (tmm) cc_final: 0.8387 (ttp) REVERT: G 20 ASP cc_start: 0.8081 (p0) cc_final: 0.7638 (p0) REVERT: G 57 TYR cc_start: 0.8312 (t80) cc_final: 0.7979 (t80) REVERT: G 94 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7466 (mm-30) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1449 time to fit residues: 66.8286 Evaluate side-chains 225 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 502 GLN A 544 GLN A 624 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 GLN H 162 ASN H 172 GLN H 187 ASN ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 ASN G 213 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109888 restraints weight = 27599.576| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.86 r_work: 0.3057 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19966 Z= 0.143 Angle : 0.664 16.015 27039 Z= 0.351 Chirality : 0.048 0.408 2914 Planarity : 0.005 0.086 3486 Dihedral : 6.907 59.425 2722 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.13 % Allowed : 6.05 % Favored : 92.82 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2420 helix: -0.32 (0.25), residues: 412 sheet: 0.03 (0.18), residues: 811 loop : -1.46 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 107 TYR 0.026 0.002 TYR I 163 PHE 0.027 0.002 PHE D 94 TRP 0.017 0.002 TRP A 706 HIS 0.003 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00319 (19964) covalent geometry : angle 0.66450 (27039) hydrogen bonds : bond 0.04154 ( 577) hydrogen bonds : angle 5.30809 ( 1533) Misc. bond : bond 0.00129 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 TYR cc_start: 0.7623 (t80) cc_final: 0.7305 (t80) REVERT: A 735 MET cc_start: 0.8800 (ttp) cc_final: 0.8570 (tmm) REVERT: D 160 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6597 (t0) REVERT: D 202 ASP cc_start: 0.8320 (t0) cc_final: 0.7737 (t0) REVERT: F 286 ASP cc_start: 0.8129 (t70) cc_final: 0.7503 (t70) REVERT: H 127 LYS cc_start: 0.6517 (ttmt) cc_final: 0.6247 (ttmm) REVERT: H 145 MET cc_start: 0.7631 (ttp) cc_final: 0.7339 (ttp) REVERT: H 274 ASP cc_start: 0.8949 (t0) cc_final: 0.8564 (t0) REVERT: H 323 ILE cc_start: 0.8404 (mm) cc_final: 0.7987 (pt) REVERT: H 400 THR cc_start: 0.8177 (p) cc_final: 0.7867 (t) REVERT: J 74 ASP cc_start: 0.8276 (t0) cc_final: 0.7195 (t0) REVERT: J 78 MET cc_start: 0.8802 (tmm) cc_final: 0.8539 (ttp) REVERT: J 112 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: G 38 LYS cc_start: 0.7660 (mmmm) cc_final: 0.7279 (tttt) REVERT: G 57 TYR cc_start: 0.8425 (t80) cc_final: 0.8085 (t80) REVERT: G 94 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7959 (mm-30) REVERT: G 123 LYS cc_start: 0.8468 (ptmt) cc_final: 0.8246 (pttm) REVERT: G 177 ASN cc_start: 0.8238 (m110) cc_final: 0.8017 (m110) REVERT: G 282 MET cc_start: 0.9032 (ttm) cc_final: 0.8829 (ttp) REVERT: G 292 ASP cc_start: 0.7835 (t70) cc_final: 0.7428 (m-30) outliers start: 24 outliers final: 11 residues processed: 261 average time/residue: 0.1400 time to fit residues: 55.9197 Evaluate side-chains 218 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 142 TRP Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain G residue 488 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 114 optimal weight: 0.0980 chunk 167 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106326 restraints weight = 27803.180| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.97 r_work: 0.2994 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19966 Z= 0.173 Angle : 0.626 13.951 27039 Z= 0.329 Chirality : 0.047 0.364 2914 Planarity : 0.004 0.050 3486 Dihedral : 6.401 58.922 2722 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.47 % Allowed : 8.84 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.17), residues: 2420 helix: 0.05 (0.26), residues: 404 sheet: -0.03 (0.18), residues: 847 loop : -1.45 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 423 TYR 0.023 0.002 TYR A 307 PHE 0.027 0.002 PHE D 94 TRP 0.018 0.002 TRP F 424 HIS 0.004 0.001 HIS G 503 Details of bonding type