Starting phenix.real_space_refine on Mon Aug 25 09:18:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c67_45241/08_2025/9c67_45241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c67_45241/08_2025/9c67_45241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c67_45241/08_2025/9c67_45241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c67_45241/08_2025/9c67_45241.map" model { file = "/net/cci-nas-00/data/ceres_data/9c67_45241/08_2025/9c67_45241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c67_45241/08_2025/9c67_45241.cif" } resolution = 3.6 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 156 5.16 5 C 17072 2.51 5 N 4609 2.21 5 O 4940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 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: 26783 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4666 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "B" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4268 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 22, 'TRANS': 517} Chain breaks: 2 Chain: "C" Number of atoms: 4654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4654 Classifications: {'peptide': 590} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 562} Chain breaks: 1 Chain: "D" Number of atoms: 4254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4254 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 22, 'TRANS': 515} Chain breaks: 2 Chain: "E" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4674 Classifications: {'peptide': 593} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 565} Chain breaks: 1 Chain: "F" Number of atoms: 4261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4261 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.26, per 1000 atoms: 0.23 Number of scatterers: 26783 At special positions: 0 Unit cell: (205.352, 197.904, 88.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 Mg 6 11.99 O 4940 8.00 N 4609 7.00 C 17072 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: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6394 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 17 sheets defined 54.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 14 through 23 removed outlier: 4.545A pdb=" N GLU A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 removed outlier: 4.364A pdb=" N LEU A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 87 Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.615A pdb=" N LEU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.721A pdb=" N TYR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 347 through 369 removed outlier: 3.706A pdb=" N LYS A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 4.122A pdb=" N SER A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.732A pdb=" N ALA A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.595A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 4.317A pdb=" N LEU A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 478 " --> pdb=" O ASN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 557 through 571 Processing helix chain 'A' and resid 575 through 596 Processing helix chain 'B' and resid 14 through 23 removed outlier: 4.112A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.870A pdb=" N PHE B 178 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 198 Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 307 through 325 removed outlier: 3.520A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'B' and resid 347 through 369 removed outlier: 3.553A pdb=" N LYS B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 4.511A pdb=" N SER B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.539A pdb=" N ARG B 427 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 441 removed outlier: 4.270A pdb=" N ALA B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 464 removed outlier: 3.543A pdb=" N ILE B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.601A pdb=" N LEU B 476 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 478 " --> pdb=" O ASN B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 473 through 478' Processing helix chain 'B' and resid 479 through 490 Processing helix chain 'B' and resid 496 through 502 Processing helix chain 'B' and resid 517 through 525 Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 575 through 600 removed outlier: 3.909A pdb=" N LYS B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 600 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 20 removed outlier: 3.842A pdb=" N GLU C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.965A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 89 Processing helix chain 'C' and resid 103 through 118 Processing helix chain 'C' and resid 133 through 143 removed outlier: 4.481A pdb=" N ASP C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 180 through 188 removed outlier: 4.566A pdb=" N GLU C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.684A pdb=" N LEU C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.649A pdb=" N LEU C 268 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 307 through 325 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 347 through 369 removed outlier: 3.740A pdb=" N LYS C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 4.110A pdb=" N SER C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 442 removed outlier: 3.823A pdb=" N CYS C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 