Starting phenix.real_space_refine on Tue Aug 26 10:59:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ilb_35532/08_2025/8ilb_35532_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ilb_35532/08_2025/8ilb_35532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ilb_35532/08_2025/8ilb_35532_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ilb_35532/08_2025/8ilb_35532_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ilb_35532/08_2025/8ilb_35532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ilb_35532/08_2025/8ilb_35532.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 220 5.16 5 C 22990 2.51 5 N 6364 2.21 5 O 6748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 232 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36322 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "B" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3541 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain: "C" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "D" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "F" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "G" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "H" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "I" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 569 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "J" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "K" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3541 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain: "L" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "M" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "N" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "O" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "P" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Q" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 569 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Time building chain proxies: 7.36, per 1000 atoms: 0.20 Number of scatterers: 36322 At special positions: 0 Unit cell: (151.716, 143.108, 136.652, 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 220 16.00 O 6748 8.00 N 6364 7.00 C 22990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8396 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 32 sheets defined 40.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.779A pdb=" N ALA A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.894A pdb=" N ILE A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.710A pdb=" N GLY A 193 " --> pdb=" O CYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.642A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.760A pdb=" N ASN A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.990A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 removed outlier: 4.066A pdb=" N SER A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 400 through 405 removed outlier: 4.307A pdb=" N LEU A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.759A pdb=" N ALA B 50 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 119 removed outlier: 3.934A pdb=" N ILE B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 152 through 160 removed outlier: 3.820A pdb=" N LEU B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.833A pdb=" N GLY B 193 " --> pdb=" O CYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.633A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.646A pdb=" N GLY B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.666A pdb=" N ASN B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.890A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 348 removed outlier: 3.704A pdb=" N MET B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.533A pdb=" N GLY B 358 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.706A pdb=" N LEU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 449 through 459 Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 109 through 118 removed outlier: 3.677A pdb=" N ILE C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 152 through 160 removed outlier: 3.689A pdb=" N LEU C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 192 Processing helix chain 'C' and resid 210 through 230 removed outlier: 3.639A pdb=" N ARG C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 258 removed outlier: 3.543A pdb=" N GLY C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.682A pdb=" N ASN C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.855A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 400 through 405 removed outlier: 3.894A pdb=" N LEU C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 437 through 446 Processing helix chain 'C' and resid 449 through 459 Processing helix chain 'D' and resid 46 through 58 removed outlier: 3.808A pdb=" N ALA D 50 " --> pdb=" O PRO D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 105 removed outlier: 3.976A pdb=" N LEU D 104 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 105 " --> pdb=" O LEU D 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 101 through 105' Processing helix chain 'D' and resid 109 through 118 removed outlier: 3.930A pdb=" N ILE D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.842A pdb=" N GLY D 193 " --> pdb=" O CYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.608A pdb=" N ARG D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.641A pdb=" N ASN D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.869A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 346 removed outlier: 3.692A pdb=" N THR D 339 " --> pdb=" O ASP D 335 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 346 " --> pdb=" O PHE D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 391 Processing helix chain 'D' and resid 400 through 405 removed outlier: 3.722A pdb=" N LEU D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 430 removed outlier: 3.572A pdb=" N GLU D 430 " --> pdb=" O GLN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 449 through 459 removed outlier: 3.624A pdb=" N TRP D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.685A pdb=" N ARG E 80 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 97 through 109 Proline residue: E 103 - end of helix Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 125 through 144 removed outlier: 3.595A pdb=" N GLN E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 165 through 169 removed outlier: 4.070A pdb=" N LEU E 168 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.839A pdb=" N ARG E 184 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 Processing helix chain 'E' and resid 217 through 231 removed outlier: 3.709A pdb=" N CYS E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 249 removed outlier: 3.553A pdb=" N MET E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 Processing helix chain 'J' and resid 46 through 58 removed outlier: 3.779A pdb=" N ALA J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.894A pdb=" N ILE J 113 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 143 Processing helix chain 'J' and resid 152 through 160 Processing helix chain 'J' and resid 178 through 193 removed outlier: 3.710A pdb=" N GLY J 193 " --> pdb=" O CYS J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.641A pdb=" N ARG J 214 " --> pdb=" O ARG J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 257 Processing helix chain 'J' and resid 270 through 285 removed outlier: 3.759A pdb=" N ASN J 274 " --> pdb=" O GLY J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 319 removed outlier: 3.990A pdb=" N LEU J 311 " --> pdb=" O HIS J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 345 removed outlier: 4.066A pdb=" N SER J 338 " --> pdb=" O GLY J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 358 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 391 Processing helix chain 'J' and resid 400 through 405 removed outlier: 4.307A pdb=" N LEU J 404 " --> pdb=" O GLY J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 430 Processing helix chain 'J' and resid 437 through 446 Processing helix chain 'J' and resid 449 through 459 Processing helix chain 'K' and resid 46 through 58 removed outlier: 3.759A pdb=" N ALA K 50 " --> pdb=" O PRO K 46 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER K 58 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 119 removed outlier: 3.934A pdb=" N ILE K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 143 Processing helix chain 'K' and resid 152 through 160 removed outlier: 3.821A pdb=" N LEU K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.833A pdb=" N GLY K 193 " --> pdb=" O CYS K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 230 removed outlier: 3.633A pdb=" N ARG K 214 " --> pdb=" O ARG K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 258 removed outlier: 3.646A pdb=" N GLY K 258 " --> pdb=" O ALA K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 285 removed outlier: 3.666A pdb=" N ASN K 274 " --> pdb=" O GLY K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 319 removed outlier: 3.889A pdb=" N LEU K 311 " --> pdb=" O HIS K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 348 removed outlier: 3.704A pdb=" N MET K 346 " --> pdb=" O PHE K 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 358 removed outlier: 3.533A pdb=" N GLY K 358 " --> pdb=" O ARG K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 391 Processing helix chain 'K' and resid 400 through 405 removed outlier: 3.706A pdb=" N LEU K 404 " --> pdb=" O GLY K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 430 Processing helix chain 'K' and resid 437 through 446 Processing helix chain 'K' and resid 449 through 459 Processing helix chain 'L' and resid 46 through 58 Processing helix chain 'L' and resid 109 through 118 removed outlier: 3.676A pdb=" N ILE L 113 " --> pdb=" O SER L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 124 Processing helix chain 'L' and resid 138 through 143 Processing helix chain 'L' and resid 152 through 160 removed outlier: 3.689A pdb=" N LEU L 159 " --> pdb=" O GLU L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 192 Processing helix chain 'L' and resid 210 through 230 removed outlier: 3.639A pdb=" N ARG L 214 " --> pdb=" O ARG L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 258 removed outlier: 3.543A pdb=" N GLY L 258 " --> pdb=" O ALA L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 285 removed outlier: 3.681A pdb=" N ASN L 274 " --> pdb=" O GLY L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 319 removed outlier: 3.855A pdb=" N LEU L 311 " --> pdb=" O HIS L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 345 Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 391 Processing helix chain 'L' and resid 400 through 405 removed outlier: 3.894A pdb=" N LEU L 404 " --> pdb=" O GLY L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 430 Processing helix chain 'L' and resid 437 through 446 Processing helix chain 'L' and resid 449 through 459 Processing helix chain 'M' and resid 46 through 58 removed outlier: 3.808A pdb=" N ALA M 50 " --> pdb=" O PRO M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 105 removed outlier: 3.976A pdb=" N LEU M 104 " --> pdb=" O PRO M 101 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE M 105 " --> pdb=" O LEU M 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 101 through 105' Processing helix chain 'M' and resid 109 through 118 removed outlier: 3.930A pdb=" N ILE M 113 " --> pdb=" O SER M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 124 Processing helix chain 'M' and resid 138 through 143 Processing helix chain 'M' and resid 152 through 160 Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.841A pdb=" N GLY M 193 " --> pdb=" O CYS M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 230 removed outlier: 3.608A pdb=" N ARG M 214 " --> pdb=" O ARG M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 257 Processing helix chain 'M' and resid 266 through 270 Processing helix chain 'M' and resid 270 through 285 removed outlier: 3.642A pdb=" N ASN M 274 " --> pdb=" O GLY M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 319 removed outlier: 3.870A pdb=" N LEU M 311 " --> pdb=" O HIS M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 346 removed outlier: 3.692A pdb=" N THR M 339 " --> pdb=" O ASP M 335 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET M 346 " --> pdb=" O PHE M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 358 Processing helix chain 'M' and resid 380 through 382 No H-bonds generated for 'chain 'M' and resid 380 through 382' Processing helix chain 'M' and resid 383 through 391 Processing helix chain 'M' and resid 400 through 405 removed outlier: 3.722A pdb=" N LEU M 404 " --> pdb=" O GLY M 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 409 through 430 removed outlier: 3.572A pdb=" N GLU M 430 " --> pdb=" O GLN M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 437 through 447 Processing helix chain 'M' and resid 449 through 459 removed outlier: 3.625A pdb=" N TRP M 459 " --> pdb=" O ALA M 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 80 removed outlier: 3.685A pdb=" N ARG N 80 " --> pdb=" O THR N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 93 Processing helix chain 'N' and resid 97 through 109 Proline residue: N 103 - end of helix Processing helix chain 'N' and resid 110 through 112 No H-bonds generated for 'chain 'N' and resid 110 through 112' Processing helix chain 'N' and resid 114 through 122 Processing helix chain 'N' and resid 125 through 144 removed outlier: 3.595A pdb=" N GLN N 144 " --> pdb=" O ASP N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 164 Processing helix chain 'N' and resid 165 through 169 removed outlier: 4.070A pdb=" N LEU N 168 " --> pdb=" O GLU N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 173 Processing helix chain 'N' and resid 174 through 184 removed outlier: 3.840A pdb=" N ARG N 184 " --> pdb=" O PHE N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 200 Processing helix chain 'N' and resid 217 through 231 removed outlier: 3.709A pdb=" N CYS N 221 " --> pdb=" O LEU N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 249 removed outlier: 3.554A pdb=" N MET N 243 " --> pdb=" O GLN N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 removed outlier: 6.067A pdb=" N CYS A 81 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA A 99 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 83 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 34 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE A 135 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 36 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 129 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N GLY A 305 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 130 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 6.610A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR A 197 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ASN A 238 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS A 235 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET A 263 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ASP A 265 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N HIS A 291 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS A 264 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS A 324 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE A 399 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY A 168 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 83 removed outlier: 5.911A pdb=" N CYS B 81 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA B 99 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS B 83 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 34 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP B 134 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA B 36 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU B 132 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG B 38 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 130 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 40 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY B 305 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 130 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 170 removed outlier: 6.565A pdb=" N LEU B 167 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS B 198 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS B 169 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASP B 265 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS B 291 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS B 264 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS B 324 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN B 398 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 375 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 86 removed outlier: 5.899A pdb=" N CYS C 81 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA C 99 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS C 83 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU C 34 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP C 134 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA C 36 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU C 132 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG C 38 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 130 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER C 40 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 305 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 166 through 170 removed outlier: 6.644A pdb=" N LEU C 167 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS C 198 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS C 169 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR C 197 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASN C 238 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N HIS C 235 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET C 263 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 237 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASP C 265 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 262 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS C 291 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS C 264 " --> pdb=" O HIS C 291 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS C 324 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN C 398 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 375 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 83 removed outlier: 5.990A pdb=" N CYS D 81 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA D 99 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS D 83 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D 34 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE D 135 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA D 36 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 305 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 234 through 236 removed outlier: 6.950A pdb=" N THR D 197 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 196 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN D 398 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA D 375 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU D 323 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS D 324 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE D 262 " --> pdb=" O HIS D 289 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS D 291 