rmsd covalent geometry : bond 0.00402 (19964) covalent geometry : angle 0.62631 (27039) hydrogen bonds : bond 0.03909 ( 577) hydrogen bonds : angle 5.07381 ( 1533) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 TYR cc_start: 0.7734 (t80) cc_final: 0.7430 (t80) REVERT: A 628 TRP cc_start: 0.7017 (t-100) cc_final: 0.6545 (t-100) REVERT: A 735 MET cc_start: 0.8894 (ttp) cc_final: 0.8685 (tmm) REVERT: D 160 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6734 (t0) REVERT: D 202 ASP cc_start: 0.8430 (t0) cc_final: 0.7768 (t0) REVERT: F 286 ASP cc_start: 0.8278 (t70) cc_final: 0.7669 (t70) REVERT: H 38 ARG cc_start: 0.6980 (mmt90) cc_final: 0.6687 (mmm-85) REVERT: H 56 ASP cc_start: 0.7813 (t0) cc_final: 0.7515 (t0) REVERT: H 79 ILE cc_start: 0.8370 (tp) cc_final: 0.7958 (tp) REVERT: H 127 LYS cc_start: 0.6692 (ttmt) cc_final: 0.6386 (ttmm) REVERT: H 274 ASP cc_start: 0.8929 (t0) cc_final: 0.8597 (t0) REVERT: H 323 ILE cc_start: 0.8510 (mm) cc_final: 0.8094 (pt) REVERT: H 400 THR cc_start: 0.8233 (p) cc_final: 0.7941 (t) REVERT: H 427 MET cc_start: 0.8689 (mmt) cc_final: 0.8291 (mmt) REVERT: J 74 ASP cc_start: 0.8353 (t0) cc_final: 0.7535 (t0) REVERT: J 78 MET cc_start: 0.8777 (tmm) cc_final: 0.8575 (ttp) REVERT: G 29 MET cc_start: 0.9110 (ptp) cc_final: 0.8721 (ptp) REVERT: G 38 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7939 (ttpt) REVERT: G 94 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7978 (mm-30) REVERT: G 177 ASN cc_start: 0.8333 (m110) cc_final: 0.8099 (m110) REVERT: G 292 ASP cc_start: 0.7914 (t70) cc_final: 0.7511 (m-30) REVERT: G 456 LYS cc_start: 0.7922 (tmmt) cc_final: 0.7435 (ttmt) outliers start: 31 outliers final: 21 residues processed: 228 average time/residue: 0.1441 time to fit residues: 49.8940 Evaluate side-chains 217 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 142 TRP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 488 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 160 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 4 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 190 optimal weight: 0.4980 chunk 159 optimal weight: 6.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 313 ASN A 509 GLN A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.154834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121820 restraints weight = 26913.198| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.91 r_work: 0.2935 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19966 Z= 0.103 Angle : 0.560 13.625 27039 Z= 0.293 Chirality : 0.044 0.189 2914 Planarity : 0.004 0.059 3486 Dihedral : 5.933 59.016 2722 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.18 % Allowed : 10.78 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2420 helix: 0.34 (0.26), residues: 404 sheet: 0.08 (0.18), residues: 837 loop : -1.31 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 107 TYR 0.018 0.001 TYR D 200 PHE 0.024 0.001 PHE D 94 TRP 0.014 0.001 TRP J 156 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00225 (19964) covalent geometry : angle 0.55963 (27039) hydrogen bonds : bond 0.03235 ( 577) hydrogen bonds : angle 4.82112 ( 1533) Misc. bond : bond 0.00080 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 TYR cc_start: 0.7643 (t80) cc_final: 0.7409 (t80) REVERT: A 628 TRP cc_start: 0.7065 (t-100) cc_final: 0.6602 (t-100) REVERT: D 202 ASP cc_start: 0.8258 (t0) cc_final: 0.7674 (t0) REVERT: F 286 ASP cc_start: 0.8176 (t70) cc_final: 0.7733 (t70) REVERT: H 56 ASP cc_start: 0.8022 (t0) cc_final: 0.7762 (t0) REVERT: H 127 LYS cc_start: 0.6874 (ttmt) cc_final: 0.6477 (ttmm) REVERT: H 145 MET cc_start: 0.7871 (ttp) cc_final: 0.7603 (ttp) REVERT: H 323 ILE cc_start: 0.8648 (mm) cc_final: 0.8314 (pt) REVERT: H 400 THR cc_start: 0.8266 (p) cc_final: 0.7932 (t) REVERT: H 427 MET cc_start: 0.8749 (mmt) cc_final: 0.8447 (mmt) REVERT: J 74 ASP cc_start: 0.8409 (t0) cc_final: 0.7817 (t0) REVERT: J 78 MET cc_start: 0.8921 (tmm) cc_final: 0.8556 (ttp) REVERT: G 94 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8042 (mm-30) REVERT: G 112 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7937 (mmt180) REVERT: G 123 LYS cc_start: 0.8518 (ptmt) cc_final: 0.8296 (pttm) REVERT: G 177 ASN cc_start: 0.8387 (m110) cc_final: 0.8171 (m110) REVERT: G 292 ASP cc_start: 0.7856 (t70) cc_final: 0.7440 (m-30) REVERT: G 456 LYS cc_start: 0.8154 (tmmt) cc_final: 0.7636 (ttmt) outliers start: 25 outliers final: 14 residues processed: 231 average time/residue: 0.1413 time to fit residues: 49.9779 Evaluate side-chains 208 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 142 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 142 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 183 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 115 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122319 restraints weight = 26811.873| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.87 r_work: 0.3120 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19966 Z= 0.098 Angle : 0.540 12.529 27039 Z= 0.284 Chirality : 0.044 0.181 2914 Planarity : 0.004 0.047 3486 Dihedral : 5.689 58.515 2722 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 1.42 % Allowed : 11.72 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.17), residues: 2420 helix: 0.50 (0.26), residues: 403 sheet: 0.12 (0.18), residues: 831 loop : -1.25 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 423 TYR 0.015 0.001 TYR D 200 PHE 0.025 0.001 PHE D 94 TRP 0.013 0.001 TRP J 156 HIS 0.003 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00214 (19964) covalent geometry : angle 0.53973 (27039) hydrogen bonds : bond 0.03085 ( 577) hydrogen bonds : angle 4.68592 ( 1533) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 TRP cc_start: 0.7045 (t-100) cc_final: 0.6703 (t-100) REVERT: F 286 ASP cc_start: 0.7842 (t70) cc_final: 0.7589 (t70) REVERT: H 127 LYS cc_start: 0.7000 (ttmt) cc_final: 0.6647 (ttmm) REVERT: H 145 MET cc_start: 0.7764 (ttp) cc_final: 0.7499 (ttp) REVERT: H 323 ILE cc_start: 0.8718 (mm) cc_final: 0.8442 (pt) REVERT: H 400 THR cc_start: 0.8148 (p) cc_final: 0.7803 (t) REVERT: I 112 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7970 (mmtt) REVERT: J 74 ASP cc_start: 0.8218 (t0) cc_final: 0.7800 (t0) REVERT: J 78 MET cc_start: 0.8901 (tmm) cc_final: 0.8460 (ttp) REVERT: G 112 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7974 (mmt180) REVERT: G 292 ASP cc_start: 0.7575 (t70) cc_final: 0.7333 (m-30) REVERT: G 456 LYS cc_start: 0.8176 (tmmt) cc_final: 0.7689 (ttmt) outliers start: 30 outliers final: 17 residues processed: 222 average time/residue: 0.1437 time to fit residues: 48.8261 Evaluate side-chains 202 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 142 TRP Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 488 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 235 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 193 optimal weight: 0.0030 chunk 212 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 150 optimal weight: 0.0570 chunk 157 optimal weight: 5.9990 overall best weight: 0.9912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN H 280 HIS G 177 ASN G 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121020 restraints weight = 26753.663| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.87 r_work: 0.3104 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19966 Z= 0.122 Angle : 0.552 11.467 27039 Z= 0.289 Chirality : 0.045 0.179 2914 Planarity : 0.004 0.046 3486 Dihedral : 5.612 57.800 2722 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 1.47 % Allowed : 12.57 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.17), residues: 2420 helix: 0.53 (0.26), residues: 405 sheet: 0.04 (0.18), residues: 854 loop : -1.26 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 423 TYR 0.034 0.001 TYR A 725 PHE 0.029 0.001 PHE D 94 TRP 0.013 0.001 TRP J 156 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00283 (19964) covalent geometry : angle 0.55237 (27039) hydrogen bonds : bond 0.03079 ( 577) hydrogen bonds : angle 4.67243 ( 1533) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 TRP cc_start: 0.7021 (t-100) cc_final: 0.6642 (t-100) REVERT: F 286 ASP cc_start: 0.7893 (t70) cc_final: 0.7672 (t70) REVERT: H 121 ASN cc_start: 0.8687 (p0) cc_final: 0.8415 (p0) REVERT: H 127 LYS cc_start: 0.7028 (ttmt) cc_final: 0.6692 (ttmm) REVERT: H 139 TYR cc_start: 0.7501 (m-80) cc_final: 0.7288 (m-80) REVERT: H 145 MET cc_start: 0.7832 (ttp) cc_final: 0.7597 (ttp) REVERT: H 323 ILE cc_start: 0.8749 (mm) cc_final: 0.8481 (pt) REVERT: H 400 THR cc_start: 0.8217 (p) cc_final: 0.7863 (t) REVERT: I 112 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8057 (mmtt) REVERT: J 74 ASP cc_start: 0.8275 (t0) cc_final: 0.7910 (t0) REVERT: J 78 MET cc_start: 0.8900 (tmm) cc_final: 0.8499 (ttp) REVERT: G 112 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7918 (mmt180) REVERT: G 456 LYS cc_start: 0.8163 (tmmt) cc_final: 0.7708 (ttmt) outliers start: 31 outliers final: 23 residues processed: 221 average time/residue: 0.1403 time to fit residues: 47.0262 Evaluate side-chains 212 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 142 TRP Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 492 THR Chi-restraints excluded: chain G residue 530 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.097145 restraints weight = 28310.747| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.44 r_work: 0.2882 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 19966 Z= 0.385 Angle : 0.759 10.699 27039 Z= 0.397 Chirality : 0.052 0.224 2914 Planarity : 0.005 0.055 3486 Dihedral : 6.337 59.001 2722 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.07 % Favored : 92.89 % Rotamer: Outliers : 2.36 % Allowed : 12.52 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 2420 helix: 0.00 (0.25), residues: 413 sheet: -0.31 (0.18), residues: 844 loop : -1.66 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 839 TYR 0.045 0.002 TYR A 725 PHE 0.028 0.003 PHE D 94 TRP 0.022 0.002 TRP J 156 HIS 0.004 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00947 (19964) covalent geometry : angle 0.75868 (27039) hydrogen bonds : bond 0.04310 ( 577) hydrogen bonds : angle 5.27262 ( 1533) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 628 TRP cc_start: 0.7060 (t-100) cc_final: 0.6488 (t-100) REVERT: D 122 ARG cc_start: 0.7438 (ptt-90) cc_final: 0.6161 (ptp-110) REVERT: F 286 ASP cc_start: 0.8411 (t70) cc_final: 0.7913 (t70) REVERT: H 127 LYS cc_start: 0.6860 (ttmt) cc_final: 0.6529 (ttmm) REVERT: H 139 TYR cc_start: 0.7508 (m-80) cc_final: 0.7283 (m-80) REVERT: H 427 MET cc_start: 0.8653 (mmt) cc_final: 0.8161 (mmt) REVERT: I 53 ARG cc_start: 0.6744 (mmt-90) cc_final: 0.6335 (mmt-90) REVERT: I 112 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7481 (mmtt) REVERT: J 32 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6424 (mp0) REVERT: J 74 ASP cc_start: 0.8614 (t0) cc_final: 0.7913 (t0) REVERT: J 78 MET cc_start: 0.8669 (tmm) cc_final: 0.8302 (ttt) REVERT: G 38 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8085 (mtmm) REVERT: G 456 LYS cc_start: 0.7897 (tmmt) cc_final: 0.7469 (ttmt) outliers start: 50 outliers final: 37 residues processed: 237 average time/residue: 0.1510 time to fit residues: 54.2430 Evaluate side-chains 226 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 142 TRP Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain G residue 18 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 492 THR Chi-restraints excluded: chain G residue 530 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 173 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 218 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 226 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN G 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104701 restraints weight = 27660.571| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.91 r_work: 0.2951 