464 removed outlier: 3.980A pdb=" N GLN C 460 " --> pdb=" O GLU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 478 Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 517 through 525 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 557 through 571 Processing helix chain 'C' and resid 575 through 597 Processing helix chain 'C' and resid 598 through 600 No H-bonds generated for 'chain 'C' and resid 598 through 600' Processing helix chain 'D' and resid 14 through 23 removed outlier: 4.180A pdb=" N GLU D 18 " --> pdb=" O MET D 14 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 52 removed outlier: 3.716A pdb=" N LEU D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 87 Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 158 through 165 removed outlier: 4.326A pdb=" N LEU D 163 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS D 164 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 165 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 199 Processing helix chain 'D' and resid 200 through 205 removed outlier: 4.187A pdb=" N GLN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 308 through 325 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 347 through 369 Processing helix chain 'D' and resid 390 through 405 removed outlier: 4.524A pdb=" N SER D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN D 405 " --> pdb=" O ILE D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 removed outlier: 4.133A pdb=" N TYR D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 473 through 478 removed outlier: 3.620A pdb=" N LEU D 476 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 477 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 489 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 517 through 525 Processing helix chain 'D' and resid 534 through 539 removed outlier: 3.521A pdb=" N SER D 538 " --> pdb=" O ASN D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 553 removed outlier: 3.762A pdb=" N LEU D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA D 550 " --> pdb=" O LEU D 546 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 571 removed outlier: 3.778A pdb=" N VAL D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 562 " --> pdb=" O ARG D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 598 Processing helix chain 'E' and resid 14 through 21 removed outlier: 4.046A pdb=" N GLU E 18 " --> pdb=" O MET E 14 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 removed outlier: 4.578A pdb=" N LEU E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 88 Processing helix chain 'E' and resid 103 through 118 Processing helix chain 'E' and resid 133 through 144 removed outlier: 4.294A pdb=" N MET E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 Processing helix chain 'E' and resid 180 through 190 removed outlier: 4.452A pdb=" N LEU E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.737A pdb=" N LEU E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 336 through 340 Processing helix chain 'E' and resid 347 through 369 removed outlier: 3.591A pdb=" N LYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 407 removed outlier: 4.356A pdb=" N SER E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 435 through 442 removed outlier: 3.680A pdb=" N GLY E 442 " --> pdb=" O VAL E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 464 Processing helix chain 'E' and resid 475 through 478 Processing helix chain 'E' and resid 479 through 490 Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'E' and resid 517 through 525 Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 541 through 548 Processing helix chain 'E' and resid 548 through 553 Processing helix chain 'E' and resid 559 through 571 Processing helix chain 'E' and resid 575 through 598 removed outlier: 4.544A pdb=" N ILE E 598 " --> pdb=" O CYS E 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 removed outlier: 4.104A pdb=" N GLU F 18 " --> pdb=" O MET F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 70 through 87 Processing helix chain 'F' and resid 103 through 118 removed outlier: 3.790A pdb=" N SER F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 144 removed outlier: 3.672A pdb=" N MET F 137 " --> pdb=" O ASN F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 163 removed outlier: 3.542A pdb=" N ARG F 161 " --> pdb=" O ALA F 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU F 163 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 199 Processing helix chain 'F' and resid 215 through 224 Processing helix chain 'F' and resid 230 through 237 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 301 through 306 Processing helix chain 'F' and resid 307 through 325 Processing helix chain 'F' and resid 336 through 340 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 347 through 369 Processing helix chain 'F' and resid 390 through 404 removed outlier: 4.345A pdb=" N SER F 394 " --> pdb=" O LEU F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 429 through 435 removed outlier: 4.291A pdb=" N HIS F 433 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 465 removed outlier: 3.528A pdb=" N ILE F 458 " --> pdb=" O ASP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 478 removed outlier: 3.712A pdb=" N LEU F 476 " --> pdb=" O ALA F 473 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU F 477 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU F 478 " --> pdb=" O ASN F 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 473 through 478' Processing helix chain 'F' and resid 479 through 489 removed outlier: 3.696A pdb=" N ARG F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 502 Processing helix chain 'F' and resid 517 through 525 Processing helix chain 'F' and resid 534 through 539 removed outlier: 3.638A pdb=" N SER F 538 " --> pdb=" O ASN F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 553 removed outlier: 4.126A pdb=" N LEU F 549 " --> pdb=" O ASN F 545 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA F 550 " --> pdb=" O LEU F 546 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 571 removed outlier: 3.994A pdb=" N VAL F 561 " --> pdb=" O SER F 557 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU F 562 " --> pdb=" O ARG F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 600 removed outlier: 3.895A pdb=" N LYS F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 600 " --> pdb=" O ILE F 596 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 62 removed outlier: 7.022A pdb=" N VAL A 30 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N THR A 60 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 32 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS A 62 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 34 " --> pdb=" O CYS A 62 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU A 5 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N PHE A 33 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS A 7 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR A 35 " --> pdb=" O CYS A 7 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL A 4 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS A 98 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU A 6 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 123 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 245 removed outlier: 4.511A pdb=" N VAL A 240 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLU A 331 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU A 242 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG A 333 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS A 244 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N VAL A 376 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N GLY A 415 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU A 378 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASP A 417 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 380 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 418 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 469 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU A 470 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 493 " --> pdb=" O SER A 529 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 62 removed outlier: 6.728A pdb=" N VAL B 30 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N THR B 60 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 32 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS B 62 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR B 34 " --> pdb=" O CYS B 62 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 5 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE B 33 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS B 7 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N THR B 35 " --> pdb=" O CYS B 7 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 4 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N CYS B 98 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 6 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 97 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL B 125 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLN B 120 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 153 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 122 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET B 151 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 245 removed outlier: 6.595A pdb=" N LYS B 239 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N GLU B 331 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B 241 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ARG B 333 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N HIS B 243 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 328 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ASN B 377 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 330 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 379 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 332 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 381 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS B 334 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N VAL B 376 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLY B 415 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 378 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASP B 417 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 380 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 414 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR B 446 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 416 " --> pdb=" O THR B 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 471 removed outlier: 7.730A pdb=" N LEU B 470 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 493 " --> pdb=" O