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS D 264 " --> pdb=" O HIS D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB4, first strand: chain 'F' and resid 80 through 82 Processing sheet with id=AB5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AB6, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AB7, first strand: chain 'I' and resid 80 through 82 Processing sheet with id=AB8, first strand: chain 'J' and resid 80 through 86 removed outlier: 6.068A pdb=" N CYS J 81 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA J 99 " --> pdb=" O CYS J 81 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS J 83 " --> pdb=" O PHE J 97 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU J 34 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE J 135 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA J 36 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER J 129 " --> pdb=" O SER J 40 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N GLY J 305 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU J 130 " --> pdb=" O GLY J 305 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 166 through 170 removed outlier: 6.610A pdb=" N LEU J 167 " --> pdb=" O PHE J 196 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS J 198 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS J 169 " --> pdb=" O LYS J 198 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR J 197 " --> pdb=" O TYR J 236 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASN J 238 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS J 235 " --> pdb=" O ILE J 261 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET J 263 " --> pdb=" O HIS J 235 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU J 237 " --> pdb=" O MET J 263 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ASP J 265 " --> pdb=" O LEU J 237 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE J 262 " --> pdb=" O HIS J 289 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N HIS J 291 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS J 264 " --> pdb=" O HIS J 291 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS J 324 " --> pdb=" O ILE J 290 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET J 166 " --> pdb=" O LEU J 397 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE J 399 " --> pdb=" O MET J 166 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY J 168 " --> pdb=" O PHE J 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 350 through 351 Processing sheet with id=AC2, first strand: chain 'K' and resid 80 through 83 removed outlier: 5.912A pdb=" N CYS K 81 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA K 99 " --> pdb=" O CYS K 81 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS K 83 " --> pdb=" O PHE K 97 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU K 34 " --> pdb=" O ASP K 134 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP K 134 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA K 36 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU K 132 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG K 38 " --> pdb=" O LEU K 130 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU K 130 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER K 40 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY K 305 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU K 130 " --> pdb=" O GLY K 305 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 166 through 170 removed outlier: 6.565A pdb=" N LEU K 167 " --> pdb=" O PHE K 196 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS K 198 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS K 169 " --> pdb=" O LYS K 198 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR K 197 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASN K 238 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS K 235 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET K 263 " --> pdb=" O HIS K 235 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU K 237 " --> pdb=" O MET K 263 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASP K 265 " --> pdb=" O LEU K 237 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE K 262 " --> pdb=" O HIS K 289 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS K 291 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS K 264 " --> pdb=" O HIS K 291 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS K 324 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN K 398 " --> pdb=" O PRO K 373 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA K 375 " --> pdb=" O GLN K 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 350 through 351 Processing sheet with id=AC5, first strand: chain 'L' and resid 80 through 86 removed outlier: 5.899A pdb=" N CYS L 81 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA L 99 " --> pdb=" O CYS L 81 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS L 83 " --> pdb=" O PHE L 97 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU L 34 " --> pdb=" O ASP L 134 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP L 134 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA L 36 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU L 132 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG L 38 " --> pdb=" O LEU L 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU L 130 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER L 40 " --> pdb=" O ARG L 128 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY L 305 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 234 through 236 removed outlier: 6.940A pdb=" N THR L 197 " --> pdb=" O TYR L 236 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU L 167 " --> pdb=" O PHE L 196 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LYS L 198 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N CYS L 169 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN L 398 " --> pdb=" O PRO L 373 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA L 375 " --> pdb=" O GLN L 398 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS L 324 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE L 262 " --> pdb=" O HIS L 289 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N HIS L 291 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS L 264 " --> pdb=" O HIS L 291 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 350 through 351 Processing sheet with id=AC8, first strand: chain 'M' and resid 80 through 83 removed outlier: 5.991A pdb=" N CYS M 81 " --> pdb=" O ALA M 99 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA M 99 " --> pdb=" O CYS M 81 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS M 83 " --> pdb=" O PHE M 97 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU M 34 " --> pdb=" O ILE M 135 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE M 135 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA M 36 " --> pdb=" O GLU M 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY M 305 " --> pdb=" O LEU M 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 234 through 236 removed outlier: 6.995A pdb=" N THR M 197 " --> pdb=" O TYR M 236 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE M 196 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN M 398 " --> pdb=" O PRO M 373 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA M 375 " --> pdb=" O GLN M 398 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU M 323 " --> pdb=" O VAL M 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS M 324 " --> pdb=" O ILE M 290 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE M 262 " --> pdb=" O HIS M 289 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS M 291 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS M 264 " --> pdb=" O HIS M 291 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 350 through 351 Processing sheet with id=AD2, first strand: chain 'O' and resid 80 through 82 Processing sheet with id=AD3, first strand: chain 'P' and resid 80 through 81 Processing sheet with id=AD4, first strand: chain 'Q' and resid 80 through 82 Processing sheet with id=AD5, first strand: chain 'R' and resid 80 through 82 1351 hydrogen bonds defined for protein. 3873 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: 6.16 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11980 1.34 - 1.45: 5703 1.45 - 1.57: 19195 1.57 - 1.69: 0 1.69 - 1.81: 310 Bond restraints: 37188 Sorted by residual: bond pdb=" C LYS O 66 " pdb=" N PRO O 67 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.12e-02 7.97e+03 2.05e+01 bond pdb=" C ALA C 241 " pdb=" N PRO C 242 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" CA ALA G 124 " pdb=" C ALA G 124 " ideal model delta sigma weight residual 1.521 1.495 0.026 1.19e-02 7.06e+03 4.74e+00 bond pdb=" CA ASP K 299 " pdb=" CB ASP K 299 " ideal model delta sigma weight residual 1.539 1.434 0.106 4.88e-02 4.20e+02 4.68e+00 bond pdb=" CA ASP B 299 " pdb=" CB ASP B 299 " ideal model delta sigma weight residual 1.539 1.434 0.106 4.88e-02 4.20e+02 4.68e+00 ... (remaining 37183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 49456 2.31 - 4.61: 772 4.61 - 6.92: 86 6.92 - 9.22: 12 9.22 - 11.53: 8 Bond angle restraints: 50334 Sorted by residual: angle pdb=" N GLY G 119 " pdb=" CA GLY G 119 " pdb=" C GLY G 119 " ideal model delta sigma weight residual 112.49 119.79 -7.30 1.21e+00 6.83e-01 3.64e+01 angle pdb=" N GLY H 119 " pdb=" CA GLY H 119 " pdb=" C GLY H 119 " ideal model delta sigma weight residual 112.73 119.95 -7.22 1.20e+00 6.94e-01 3.62e+01 angle pdb=" N LYS D 198 " pdb=" CA LYS D 198 " pdb=" C LYS D 198 " ideal model delta sigma weight residual 108.76 118.09 -9.33 1.69e+00 3.50e-01 3.04e+01 angle pdb=" N ILE F 127 " pdb=" CA ILE F 127 " pdb=" C ILE F 127 " ideal model delta sigma weight