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19966 Z= 0.111 Angle : 0.576 12.375 27039 Z= 0.302 Chirality : 0.045 0.167 2914 Planarity : 0.004 0.048 3486 Dihedral : 5.811 57.900 2722 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 1.37 % Allowed : 13.94 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2420 helix: 0.37 (0.26), residues: 405 sheet: -0.17 (0.18), residues: 843 loop : -1.42 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 423 TYR 0.030 0.001 TYR A 620 PHE 0.036 0.001 PHE F 426 TRP 0.026 0.002 TRP F 424 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00246 (19964) covalent geometry : angle 0.57585 (27039) hydrogen bonds : bond 0.03209 ( 577) hydrogen bonds : angle 4.83254 ( 1533) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.785 Fit side-chains REVERT: A 628 TRP cc_start: 0.7054 (t-100) cc_final: 0.6564 (t-100) REVERT: F 286 ASP cc_start: 0.8409 (t70) cc_final: 0.8047 (t0) REVERT: H 127 LYS cc_start: 0.6811 (ttmt) cc_final: 0.6427 (ttmm) REVERT: H 139 TYR cc_start: 0.7119 (m-80) cc_final: 0.6834 (m-80) REVERT: H 400 THR cc_start: 0.8222 (p) cc_final: 0.7943 (t) REVERT: I 112 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7640 (mmtt) REVERT: J 32 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6929 (tm-30) REVERT: J 74 ASP cc_start: 0.8591 (t0) cc_final: 0.7864 (t0) REVERT: G 38 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8125 (mtmm) REVERT: G 456 LYS cc_start: 0.7873 (tmmt) cc_final: 0.7429 (ttmt) outliers start: 29 outliers final: 25 residues processed: 216 average time/residue: 0.1395 time to fit residues: 45.9553 Evaluate side-chains 211 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain D residue 102 PHE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain I residue 142 TRP Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain G residue 18 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 492 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 48 optimal weight: 0.0970 chunk 166 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 chunk 236 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 185 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN G 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105170 restraints weight = 27310.206| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.89 r_work: 0.2989 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19966 Z= 0.109 Angle : 0.560 12.559 27039 Z= 0.294 Chirality : 0.044 0.176 2914 Planarity : 0.004 0.048 3486 Dihedral : 5.589 58.871 2722 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 1.47 % Allowed : 13.94 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.17), residues: 2420 helix: 0.51 (0.26), residues: 405 sheet: -0.11 (0.18), residues: 838 loop : -1.34 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 423 TYR 0.022 0.001 TYR A 725 PHE 0.032 0.001 PHE F 426 TRP 0.019 0.001 TRP F 424 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00239 (19964) covalent geometry : angle 0.56034 (27039) hydrogen bonds : bond 0.03044 ( 577) hydrogen bonds : angle 4.72499 ( 1533) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 TRP cc_start: 0.7017 (t-100) cc_final: 0.6498 (t-100) REVERT: F 286 ASP cc_start: 0.8405 (t70) cc_final: 0.8063 (t0) REVERT: H 127 LYS cc_start: 0.6657 (ttmt) cc_final: 0.6263 (ttmm) REVERT: H 139 TYR cc_start: 0.7114 (m-80) cc_final: 0.6831 (m-80) REVERT: H 400 THR cc_start: 0.8262 (p) cc_final: 0.7988 (t) REVERT: H 427 MET cc_start: 0.8747 (mmt) cc_final: 0.8311 (mmt) REVERT: I 112 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7742 (mmtt) REVERT: J 32 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6881 (tm-30) REVERT: J 74 ASP cc_start: 0.8561 (t0) cc_final: 0.7829 (t0) REVERT: G 38 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8134 (mtmm) REVERT: G 123 LYS cc_start: 0.8586 (ptmt) cc_final: 0.8269 (pttm) REVERT: G 456 LYS cc_start: 0.7854 (tmmt) cc_final: 0.7424 (ttmt) outliers start: 31 outliers final: 28 residues processed: 216 average