SER B 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 62 removed outlier: 3.644A pdb=" N THR C 34 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU C 5 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE C 33 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N CYS C 7 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR C 35 " --> pdb=" O CYS C 7 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL C 4 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N CYS C 98 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 6 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 123 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLN C 120 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR C 153 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N VAL C 122 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET C 151 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 239 through 245 removed outlier: 4.408A pdb=" N VAL C 240 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU C 331 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU C 242 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG C 333 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS C 244 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE C 413 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 378 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY C 415 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 380 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 419 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 446 through 447 removed outlier: 7.289A pdb=" N ALA C 447 " --> pdb=" O GLY C 471 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU C 470 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL C 493 " --> pdb=" O SER C 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 56 through 62 removed outlier: 6.900A pdb=" N VAL D 30 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR D 60 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 32 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS D 62 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR D 34 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR D 35 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL D 4 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N CYS D 98 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU D 6 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 97 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL D 125 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL D 122 " --> pdb=" O MET D 151 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS D 147 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 239 through 245 removed outlier: 4.396A pdb=" N VAL D 240 " --> pdb=" O TYR D 329 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLU D 331 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU D 242 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG D 333 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS D 244 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA D 328 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASN D 377 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 330 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 379 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE D 332 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE D 413 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU D 378 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY D 415 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 493 through 495 removed outlier: 6.338A pdb=" N VAL D 493 " --> pdb=" O SER D 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 56 through 62 removed outlier: 7.290A pdb=" N VAL E 30 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR E 60 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 32 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N CYS E 62 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR E 34 " --> pdb=" O CYS E 62 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU E 5 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE E 33 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS E 7 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR E 35 " --> pdb=" O CYS E 7 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL E 4 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS E 98 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU E 6 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL E 97 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL E 125 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 239 through 245 removed outlier: 4.421A pdb=" N VAL E 240 " --> pdb=" O TYR E 329 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU E 331 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU E 242 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG E 333 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS E 244 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E 413 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU E 378 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY E 415 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA E 419 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL E 414 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR E 446 " --> pdb=" O VAL E 414 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 416 " --> pdb=" O