residual 111.58 117.33 -5.75 1.06e+00 8.90e-01 2.94e+01 angle pdb=" N GLY P 119 " pdb=" CA GLY P 119 " pdb=" C GLY P 119 " ideal model delta sigma weight residual 112.49 118.93 -6.44 1.21e+00 6.83e-01 2.84e+01 ... (remaining 50329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 19760 17.25 - 34.50: 1678 34.50 - 51.76: 307 51.76 - 69.01: 83 69.01 - 86.26: 30 Dihedral angle restraints: 21858 sinusoidal: 8678 harmonic: 13180 Sorted by residual: dihedral pdb=" CA ASN E 235 " pdb=" C ASN E 235 " pdb=" N PRO E 236 " pdb=" CA PRO E 236 " ideal model delta harmonic sigma weight residual -180.00 -146.52 -33.48 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA ASN N 235 " pdb=" C ASN N 235 " pdb=" N PRO N 236 " pdb=" CA PRO N 236 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA ILE B 462 " pdb=" C ILE B 462 " pdb=" N LYS B 463 " pdb=" CA LYS B 463 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 21855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4650 0.073 - 0.147: 666 0.147 - 0.220: 46 0.220 - 0.293: 4 0.293 - 0.367: 2 Chirality restraints: 5368 Sorted by residual: chirality pdb=" CA ASP L 69 " pdb=" N ASP L 69 " pdb=" C ASP L 69 " pdb=" CB ASP L 69 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA LEU C 71 " pdb=" N LEU C 71 " pdb=" C LEU C 71 " pdb=" CB LEU C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE F 127 " pdb=" N ILE F 127 " pdb=" C ILE F 127 " pdb=" CB ILE F 127 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5365 not shown) Planarity restraints: 6622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 128 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C GLY F 128 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY F 128 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY F 129 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 241 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO C 242 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 242 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 242 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET J 259 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO J 260 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO J 260 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 260 " 0.026 5.00e-02 4.00e+02 ... (remaining 6619 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3222 2.73 - 3.27: 34643 3.27 - 3.82: 55803 3.82 - 4.36: 70189 4.36 - 4.90: 126041 Nonbonded interactions: 289898 Sorted by model distance: nonbonded pdb=" O LEU L 70 " pdb=" CG LEU L 71 " model vdw 2.190 3.470 nonbonded pdb=" OH TYR N 201 " pdb=" O PHE N 213 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR E 201 " pdb=" O PHE E 213 " model vdw 2.213 3.040 nonbonded pdb=" N GLY K 330 " pdb=" O GLU O 136 " model vdw 2.219 3.120 nonbonded pdb=" N GLY B 330 " pdb=" O GLU F 136 " model vdw 2.219 3.120 ... (remaining 289893 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 466) selection = chain 'B' selection = (chain 'C' and resid 16 through 466) selection = (chain 'D' and resid 16 through 466) selection = (chain 'J' and resid 16 through 466) selection = chain 'K' selection = (chain 'L' and resid 16 through 466) selection = (chain 'M' and resid 16 through 466) } ncs_group { reference = chain 'E' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 58 through 136) selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = (chain 'R' and resid 58 through 136) } 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: 0.010 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.890 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 37188 Z= 0.296 Angle : 0.736 11.531 50334 Z= 0.423 Chirality : 0.051 0.367 5368 Planarity : 0.005 0.047 6622 Dihedral : 13.727 86.259 13462 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.94 % Favored : 91.02 % Rotamer: Outliers : 1.56 % Allowed : 4.44 % Favored : 94.01 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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 aren not related in a simple way. whole: -3.03 (0.11), residues: 4644 helix: -0.84 (0.12), residues: 1670 sheet: -0.98 (0.21), residues: 472 loop : -3.21 (0.10), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 212 TYR 0.011 0.001 TYR C 17 PHE 0.025 0.002 PHE K 342 TRP 0.025 0.002 TRP B 67 HIS 0.005 0.001 HIS M 264 Details of bonding type rmsd covalent geometry : bond 0.00686 (37188) covalent geometry : angle 0.73620 (50334) hydrogen bonds : bond 0.15625 ( 1351) hydrogen bonds : angle 5.71193 ( 3873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 459 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 MET cc_start: 0.8421 (tpp) cc_final: 0.8220 (tpp) REVERT: A 426 GLN cc_start: 0.8408 (tp40) cc_final: 0.7580 (tp-100) REVERT: B 76 ARG cc_start: 0.8383 (mtp180) cc_final: 0.8152 (ttp80) REVERT: C 354 ASP cc_start: 0.7237 (t0) cc_final: 0.6867 (t0) REVERT: C 357 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7578 (mmm-85) REVERT: C 426 GLN cc_start: 0.8014 (tp40) cc_final: 0.7235 (tp-100) REVERT: D 342 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8520 (t80) REVERT: D 354 ASP cc_start: 0.7714 (t0) cc_final: 0.7229 (t70) REVERT: D 426 GLN cc_start: 0.8306 (tt0) cc_final: 0.7834 (tp-100) REVERT: D 444 GLU cc_start: 0.8051 (mp0) cc_final: 0.7845 (mp0) REVERT: E 238 ASP cc_start: 0.6997 (m-30) cc_final: 0.6688 (m-30) REVERT: F 74 ASN cc_start: 0.7299 (OUTLIER) cc_final: 0.7054 (t160) REVERT: F 76 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: G 120 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8015 (p0) REVERT: H 74 ASN cc_start: 0.7812 (t0) cc_final: 0.7327 (t0) REVERT: I 78 GLU cc_start: 0.7756 (pt0) cc_final: 0.7446 (pt0) REVERT: I 80 CYS cc_start: 0.7841 (m) cc_final: 0.7575 (p) REVERT: I 111 ARG cc_start: 0.8956 (mmt90) cc_final: 0.8630 (mmt-90) REVERT: J 426 GLN cc_start: 0.8408 (tp40) cc_final: 0.7588 (tp-100) REVERT: K 76 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8144 (ttp80) REVERT: K 178 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7972 (p) REVERT: L 71 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6806 (mm) REVERT: L 354 ASP cc_start: 0.7233 (t0) cc_final: 0.6865 (t0) REVERT: L 357 ARG cc_start: 0.7832 (mtt-85) cc_final: 0.7582 (mmm-85) REVERT: L 426 GLN cc_start: 0.8077 (tp40) cc_final: 0.7292 (tp-100) REVERT: M 342 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8426 (t80) REVERT: M 354 ASP cc_start: 0.7725 (t0) cc_final: 0.7229 (t70) REVERT: M 426 GLN cc_start: 0.8314 (tt0) cc_final: 0.7760 (tp-100) REVERT: M 444 GLU cc_start: 0.8052 (mp0) cc_final: 0.7848 (mp0) REVERT: N 238 ASP cc_start: 0.7045 (m-30) cc_final: 0.6742 (m-30) REVERT: O 74 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7373 (t160) REVERT: R 78 GLU cc_start: 0.7765 (pt0) cc_final: 0.7456 (pt0) REVERT: R 80 CYS cc_start: 0.7854 (m) cc_final: 0.7594 (p) REVERT: R 111 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8647 (mmt-90) outliers start: 59 outliers final: 7 residues processed: 493 average time/residue: 0.7682 time to fit residues: 442.9131 Evaluate side-chains 332 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 317 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 74 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 150 HIS A 209 GLN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN B 324 HIS B 350 HIS C 92 ASN C 209 GLN C 264 HIS C 417 ASN D 322 HIS D 426 GLN E 63 GLN E 137 GLN F 122 ASN G 68 ASN J 92 ASN J 150 HIS J 209 GLN J 417 ASN K 324 HIS K 350 HIS L 92 ASN L 209 GLN L 264 HIS L 417 ASN M 160 ASN M 322 HIS M 426 GLN N 63 GLN N 137 GLN O 68 ASN O 122 ASN P 68 ASN P 74 ASN P 122 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.081098 restraints weight = 50050.562| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.79 r_work: 0.2811 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37188 Z= 0.173 Angle : 0.614 9.870 50334 Z= 0.316 Chirality : 0.045 0.191 5368 Planarity : 0.005 0.045 6622 Dihedral : 5.637 80.958 5068 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.48 % Allowed : 9.71 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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 aren not related in a simple way. whole: -1.80 (0.12), residues: 4644 helix: 0.43 (0.13), residues: 1704 sheet: -0.77 (0.21), residues: 534 loop : -2.63 (0.11), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 302 TYR 0.018 0.001 TYR N 101 PHE 0.023 0.001 PHE B 342 TRP 0.018 0.001 TRP C 408 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00418 (37188) covalent geometry : angle 0.61369 (50334) hydrogen bonds : bond 0.04981 ( 1351) hydrogen bonds : angle 4.02921 ( 3873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 370 time to evaluate : 1.386 Fit side-chains REVERT: A 426 GLN cc_start: 0.7972 (tp40) cc_final: 0.7252 (tp-100) REVERT: B 76 ARG cc_start: 0.8603 (mtp180) cc_final: 0.8334 (ttp80) REVERT: B 283 ASP cc_start: 0.7951 (m-30) cc_final: 0.7681 (m-30) REVERT: B 444 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8004 (mt-10) REVERT: C 246 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: C 357 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7435 (mmm-85) REVERT: C 426 GLN cc_start: 0.7762 (tp40) cc_final: 0.7355 (tm-30) REVERT: D 74 MET cc_start: 0.7327 (mtp) cc_final: 0.6988 (mmt) REVERT: D 342 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8055 (t80) REVERT: D 354 ASP cc_start: 0.7486 (t0) cc_final: 0.6827 (t70) REVERT: D 426 GLN cc_start: 0.7824 (tt0) cc_final: 0.7282 (tp-100) REVERT: D 444 GLU cc_start: 0.7953 (mp0) cc_final: 0.7701 (mp0) REVERT: F 74 ASN cc_start: 0.6750 (t0) cc_final: 0.6397 (t0) REVERT: F 76 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: F 78 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7078 (tt0) REVERT: G 76 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7936 (mm-30) REVERT: G 120 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7927 (p0) REVERT: I 68 ASN cc_start: 0.7192 (m-40) cc_final: 0.6777 (p0) REVERT: I 78 GLU cc_start: 0.7565 (pt0) cc_final: 0.7134 (pt0) REVERT: I 80 CYS cc_start: 0.7795 (m) cc_final: 0.7018 (p) REVERT: I 111 ARG cc_start: 0.8414 (mmt90) cc_final: 0.8159 (mmt-90) REVERT: J 76 ARG cc_start: 0.8758 (ptm160) cc_final: 0.8514 (ptm160) REVERT: J 426 GLN cc_start: 0.7954 (tp40) cc_final: 0.7237 (tp-100) REVERT: J 436 ARG cc_start: 0.8716 (ptm160) cc_final: 0.8180 (ptm160) REVERT: K 76 ARG cc_start: 0.8602 (mtp180) cc_final: 0.8335 (ttp80) REVERT: K 283 ASP cc_start: 0.7960 (m-30) cc_final: 0.7688 (m-30) REVERT: K 444 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8011 (mt-10) REVERT: L 246 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: L 357 ARG cc_start: 0.7854 (mtt-85) cc_final: 0.7437 (mmm-85) REVERT: L 426 GLN cc_start: 0.7789 (tp40) cc_final: 0.7384 (tm-30) REVERT: M 74 MET cc_start: 0.7365 (mtp) cc_final: 0.6981 (mmt) REVERT: M 342 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8047 (t80) REVERT: M 354 ASP cc_start: 0.7499 (t0) cc_final: 0.6818 (t70) REVERT: M 426 GLN cc_start: 0.7902 (tt0) cc_final: 0.7233 (tp-100) REVERT: M 444 GLU cc_start: 0.7944 (mp0) cc_final: 0.7712 (mp0) REVERT: R 68 ASN cc_start: 0.7201 (m-40) cc_final: 0.6754 (p0) REVERT: R 78 GLU cc_start: 0.7572 (pt0) cc_final: 0.7143 (pt0) REVERT: R 80 CYS cc_start: 0.7823 (m) cc_final: 0.7039 (p) REVERT: R 111 ARG cc_start: 0.8422 (mmt90) cc_final: 0.8172 (mmt-90) outliers start: 56 outliers final: 26 residues processed: 399 average time/residue: 0.7438 time to fit residues: 348.3617 Evaluate side-chains 353 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 321 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 256 GLU Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 335 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 132 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 1 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 389 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 447 optimal weight: 20.0000 chunk 431 optimal weight: 7.9990 chunk 395 optimal weight: 4.9990 chunk 360 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN C 226 GLN D 322 HIS G 122 ASN J 209 GLN K 426 GLN L 226 GLN M 322 HIS O 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.079915 restraints weight = 50150.236| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.78 r_work: 0.2769 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 37188 Z= 0.210 Angle : 0.612 9.464 50334 Z= 0.314 Chirality : 0.045 0.174 5368 Planarity : 0.005 0.047 6622 Dihedral : 5.283 73.354 5061 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.95 % Allowed : 11.75 % Favored : 86.30 % 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 aren not related in a simple way. whole: -1.17 (0.12), residues: 4644 helix: 1.07 (0.13), residues: 1692 sheet: -0.58 (0.21), residues: 538 loop : -2.31 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 302 TYR 0.017 0.001 TYR N 101 PHE 0.026 0.002 PHE K 342 TRP 0.019 0.001 TRP C 408 HIS 0.005 0.001 HIS L 289 Details of bonding type rmsd covalent geometry : bond 0.00515 (37188) covalent geometry : angle 0.61202 (50334) hydrogen bonds : bond 0.05146 ( 1351) hydrogen bonds : angle 3.83932 ( 3873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 346 time to evaluate : 0.943 Fit side-chains REVERT: A 153 GLN cc_start: 0.7612 (mp10) cc_final: 0.7390 (mp10) REVERT: A 302 ARG cc_start: 0.8592 (ttm110) cc_final: 0.8030 (mtp-110) REVERT: A 436 ARG cc_start: 0.8720 (ptm-80) cc_final: 0.8324 (ptm160) REVERT: B 76 ARG cc_start: 0.8566 (mtp180) cc_final: 0.8321 (ttp80) REVERT: B 283 ASP cc_start: 0.8050 (m-30) cc_final: 0.7791 (m-30) REVERT: C 246 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: C 357 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7436 (mmm-85) REVERT: C 393 ASP cc_start: 0.8434 (m-30) cc_final: 0.8213 (m-30) REVERT: C 426 GLN cc_start: 0.7758 (tp40) cc_final: 0.7307 (tm-30) REVERT: D 74 MET cc_start: 0.7310 (mtp) cc_final: 0.7014 (mmt) REVERT: D 426 GLN cc_start: 0.7778 (tt0) cc_final: 0.7218 (tp-100) REVERT: F 74 ASN cc_start: 0.7161 (t0) cc_final: 0.6878 (t0) REVERT: F 76 GLU cc_start: 0.8112 (mp0) cc_final: 0.7439 (tm-30) REVERT: F 78 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7125 (tt0) REVERT: G 76 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7917 (tm-30) REVERT: G 111 ARG cc_start: 0.8442 (mpt-90) cc_final: 0.8164 (mmt90) REVERT: G 120 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8168 (p0) REVERT: I 68 ASN cc_start: 0.7114 (m-40) cc_final: 0.6782 (p0) REVERT: I 78 GLU cc_start: 0.7497 (pt0) cc_final: 0.7058 (pt0) REVERT: I 80 CYS cc_start: 0.7854 (m) cc_final: 0.7005 (p) REVERT: I 111 ARG cc_start: 0.8358 (mmt90) cc_final: 0.8096 (mmt-90) REVERT: J 302 ARG cc_start: 0.8581 (ttm110) cc_final: 0.8017 (mtp-110) REVERT: J 436 ARG cc_start: 0.8727 (ptm160) cc_final: 0.8108 (ptm160) REVERT: K 283 ASP cc_start: 0.8063 (m-30) cc_final: 0.7805 (m-30) REVERT: L 70 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5967 (pp) REVERT: L 246 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: L 357 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7454 (mmm-85) REVERT: L 393 ASP cc_start: 0.8420 (m-30) cc_final: 0.8214 (m-30) REVERT: L 426 GLN cc_start: 0.7784 (tp40) cc_final: 0.7337 (tm-30) REVERT: M 74 MET cc_start: 0.7338 (mtp) cc_final: 0.7030 (mmt) REVERT: M 354 ASP cc_start: 0.7460 (t0) cc_final: 0.6792 (t70) REVERT: M 426 GLN cc_start: 0.7703 (tt0) cc_final: 0.7152 (tp-100) REVERT: O 76 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7326 (tm-30) REVERT: P 111 ARG cc_start: 0.8440 (mpt-90) cc_final: 0.8156 (mmt90) REVERT: Q 113 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7987 (mtpp) REVERT: R 68 ASN cc_start: 0.7112 (m-40) cc_final: 0.6786 (p0) REVERT: R 78 GLU cc_start: 0.7483 (pt0) cc_final: 0.7041 (pt0) REVERT: R 80 CYS cc_start: 0.7868 (m) cc_final: 0.7015 (p) REVERT: R 111 ARG cc_start: 0.8357 (mmt90) cc_final: 0.8098 (mmt-90) outliers start: 74 outliers final: 30 residues processed: 386 average time/residue: 0.7626 time to fit residues: 344.7154 Evaluate side-chains 356 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 322 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 256 GLU Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 335 ASP Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 113 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 275 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 320 optimal weight: 4.9990 chunk 421 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 442 optimal weight: 0.7980 chunk 335 optimal weight: 3.9990 chunk 410 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS A 426 GLN C 226 GLN D 322 HIS J 426 GLN L 226 GLN M 322 HIS O 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082085 restraints weight = 49504.283| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.77 r_work: 0.2805 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 37188 Z= 0.131 Angle : 0.554 14.503 50334 Z= 0.283 Chirality : 0.043 0.173 5368 Planarity : 0.004 0.043 6622 Dihedral : 4.742 71.235 5048 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.77 % Allowed : 13.36 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.12), residues: 4644 helix: 1.51 (0.13), residues: 1696 sheet: -0.33 (0.21), residues: 538 loop : -1.99 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 302 TYR 0.017 0.001 TYR N 101 PHE 0.018 0.001 PHE K 342 TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS J 289 Details of bonding type rmsd covalent geometry : bond 0.00315 (37188) covalent geometry : angle 0.55438 (50334) hydrogen bonds : bond 0.03912 ( 1351) hydrogen bonds : angle 3.65694 ( 3873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 350 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.7569 (mp10) cc_final: 0.7361 (mp10) REVERT: A 436 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8333 (ptm160) REVERT: B 153 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7671 (mm-40) REVERT: B 283 ASP cc_start: 0.7920 (m-30) cc_final: 0.7661 (m-30) REVERT: B 444 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7959 (mt-10) REVERT: C 246 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: C 357 ARG cc_start: 0.7676 (mtt-85) cc_final: 0.7255 (mmm-85) REVERT: C 426 GLN cc_start: 0.7740 (tp40) cc_final: 0.7298 (tm-30) REVERT: D 299 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7356 (p0) REVERT: D 426 GLN cc_start: 0.7743 (tt0) cc_final: 0.7239 (tp-100) REVERT: F 74 ASN cc_start: 0.7193 (t0) cc_final: 0.6929 (t0) REVERT: F 76 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: F 78 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7136 (tt0) REVERT: G 76 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7874 (tm-30) REVERT: G 111 ARG cc_start: 0.8489 (mpt-90) cc_final: 0.8174 (mmt90) REVERT: G 120 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8136 (p0) REVERT: H 113 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8035 (mtpp) REVERT: H 115 GLU cc_start: 0.6805 (pt0) cc_final: 0.6571 (tp30) REVERT: I 68 ASN cc_start: 0.7018 (m-40) cc_final: 0.6769 (p0) REVERT: I 78 GLU cc_start: 0.7482 (pt0) cc_final: 0.7024 (pt0) REVERT: I 80 CYS cc_start: 0.7789 (m) cc_final: 0.7075 (p) REVERT: I 111 ARG cc_start: 0.8353 (mmt90) cc_final: 0.8117 (mmt-90) REVERT: J 436 ARG cc_start: 0.8703 (ptm160) cc_final: 0.8097 (ptm160) REVERT: K 283 ASP cc_start: 0.7932 (m-30) cc_final: 0.7675 (m-30) REVERT: K 444 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7937 (mt-10) REVERT: L 70 