time/residue: 0.1419 time to fit residues: 47.0153 Evaluate side-chains 214 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain D residue 102 PHE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 142 TRP Chi-restraints excluded: chain G residue 18 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 492 THR Chi-restraints excluded: chain G residue 530 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 166 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN G 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105460 restraints weight = 27456.940| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.91 r_work: 0.2970 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19966 Z= 0.116 Angle : 0.557 12.830 27039 Z= 0.291 Chirality : 0.044 0.174 2914 Planarity : 0.004 0.048 3486 Dihedral : 5.520 59.094 2722 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.17 % Favored : 94.79 % Rotamer: Outliers : 1.51 % Allowed : 13.89 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2420 helix: 0.55 (0.26), residues: 403 sheet: -0.07 (0.18), residues: 829 loop : -1.33 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 423 TYR 0.026 0.001 TYR A 620 PHE 0.033 0.001 PHE F 426 TRP 0.018 0.001 TRP F 424 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00267 (19964) covalent geometry : angle 0.55709 (27039) hydrogen bonds : bond 0.03042 ( 577) hydrogen bonds : angle 4.68577 ( 1533) Misc. bond : bond 0.00042 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 628 TRP cc_start: 0.6985 (t-100) cc_final: 0.6481 (t-100) REVERT: F 286 ASP cc_start: 0.8419 (t70) cc_final: 0.8076 (t0) REVERT: H 127 LYS cc_start: 0.6732 (ttmt) cc_final: 0.6339 (ttmm) REVERT: H 139 TYR cc_start: 0.7137 (m-80) cc_final: 0.6814 (m-80) REVERT: H 400 THR cc_start: 0.8246 (p) cc_final: 0.7967 (t) REVERT: I 58 ARG cc_start: 0.8203 (ptt-90) cc_final: 0.7342 (ptt180) REVERT: I 112 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7747 (mmtt) REVERT: J 32 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6907 (tm-30) REVERT: J 74 ASP cc_start: 0.8592 (t0) cc_final: 0.7859 (t0) REVERT: G 38 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8471 (pttp) REVERT: G 123 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8294 (pttm) REVERT: G 456 LYS cc_start: 0.7879 (tmmt) cc_final: 0.7449 (ttmt) outliers start: 32 outliers final: 30 residues processed: 213 average time/residue: 0.1438 time to fit residues: 46.9079 Evaluate side-chains 217 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 102 PHE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 142 TRP Chi-restraints excluded: chain G residue 18 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 492 THR Chi-restraints excluded: chain G residue 530 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 65 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 174 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN G 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105067 restraints weight = 27581.562| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.90 r_work: 0.2967 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 19966 Z= 0.181 Angle : 0.722 59.200 27039 Z= 0.414 Chirality : 0.046 0.246 2914 Planarity : 0.004 0.066 3486 Dihedral : 5.598 59.046 2722 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 1.56 % Allowed : 13.89 % Favored : 84.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2420 helix: 0.54 (0.26), residues: 403 sheet: -0.07 (0.18), residues: 830 loop : -1.33 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 423 TYR 0.021 0.001 TYR A 725 PHE 0.030 0.001 PHE F 426 TRP 0.018 0.002 TRP F 424 HIS 0.003 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00402 (19964) covalent geometry : angle 0.72246 (27039) hydrogen bonds : bond 0.03086 ( 577) hydrogen bonds : angle 4.68689 ( 1533) Misc. bond : bond 0.00060 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5546.00 seconds wall clock time: 95 minutes 27.50 seconds (5727.50 seconds total)