THR E 446 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS E 448 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU E 418 " --> pdb=" O HIS E 448 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 469 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL E 493 " --> pdb=" O SER E 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.509A pdb=" N THR F 60 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU F 5 " --> pdb=" O HIS F 31 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE F 33 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS F 7 " --> pdb=" O PHE F 33 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 4 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N CYS F 98 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU F 6 " --> pdb=" O CYS F 98 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER F 121 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY F 152 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE F 123 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU F 150 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL F 125 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE F 148 " --> pdb=" O VAL F 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 240 through 245 removed outlier: 6.753A pdb=" N ASP F 241 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ARG F 333 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N HIS F 243 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N VAL F 376 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N GLY F 415 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU F 378 " --> pdb=" O GLY F 415 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASP F 417 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL F 380 " --> pdb=" O ASP F 417 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 446 through 447 removed outlier: 4.032A pdb=" N ALA F 447 " --> pdb=" O ARG F 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 493 through 495 removed outlier: 6.438A pdb=" N VAL F 493 " --> pdb=" O SER F 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 1177 hydrogen bonds defined for protein. 3360 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: 5.75 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6990 1.33 - 1.45: 4991 1.45 - 1.58: 15145 1.58 - 1.70: 2 1.70 - 1.82: 234 Bond restraints: 27362 Sorted by residual: bond pdb=" CB PRO B 207 " pdb=" CG PRO B 207 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CB PRO F 90 " pdb=" CG PRO F 90 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.72e+00 bond pdb=" C LEU B 167 " pdb=" N PRO B 168 " ideal model delta sigma weight residual 1.331 1.351 -0.019 1.21e-02 6.83e+03 2.55e+00 bond pdb=" N MET D 89 " pdb=" CA MET D 89 " ideal model delta sigma weight residual 1.454 1.474 -0.020 1.29e-02 6.01e+03 2.47e+00 bond pdb=" CA ASN A 452 " pdb=" CB ASN A 452 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.47e-02 4.63e+03 2.44e+00 ... (remaining 27357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 36659 3.07 - 6.14: 323 6.14 - 9.21: 58 9.21 - 12.28: 12 12.28 - 15.35: 6 Bond angle restraints: 37058 Sorted by residual: angle pdb=" CA PRO B 207 " pdb=" N PRO B 207 " pdb=" CD PRO B 207 " ideal model delta sigma weight residual 112.00 96.65 15.35 1.40e+00 5.10e-01 1.20e+02 angle pdb=" N ILE F 213 " pdb=" CA ILE F 213 " pdb=" C ILE F 213 " ideal model delta sigma weight residual 113.20 107.58 5.62 9.60e-01 1.09e+00 3.43e+01 angle pdb=" C PHE D 386 " pdb=" CA PHE D 386 " pdb=" CB PHE D 386 " ideal model delta sigma weight residual 117.23 109.81 7.42 1.36e+00 5.41e-01 2.97e+01 angle pdb=" CA GLN C 405 " pdb=" CB GLN C 405 " pdb=" CG GLN C 405 " ideal model delta sigma weight residual 114.10 124.41 -10.31 2.00e+00 2.50e-01 2.66e+01 angle pdb=" CA MET D 89 " pdb=" CB MET D 89 " pdb=" CG MET D 89 " ideal model delta sigma weight residual 114.10 123.78 -9.68 2.00e+00 2.50e-01 2.34e+01 ... (remaining 37053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 13728 17.69 - 35.38: 2043 35.38 - 53.08: 565 53.08 - 70.77: 106 70.77 - 88.46: 33 Dihedral angle restraints: 16475 sinusoidal: 6605 harmonic: 9870 Sorted by residual: dihedral pdb=" CA MET F 89 " pdb=" C MET F 89 " pdb=" N PRO F 90 " pdb=" CA PRO F 90 " ideal model delta harmonic sigma weight residual -180.00 -138.17 -41.83 0 5.00e+00 4.00e-02 7.00e+01 dihedral pdb=" CA PHE D 208 " pdb=" C PHE D 208 " pdb=" N PRO D 209 " pdb=" CA PRO D 209 " ideal model delta harmonic sigma weight residual -180.00 -143.94 -36.06 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA SER F 210 " pdb=" C SER F 210 " pdb=" N LEU F 211 " pdb=" CA LEU F 211 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 16472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3350 0.054 - 0.109: 698 0.109 - 0.163: 67 0.163 - 0.217: 4 0.217 - 0.272: 4 Chirality restraints: 4123 Sorted by residual: chirality pdb=" CB ILE E 217 " pdb=" CA ILE E 217 " pdb=" CG1 ILE E 217 " pdb=" CG2 ILE E 217 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CG LEU D 522 " pdb=" CB LEU D 522 " pdb=" CD1 LEU D 522 " pdb=" CD2 LEU D 522 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 5 " pdb=" CB LEU A 5 " pdb=" CD1 LEU A 5 " pdb=" CD2 LEU A 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 4120 not shown) Planarity restraints: 4799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET F 89 " 0.098 5.00e-02 4.00e+02 