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5759 (pp) REVERT: L 357 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7259 (mmm-85) REVERT: L 426 GLN cc_start: 0.7763 (tp40) cc_final: 0.7321 (tm-30) REVERT: M 342 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8152 (OUTLIER) REVERT: M 426 GLN cc_start: 0.7712 (tt0) cc_final: 0.7198 (tp-100) REVERT: O 76 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7353 (tm-30) REVERT: P 111 ARG cc_start: 0.8488 (mpt-90) cc_final: 0.8164 (mmt90) REVERT: Q 113 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7961 (mtpp) REVERT: Q 115 GLU cc_start: 0.6755 (pt0) cc_final: 0.6537 (tp30) REVERT: R 68 ASN cc_start: 0.7013 (m-40) cc_final: 0.6752 (p0) REVERT: R 78 GLU cc_start: 0.7490 (pt0) cc_final: 0.7033 (pt0) REVERT: R 80 CYS cc_start: 0.7796 (m) cc_final: 0.7076 (p) REVERT: R 111 ARG cc_start: 0.8345 (mmt90) cc_final: 0.8114 (mmt-90) outliers start: 67 outliers final: 27 residues processed: 390 average time/residue: 0.7496 time to fit residues: 340.7281 Evaluate side-chains 357 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 322 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 256 GLU Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 335 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 113 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 146 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 406 optimal weight: 9.9990 chunk 224 optimal weight: 0.0470 chunk 456 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 392 optimal weight: 0.9980 chunk 221 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 209 GLN B 426 GLN D 322 HIS E 129 GLN J 426 GLN K 426 GLN L 209 GLN L 226 GLN M 322 HIS N 129 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.083393 restraints weight = 49348.559| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.78 r_work: 0.2828 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37188 Z= 0.107 Angle : 0.539 15.261 50334 Z= 0.273 Chirality : 0.042 0.215 5368 Planarity : 0.004 0.044 6622 Dihedral : 4.499 67.668 5048 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.82 % Allowed : 14.04 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.13), residues: 4644 helix: 1.85 (0.13), residues: 1696 sheet: -0.22 (0.20), residues: 562 loop : -1.76 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 302 TYR 0.017 0.001 TYR E 101 PHE 0.017 0.001 PHE F 130 TRP 0.013 0.001 TRP L 211 HIS 0.004 0.001 HIS L 289 Details of bonding type rmsd covalent geometry : bond 0.00252 (37188) covalent geometry : angle 0.53926 (50334) hydrogen bonds : bond 0.03387 ( 1351) hydrogen bonds : angle 3.53502 ( 3873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 349 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.7557 (mp10) cc_final: 0.7353 (mp10) REVERT: A 436 ARG cc_start: 0.8668 (ptm-80) cc_final: 0.8305 (ptm-80) REVERT: A 469 MET cc_start: 0.0763 (tpt) cc_final: 0.0293 (tpt) REVERT: B 203 ILE cc_start: 0.8184 (mm) cc_final: 0.7890 (pt) REVERT: B 283 ASP cc_start: 0.7876 (m-30) cc_final: 0.7605 (m-30) REVERT: C 246 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: C 357 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7233 (mmm-85) REVERT: C 426 GLN cc_start: 0.7799 (tp40) cc_final: 0.7356 (tm-30) REVERT: D 342 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8166 (t80) REVERT: D 426 GLN cc_start: 0.7696 (tt0) cc_final: 0.7226 (tp-100) REVERT: F 74 ASN cc_start: 0.7249 (t0) cc_final: 0.6962 (t0) REVERT: F 76 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: F 78 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7073 (tt0) REVERT: G 120 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8156 (p0) REVERT: H 113 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7955 (mtpm) REVERT: H 115 GLU cc_start: 0.6767 (pt0) cc_final: 0.6544 (tp30) REVERT: I 78 GLU cc_start: 0.7456 (pt0) cc_final: 0.7016 (pt0) REVERT: I 80 CYS cc_start: 0.7723 (m) cc_final: 0.7160 (p) REVERT: J 436 ARG cc_start: 0.8689 (ptm160) cc_final: 0.8056 (ptm160) REVERT: K 153 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7674 (mm-40) REVERT: K 203 ILE cc_start: 0.8183 (mm) cc_final: 0.7901 (pt) REVERT: K 283 ASP cc_start: 0.7879 (m-30) cc_final: 0.7623 (m-30) REVERT: L 246 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: L 357 ARG cc_start: 0.7623 (mtt-85) cc_final: 0.7239 (mmm-85) REVERT: L 426 GLN cc_start: 0.7816 (tp40) cc_final: 0.7373 (tm-30) REVERT: M 342 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8162 (t80) REVERT: M 426 GLN cc_start: 0.7704 (tt0) cc_final: 0.7232 (tp-100) REVERT: O 76 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7525 (tm-30) REVERT: O 78 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7531 (tt0) REVERT: Q 113 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7968 (mtpm) REVERT: Q 115 GLU cc_start: 0.6719 (pt0) cc_final: 0.6505 (tp30) REVERT: R 78 GLU cc_start: 0.7464 (pt0) cc_final: 0.7024 (pt0) REVERT: R 80 CYS cc_start: 0.7745 (m) cc_final: 0.7169 (p) outliers start: 69 outliers final: 30 residues processed: 391 average time/residue: 0.7477 time to fit residues: 342.4738 Evaluate side-chains 365 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 205 SER Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 400 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 452 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 410 optimal weight: 0.0000 chunk 343 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 426 GLN C 209 GLN D 322 HIS J 426 GLN K 426 GLN M 322 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087753 restraints weight = 50474.666| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.81 r_work: 0.2945 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 37188 Z= 0.098 Angle : 0.522 12.315 50334 Z= 0.265 Chirality : 0.041 0.298 5368 Planarity : 0.004 0.048 6622 Dihedral : 4.255 64.261 5046 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.72 % Allowed : 14.60 % Favored : 83.69 % 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 aren not related in a simple way. whole: 0.06 (0.13), residues: 4644 helix: 2.11 (0.13), residues: 1696 sheet: -0.00 (0.21), residues: 564 loop : -1.59 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 302 TYR 0.017 0.001 TYR N 101 PHE 0.021 0.001 PHE O 130 TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS J 289 Details of bonding type rmsd covalent geometry : bond 0.00230 (37188) covalent geometry : angle 0.52156 (50334) hydrogen bonds : bond 0.03020 ( 1351) hydrogen bonds : angle 3.44053 ( 3873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 349 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.7529 (mp10) cc_final: 0.7311 (mp10) REVERT: A 203 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7760 (tt) REVERT: A 436 ARG cc_start: 0.8577 (ptm-80) cc_final: 0.8278 (ptm-80) REVERT: B 283 ASP cc_start: 0.7829 (m-30) cc_final: 0.7555 (m-30) REVERT: B 444 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7920 (mt-10) REVERT: C 246 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: C 357 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7298 (mmm-85) REVERT: C 426 GLN cc_start: 0.7748 (tp40) cc_final: 0.7304 (tm-30) REVERT: D 342 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8223 (t80) REVERT: D 426 GLN cc_start: 0.7743 (tt0) cc_final: 0.7311 (tp-100) REVERT: E 95 MET cc_start: 0.7768 (mtt) cc_final: 0.7377 (mpt) REVERT: F 74 ASN cc_start: 0.7360 (t0) cc_final: 0.7071 (t0) REVERT: F 76 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: F 78 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7052 (tt0) REVERT: G 120 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8261 (p0) REVERT: H 78 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7848 (tp30) REVERT: H 113 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7964 (mtpm) REVERT: I 78 GLU cc_start: 0.7433 (pt0) cc_final: 0.6988 (pt0) REVERT: I 80 CYS cc_start: 0.7743 (m) cc_final: 0.7263 (p) REVERT: J 203 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7771 (tt) REVERT: J 436 ARG cc_start: 0.8590 (ptm160) cc_final: 0.8011 (ptm160) REVERT: K 153 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7585 (mm-40) REVERT: K 283 ASP cc_start: 0.7828 (m-30) cc_final: 0.7577 (m-30) REVERT: K 444 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7888 (mt-10) REVERT: L 246 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7118 (mm-30) REVERT: L 357 ARG cc_start: 0.7674 (mtt-85) cc_final: 0.7326 (mmm-85) REVERT: L 426 GLN cc_start: 0.7760 (tp40) cc_final: 0.7315 (tm-30) REVERT: M 203 ILE cc_start: 0.8394 (mm) cc_final: 0.7999 (pt) REVERT: M 342 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8196 (t80) REVERT: M 426 GLN cc_start: 0.7706 (tt0) cc_final: 0.7273 (tp-100) REVERT: O 76 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7518 (tm-30) REVERT: O 78 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7604 (tt0) REVERT: Q 113 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7976 (mtpm) REVERT: R 78 GLU cc_start: 0.7499 (pt0) cc_final: 0.7047 (pt0) REVERT: R 80 CYS cc_start: 0.7750 (m) cc_final: 0.7270 (p) outliers start: 65 outliers final: 30 residues processed: 391 average time/residue: 0.7284 time to fit residues: 335.3089 Evaluate side-chains 367 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 304 optimal weight: 8.9990 chunk 253 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 396 optimal weight: 4.9990 chunk 420 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS A 426 GLN B 426 GLN D 322 HIS J 264 HIS J 426 GLN K 426 GLN M 322 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.081807 restraints weight = 49700.042| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.79 r_work: 0.2804 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 37188 