1.48e-01 3.50e+01 pdb=" N PRO F 90 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO F 90 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO F 90 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 206 " 0.087 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO B 207 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 52 " -0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO B 53 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 53 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 53 " -0.049 5.00e-02 4.00e+02 ... (remaining 4796 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 395 2.59 - 3.17: 23953 3.17 - 3.74: 45772 3.74 - 4.32: 58549 4.32 - 4.90: 94778 Nonbonded interactions: 223447 Sorted by model distance: nonbonded pdb=" OD1 ASP F 533 " pdb="MG MG F 701 " model vdw 2.010 2.170 nonbonded pdb=" OD1 ASP B 533 " pdb="MG MG B 701 " model vdw 2.067 2.170 nonbonded pdb=" OD1 ASP D 533 " pdb="MG MG D 701 " model vdw 2.086 2.170 nonbonded pdb=" O PHE E 421 " pdb=" OG1 THR E 426 " model vdw 2.095 3.040 nonbonded pdb=" O GLN B 460 " pdb=" OG SER B 464 " model vdw 2.097 3.040 ... (remaining 223442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 502 or resid 515 through 701)) selection = (chain 'B' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 701)) selection = (chain 'C' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 502 or resid 515 through 701)) selection = (chain 'D' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 701)) selection = (chain 'E' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 502 or resid 515 through 701)) selection = (chain 'F' and (resid 3 through 190 or resid 200 through 701)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 26.900 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.003 0.175 27362 Z= 0.140 Angle : 0.771 15.354 37058 Z= 0.384 Chirality : 0.044 0.272 4123 Planarity : 0.005 0.148 4799 Dihedral : 18.212 88.460 10081 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.85 % Favored : 94.85 % Rotamer: Outliers : 0.48 % Allowed : 36.14 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: 0.02 (0.15), residues: 3362 helix: 0.95 (0.13), residues: 1557 sheet: -0.32 (0.28), residues: 367 loop : -0.89 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 283 TYR 0.031 0.002 TYR D 430 PHE 0.052 0.001 PHE F 208 TRP 0.046 0.002 TRP E 157 HIS 0.005 0.001 HIS D 396 Details of bonding type rmsd covalent geometry : bond 0.00323 (27362) covalent geometry : angle 0.77142 (37058) hydrogen bonds : bond 0.15802 ( 1177) hydrogen bonds : angle 6.17747 ( 3360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.9387 (t) cc_final: 0.9126 (m) REVERT: A 483 MET cc_start: 0.9404 (mmm) cc_final: 0.9125 (mmm) REVERT: B 137 MET cc_start: 0.9183 (ptp) cc_final: 0.8872 (mtt) REVERT: C 397 LEU cc_start: 0.9488 (mt) cc_final: 0.9128 (pp) REVERT: C 435 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7819 (t80) REVERT: C 483 MET cc_start: 0.8977 (mmm) cc_final: 0.8762 (mmm) REVERT: D 14 MET cc_start: 0.5831 (tpt) cc_final: 0.5372 (mmm) REVERT: D 339 TYR cc_start: 0.7729 (m-10) cc_final: 0.7485 (m-10) REVERT: D 570 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8543 (mm-30) REVERT: D 580 MET cc_start: 0.8561 (ttp) cc_final: 0.8340 (ttp) REVERT: E 14 MET cc_start: 0.7789 (ttt) cc_final: 0.7360 (ttt) REVERT: E 106 MET cc_start: 0.6802 (mpp) cc_final: 0.6283 (mpp) REVERT: E 483 MET cc_start: 0.9252 (mmm) cc_final: 0.8841 (mmm) outliers start: 14 outliers final: 5 residues processed: 247 average time/residue: 0.1615 time to fit residues: 66.9894 Evaluate side-chains 234 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain E residue 124 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 30.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 HIS A 204 ASN A 326 ASN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 GLN A 534 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 HIS E 70 ASN E 124 HIS F 92 ASN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN F 353 GLN F 406 GLN ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.062597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043241 restraints weight = 143865.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.044919 restraints weight = 92650.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.046045 restraints weight = 69142.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.046810 restraints weight = 56643.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.047352 restraints weight = 49425.963| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27362 Z= 0.142 Angle : 0.651 10.647 37058 Z= 0.323 Chirality : 0.044 0.242 4123 Planarity : 0.005 0.147 4799 Dihedral : 4.907 59.432 3636 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.03 % Favored : 94.77 % Rotamer: Outliers : 3.14 % Allowed : 31.19 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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 (0.15), residues: 3362 helix: 1.00 (0.13), residues: 1600 sheet: -0.25 (0.27), residues: 388 loop : -0.96 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 384 TYR 0.021 0.001 TYR A 463 PHE 0.028 0.001 PHE F 208 TRP 0.020 0.001 TRP E 157 HIS 0.009 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00323 (27362) covalent geometry : angle 0.65093 (37058) hydrogen bonds : bond 0.03964 ( 1177) hydrogen bonds : angle 5.07726 ( 