Z= 0.157 Angle : 0.571 12.796 50334 Z= 0.289 Chirality : 0.044 0.275 5368 Planarity : 0.004 0.055 6622 Dihedral : 4.327 62.871 5046 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.93 % Allowed : 15.07 % Favored : 83.00 % 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 aren not related in a simple way. whole: 0.07 (0.13), residues: 4644 helix: 2.09 (0.13), residues: 1694 sheet: 0.13 (0.21), residues: 538 loop : -1.58 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 302 TYR 0.016 0.001 TYR E 101 PHE 0.020 0.001 PHE F 130 TRP 0.014 0.001 TRP C 408 HIS 0.004 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00387 (37188) covalent geometry : angle 0.57147 (50334) hydrogen bonds : bond 0.04045 ( 1351) hydrogen bonds : angle 3.50754 ( 3873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 329 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.7554 (mp10) cc_final: 0.7345 (mp10) REVERT: A 203 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7674 (tt) REVERT: A 436 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8352 (ptm-80) REVERT: B 125 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8843 (mmpt) REVERT: B 153 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7685 (mm-40) REVERT: B 283 ASP cc_start: 0.7918 (m-30) cc_final: 0.7677 (m-30) REVERT: B 389 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8347 (pp20) REVERT: C 246 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: C 357 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7444 (mmm-85) REVERT: C 426 GLN cc_start: 0.7809 (tp40) cc_final: 0.7339 (tm-30) REVERT: D 18 LYS cc_start: 0.7451 (mppt) cc_final: 0.7247 (mmmm) REVERT: D 354 ASP cc_start: 0.7385 (t0) cc_final: 0.6949 (t70) REVERT: D 426 GLN cc_start: 0.7740 (tt0) cc_final: 0.7288 (tp-100) REVERT: F 74 ASN cc_start: 0.7181 (t0) cc_final: 0.6895 (t0) REVERT: F 76 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: F 78 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7092 (tt0) REVERT: G 120 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8349 (p0) REVERT: H 113 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8008 (mtpm) REVERT: H 115 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: I 78 GLU cc_start: 0.7463 (pt0) cc_final: 0.7032 (pt0) REVERT: I 80 CYS cc_start: 0.7847 (m) cc_final: 0.7283 (p) REVERT: J 203 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7684 (tt) REVERT: J 436 ARG cc_start: 0.8674 (ptm160) cc_final: 0.8095 (ptm160) REVERT: K 125 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8853 (mmpt) REVERT: K 153 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7676 (mm-40) REVERT: K 283 ASP cc_start: 0.7928 (m-30) cc_final: 0.7689 (m-30) REVERT: K 389 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8361 (pp20) REVERT: L 246 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: L 357 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.7461 (mmm-85) REVERT: L 426 GLN cc_start: 0.7840 (tp40) cc_final: 0.7371 (tm-30) REVERT: M 342 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8169 (t80) REVERT: M 354 ASP cc_start: 0.7297 (t0) cc_final: 0.6710 (t70) REVERT: M 426 GLN cc_start: 0.7733 (tt0) cc_final: 0.7279 (tp-100) REVERT: O 76 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7428 (tm-30) REVERT: O 78 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7664 (tt0) REVERT: Q 74 ASN cc_start: 0.7494 (t0) cc_final: 0.7263 (t0) REVERT: Q 78 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: Q 113 LYS cc_start: 0.8446 (mtmm) cc_final: 0.7946 (mtpm) REVERT: Q 115 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: R 78 GLU cc_start: 0.7458 (pt0) cc_final: 0.7025 (pt0) REVERT: R 80 CYS cc_start: 0.7850 (m) cc_final: 0.7284 (p) outliers start: 73 outliers final: 32 residues processed: 375 average time/residue: 0.7268 time to fit residues: 320.3523 Evaluate side-chains 372 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 323 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 389 GLU Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 29 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 405 optimal weight: 4.9990 chunk 336 optimal weight: 0.8980 chunk 269 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 225 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 426 GLN C 322 HIS D 322 HIS J 426 GLN K 426 GLN L 322 HIS M 322 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.083201 restraints weight = 49371.181| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.77 r_work: 0.2830 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 37188 Z= 0.116 Angle : 0.555 10.770 50334 Z= 0.279 Chirality : 0.042 0.336 5368 Planarity : 0.004 0.053 6622 Dihedral : 4.229 64.545 5046 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.82 % Allowed : 15.58 % Favored : 82.60 % 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 aren not related in a simple way. whole: 0.20 (0.13), residues: 4644 helix: 2.15 (0.13), residues: 1702 sheet: 0.17 (0.21), residues: 562 loop : -1.47 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 302 TYR 0.016 0.001 TYR E 101 PHE 0.024 0.001 PHE O 130 TRP 0.011 0.001 TRP L 211 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00282 (37188) covalent geometry : angle 0.55491 (50334) hydrogen bonds : bond 0.03334 ( 1351) hydrogen bonds : angle 3.45706 ( 3873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 333 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.7488 (mp10) cc_final: 0.7275 (mp10) REVERT: A 203 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7677 (tt) REVERT: A 436 ARG cc_start: 0.8584 (ptm-80) cc_final: 0.8277 (ptm-80) REVERT: B 76 ARG cc_start: 0.8433 (mtp180) cc_final: 0.8213 (ttp80) REVERT: B 125 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8775 (mmpt) REVERT: B 153 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7549 (mm-40) REVERT: B 283 ASP cc_start: 0.7730 (m-30) cc_final: 0.7485 (m-30) REVERT: B 389 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8212 (pp20) REVERT: C 155 GLU cc_start: 0.8221 (pp20) cc_final: 0.7939 (pt0) REVERT: C 246 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7126 (mm-30) REVERT: C 357 ARG cc_start: 0.7704 (mtt-85) cc_final: 0.7335 (mmm-85) REVERT: C 426 GLN cc_start: 0.7705 (tp40) cc_final: 0.7263 (tm-30) REVERT: D 18 LYS cc_start: 0.7451 (mppt) cc_final: 0.7239 (mmmm) REVERT: D 74 MET cc_start: 0.7696 (mmp) cc_final: 0.7362 (mmt) REVERT: D 299 ASP cc_start: 0.7609 (t0) cc_final: 0.7179 (p0) REVERT: D 426 GLN cc_start: 0.7676 (tt0) cc_final: 0.7265 (tp-100) REVERT: E 95 MET cc_start: 0.7780 (mtt) cc_final: 0.7359 (mpt) REVERT: F 74 ASN cc_start: 0.7218 (t0) cc_final: 0.6938 (t0) REVERT: F 76 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: F 78 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7174 (tt0) REVERT: G 120 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8337 (p0) REVERT: H 113 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7943 (mtpm) REVERT: H 115 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: I 78 GLU cc_start: 0.7416 (pt0) cc_final: 0.6965 (pt0) REVERT: I 80 CYS cc_start: 0.7783 (m) cc_final: 0.7334 (p) REVERT: J 203 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7684 (tt) REVERT: J 436 ARG cc_start: 0.8588 (ptm160) cc_final: 0.8290 (ptm-80) REVERT: K 76 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8211 (ttp80) REVERT: K 125 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8780 (mmpt) REVERT: K 153 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7562 (mm-40) REVERT: K 283 ASP cc_start: 0.7744 (m-30) cc_final: 0.7501 (m-30) REVERT: K 389 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8248 (pp20) REVERT: L 155 GLU cc_start: 0.8215 (pp20) cc_final: 0.7980 (pt0) REVERT: L 246 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: L 357 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7350 (mmm-85) REVERT: L 426 GLN cc_start: 0.7729 (tp40) cc_final: 0.7286 (tm-30) REVERT: M 74 MET cc_start: 0.7675 (mmp) cc_final: 0.7336 (mmt) REVERT: M 299 ASP cc_start: 0.7649 (t0) cc_final: 0.7200 (p0) REVERT: M 342 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8098 (t80) REVERT: M 426 GLN cc_start: 0.7680 (tt0) cc_final: 0.7264 (tp-100) REVERT: O 76 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7489 (tm-30) REVERT: O 78 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7583 (tt0) REVERT: Q 78 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: Q 113 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7941 (mtpm) REVERT: Q 115 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7187 (mm-30) REVERT: R 78 GLU cc_start: 0.7410 (pt0) cc_final: 0.6963 (pt0) REVERT: R 80 CYS cc_start: 0.7783 (m) cc_final: 0.7338 (p) outliers start: 69 outliers final: 34 residues processed: 373 average time/residue: 0.7722 time to fit residues: 336.4336 Evaluate side-chains 377 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 325 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 389 GLU Chi-restraints excluded: chain K residue 435 TYR Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain M residue 457 ASP Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 271 optimal weight: 0.9980 chunk 356 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 451 optimal weight: 0.9990 chunk 413 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 212 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 426 GLN C 322 HIS D 322 HIS J 426 GLN K 426 GLN L 322 HIS M 322 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.082979 restraints weight = 49434.936| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.78 r_work: 0.2826 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 37188 Z= 0.122 Angle : 0.558 9.967 50334 Z= 0.281 Chirality : 0.043 0.253 5368 Planarity : 0.004 0.063 6622 Dihedral : 4.214 64.102 5046 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.58 % Allowed : 16.02 % Favored : 82.39 % 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 aren not related in a simple way. whole: 0.25 (0.13), residues: 4644 helix: 2.17 (0.13), residues: 1702 sheet: 0.21 (0.21), residues: 562 loop : -1.42 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 302 TYR 0.016 0.001 TYR E 101 PHE 0.023 0.001 PHE F 130 TRP 0.011 0.001 TRP C 408 HIS 0.004 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00301 (37188) covalent geometry : angle 0.55780 (50334) hydrogen bonds : bond 0.03453 ( 1351) hydrogen bonds : angle 3.44826 ( 3873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 324 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.7481 (mp10) cc_final: 0.7267 (mp10) REVERT: A 203 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7689 (tt) REVERT: B 125 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8764 (mmpt) REVERT: B 389 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8203 (pp20) REVERT: C 74 MET cc_start: 0.7707 (ttm) cc_final: 0.7429 (ttp) REVERT: C 246 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: C 357 ARG cc_start: 0.7713 (mtt-85) cc_final: 0.7343 (mmm-85) REVERT: C 426 GLN cc_start: 0.7728 (tp40) cc_final: 0.7265 (tm-30) REVERT: D 299 ASP cc_start: 0.7650 (t0) cc_final: 0.7203 (p0) REVERT: D 426 GLN cc_start: 0.7678 (tt0) cc_final: 0.7267 (tp-100) REVERT: E 95 MET cc_start: 0.7804 (mtt) cc_final: 0.7374 (mpt) REVERT: F 74 ASN cc_start: 0.7211 (t0) cc_final: 0.6920 (t0) REVERT: F 76 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: F 78 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7181 (tt0) REVERT: G 120 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8189 (p0) REVERT: H 113 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7941 (mtpm) REVERT: H 115 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: I 78 GLU cc_start: 0.7422 (pt0) cc_final: 0.6971 (pt0) REVERT: I 80 CYS cc_start: 0.7779 (m) cc_final: 0.7339 (p) REVERT: J 203 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7698 (tt) REVERT: J 436 ARG cc_start: 0.8583 (ptm160) cc_final: 0.8262 (ptm-80) REVERT: K 125 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8769 (mmpt) REVERT: K 153 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7560 (mm-40) REVERT: K 389 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (pp20) REVERT: L 246 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: L 357 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7360 (mmm-85) REVERT: L 426 GLN cc_start: 0.7748 (tp40) cc_final: 0.7286 (tm-30) REVERT: M 18 LYS cc_start: 0.7462 (mppt) cc_final: 0.7154 (mmmm) REVERT: M 299 ASP cc_start: 0.7601 (t0) cc_final: 0.7167 (p0) REVERT: M 342 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8098 (t80) REVERT: M 354 ASP cc_start: 0.7232 (t0) cc_final: 0.6695 (t70) REVERT: M 426 GLN cc_start: 0.7681 (tt0) cc_final: 0.7266 (tp-100) REVERT: O 76 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7404 (tm-30) REVERT: O 78 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7605 (tt0) REVERT: Q 78 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7800 (tp30) REVERT: Q 113 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7932 (mtpm) REVERT: Q 115 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: R 78 GLU cc_start: 0.7490 (pt0) cc_final: 0.7033 (pt0) REVERT: R 80 CYS cc_start: 0.7776 (m) cc_final: 0.7339 (p) outliers start: 60 outliers final: 32 residues processed: 360 average time/residue: 0.7698 time to fit residues: 323.6410 Evaluate side-chains 365 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 389 GLU Chi-restraints excluded: chain K residue 435 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 64 optimal weight: 2.9990 chunk 373 optimal weight: 8.9990 chunk 422 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 400 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 chunk 428 optimal weight: 9.9990 chunk 379 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 426 GLN C 295 HIS C 322 HIS D 322 HIS J 426 GLN K 426 GLN L 295 HIS L 322 HIS M 322 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.081060 restraints weight = 49690.120| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.78 r_work: 0.2792 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 37188 Z= 0.176 Angle : 0.605 10.225 50334 Z= 0.304 Chirality : 0.044 0.255 5368 Planarity : 0.005 0.065 6622 Dihedral : 4.371 63.561 5046 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.64 % Allowed : 16.00 % Favored : 82.37 % 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 aren not related in a simple way. whole: 0.14 (0.13), residues: 4644 helix: 2.04 (0.13), residues: 1702 sheet: 0.23 (0.21), residues: 538 loop : -1.47 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 302 TYR 0.016 0.001 TYR E 101 PHE 0.024 0.001 PHE O 130 TRP 0.015 0.001 TRP C 408 HIS 0.004 0.001 HIS K 289 Details of bonding type rmsd covalent geometry : bond 0.00435 (37188) covalent geometry : angle 0.60531 (50334) hydrogen bonds : bond 0.04368 ( 1351) hydrogen bonds : angle 3.54563 ( 3873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 326 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.7559 (mp10) cc_final: 0.7354 (mp10) REVERT: A 203 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7695 (tt) REVERT: A 436 ARG cc_start: 0.8677 (ptm-80) cc_final: 0.8347 (ptm-80) REVERT: B 153 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7697 (mm-40) REVERT: B 191 ARG cc_start: 0.8344 (tpt-90) cc_final: 0.7873 (tpt90) REVERT: C 74 MET cc_start: 0.7795 (ttm) cc_final: 0.7485 (ttp) REVERT: C 246 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: C 357 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.7399 (mmm-85) REVERT: C 426 GLN cc_start: 0.7872 (tp40) cc_final: 0.7409 (tm-30) REVERT: D 74 MET cc_start: 0.7774 (mmp) cc_final: 0.6327 (ttp) REVERT: D 299 ASP cc_start: 0.7859 (t0) cc_final: 0.7425 (p0) REVERT: D 354 ASP cc_start: 0.7436 (t0) cc_final: 0.6960 (t70) REVERT: D 426 GLN cc_start: 0.7697 (tt0) cc_final: 0.7241 (tp-100) REVERT: F 74 ASN cc_start: 0.7228 (t0) cc_final: 0.6959 (t0) REVERT: F 76 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: F 78 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7391 (tt0) REVERT: H 113 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7984 (mtpm) REVERT: H 115 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: I 78 GLU cc_start: 0.7533 (pt0) cc_final: 0.7096 (pt0) REVERT: I 80 CYS cc_start: 0.7867 (m) cc_final: 0.7289 (p) REVERT: I 114 LYS cc_start: 0.8966 (mttp) cc_final: 0.8169 (mtpp) REVERT: J 203 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7678 (tt) REVERT: J 436 ARG cc_start: 0.8628 (ptm160) cc_final: 0.8346 (ptm-80) REVERT: K 153 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7704 (mm-40) REVERT: L 246 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: L 357 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.7483 (mmm-85) REVERT: L 426 GLN cc_start: 0.7891 (tp40) cc_final: 0.7379 (tm-30) REVERT: M 18 LYS cc_start: 0.7591 (mppt) cc_final: 0.7284 (mmmm) REVERT: M 74 MET cc_start: 0.7767 (mmp) cc_final: 0.6321 (ttp) REVERT: M 299 ASP cc_start: 0.7843 (t0) cc_final: 0.7417 (p0) REVERT: M 426 GLN cc_start: 0.7699 (tt0) cc_final: 0.7249 (tp-100) REVERT: O 76 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7446 (tm-30) REVERT: O 78 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7645 (tt0) REVERT: Q 78 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: Q 113 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7957 (mtpm) REVERT: Q 115 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: R 78 GLU cc_start: 0.7511 (pt0) cc_final: 0.7074 (pt0) REVERT: R 80 CYS cc_start: 0.7872 (m) cc_final: 0.7292 (p) REVERT: R 114 LYS cc_start: 0.8972 (mttp) cc_final: 0.8179 (mtpp) outliers start: 62 outliers final: 30 residues processed: 364 average time/residue: 0.7972 time to fit residues: 339.9267 Evaluate side-chains 360 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 435 TYR Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 163 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 374 optimal weight: 0.8980 chunk 419 optimal weight: 4.9990 chunk 415 optimal weight: 10.0000 chunk 375 optimal weight: 3.9990 chunk 82 optimal weight: 0.0770 chunk 105 optimal weight: 0.9990 chunk 453 optimal weight: 7.9990 chunk 251 optimal weight: 0.5980 chunk 198 optimal weight: 7.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 426 GLN B 426 GLN D 322 HIS H 68 ASN J 410 ASN J 426 GLN K 426 GLN M 322 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.082796 restraints weight = 49203.153| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.78 r_work: 0.2821 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 37188 Z= 0.123 Angle : 0.581 12.998 50334 Z= 0.292 Chirality : 0.043 0.250 5368 Planarity : 0.004 0.064 6622 Dihedral : 4.259 65.184 5044 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.29 % Allowed : 16.66 % Favored : 82.05 % 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 aren not related in a simple way. whole: 0.26 (0.13), residues: 4644 helix: 2.13 (0.13), residues: 1704 sheet: 0.22 (0.21), residues: 562 loop : -1.39 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 302 TYR 0.016 0.001 TYR E 101 PHE 0.022 0.001 PHE F 130 TRP 0.012 0.001 TRP L 211 HIS 0.004 0.001 HIS J 289 Details of bonding type rmsd covalent geometry : bond 0.00302 (37188) covalent geometry : angle 0.58059 (50334) hydrogen bonds : bond 0.03516 ( 1351) hydrogen bonds : angle 3.47641 ( 3873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10454.53 seconds wall clock time: 179 minutes 4.46 seconds (10744.46 seconds total)