3360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 243 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.9433 (t) cc_final: 0.9183 (m) REVERT: A 80 MET cc_start: 0.8796 (mmt) cc_final: 0.8400 (mmt) REVERT: A 89 MET cc_start: 0.8164 (pmm) cc_final: 0.7827 (pmm) REVERT: A 164 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7642 (ptpt) REVERT: A 498 TYR cc_start: 0.9520 (OUTLIER) cc_final: 0.8981 (t80) REVERT: B 80 MET cc_start: 0.8929 (mmt) cc_final: 0.8368 (mmt) REVERT: B 137 MET cc_start: 0.9231 (ptp) cc_final: 0.8922 (ptp) REVERT: B 151 MET cc_start: 0.7447 (mmt) cc_final: 0.7227 (mmt) REVERT: B 422 GLU cc_start: 0.5403 (OUTLIER) cc_final: 0.4142 (pt0) REVERT: B 496 CYS cc_start: 0.8636 (m) cc_final: 0.7825 (t) REVERT: C 365 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9034 (pp20) REVERT: C 404 MET cc_start: 0.8447 (tmm) cc_final: 0.7841 (tmm) REVERT: C 509 MET cc_start: 0.6992 (ppp) cc_final: 0.6690 (ppp) REVERT: C 580 MET cc_start: 0.9158 (mmm) cc_final: 0.8951 (mmm) REVERT: D 14 MET cc_start: 0.6699 (tpt) cc_final: 0.6024 (mmm) REVERT: D 80 MET cc_start: 0.8898 (mmt) cc_final: 0.8668 (mmt) REVERT: D 137 MET cc_start: 0.8697 (mmm) cc_final: 0.8295 (mmm) REVERT: D 208 PHE cc_start: 0.5362 (OUTLIER) cc_final: 0.4498 (m-80) REVERT: D 498 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: D 548 ILE cc_start: 0.9496 (mm) cc_final: 0.9169 (mm) REVERT: D 570 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8763 (mm-30) REVERT: D 580 MET cc_start: 0.8533 (ttp) cc_final: 0.8287 (ttp) REVERT: E 14 MET cc_start: 0.7372 (ttt) cc_final: 0.6781 (ttt) REVERT: E 80 MET cc_start: 0.8780 (mmm) cc_final: 0.8360 (mmp) REVERT: E 494 GLU cc_start: 0.7887 (pm20) cc_final: 0.7558 (pm20) REVERT: E 495 MET cc_start: 0.9163 (ptm) cc_final: 0.8718 (ptm) REVERT: E 498 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.9022 (t80) REVERT: E 509 MET cc_start: 0.7778 (mmt) cc_final: 0.7437 (mmt) REVERT: F 80 MET cc_start: 0.8916 (mmm) cc_final: 0.8512 (mmt) REVERT: F 89 MET cc_start: 0.8589 (mmm) cc_final: 0.8372 (mmm) REVERT: F 116 LEU cc_start: 0.9205 (tp) cc_final: 0.8989 (tp) REVERT: F 117 PHE cc_start: 0.8556 (m-80) cc_final: 0.8064 (m-80) REVERT: F 496 CYS cc_start: 0.8756 (m) cc_final: 0.8312 (t) outliers start: 92 outliers final: 37 residues processed: 314 average time/residue: 0.1458 time to fit residues: 77.7597 Evaluate side-chains 269 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 69 optimal weight: 0.0670 chunk 239 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.059467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.040493 restraints weight = 147793.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.042028 restraints weight = 95957.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.043061 restraints weight = 72291.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.043768 restraints weight = 59628.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.044261 restraints weight = 52289.815| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 27362 Z= 0.215 Angle : 0.662 13.496 37058 Z= 0.335 Chirality : 0.044 0.168 4123 Planarity : 0.005 0.150 4799 Dihedral : 4.659 41.000 3625 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.29 % Favored : 94.50 % Rotamer: Outliers : 4.88 % Allowed : 29.45 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: -0.10 (0.15), residues: 3362 helix: 0.90 (0.13), residues: 1618 sheet: -0.57 (0.26), residues: 403 loop : -1.04 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 384 TYR 0.028 0.002 TYR A 463 PHE 0.025 0.002 PHE F 208 TRP 0.016 0.002 TRP E 157 HIS 0.008 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00465 (27362) covalent geometry : angle 0.66181 (37058) hydrogen bonds : bond 0.03975 ( 1177) hydrogen bonds : angle 5.01282 ( 3360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 219 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.9453 (t) cc_final: 0.9205 (m) REVERT: A 58 SER cc_start: 0.5935 (OUTLIER) cc_final: 0.5650 (p) REVERT: A 80 MET cc_start: 0.8927 (mmt) cc_final: 0.8364 (mmt) REVERT: A 164 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8154 (ptmt) REVERT: A 483 MET cc_start: 0.9263 (mmm) cc_final: 0.9023 (mmm) REVERT: A 498 TYR cc_start: 0.9557 (OUTLIER) cc_final: 0.8885 (t80) REVERT: A 580 MET cc_start: 0.9180 (mmm) cc_final: 0.8945 (mmm) REVERT: B 80 MET cc_start: 0.8956 (mmt) cc_final: 0.8422 (mmt) REVERT: B 106 MET cc_start: 0.8580 (ptp) cc_final: 0.8356 (ptp) REVERT: B 151 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7648 (mmt) REVERT: B 196 MET cc_start: 0.8860 (tpp) cc_final: 0.8607 (tpp) REVERT: B 320 GLN cc_start: 0.9448 (OUTLIER) cc_final: 0.8650 (tp40) REVERT: B 422 GLU cc_start: 0.5633 (OUTLIER) cc_final: 0.4199 (pt0) REVERT: B 495 MET cc_start: 0.9192 (ptm) cc_final: 0.8823 (tmm) REVERT: C 221 TRP cc_start: 0.9491 (OUTLIER) cc_final: 0.9169 (t-100) REVERT: C 365 GLU cc_start: 0.9488 (OUTLIER) cc_final: 0.9116 (pp20) REVERT: C 368 GLN cc_start: 0.9615 (OUTLIER) cc_final: 0.9260 (mm-40) REVERT: C 404 MET cc_start: 0.8648 (tmm) cc_final: 0.8113 (tmm) REVERT: C 498 TYR cc_start: 0.9409 (OUTLIER) cc_final: 0.8926 (t80) REVERT: C 512 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8459 (m-10) REVERT: C 559 MET cc_start: 0.9416 (tpt) cc_final: 0.8889 (tpp) REVERT: C 580 MET cc_start: 0.9225 (mmm) cc_final: 0.8952 (mmm) REVERT: D 80 MET cc_start: 0.9053 (mmt) cc_final: 0.8713 (mmt) REVERT: D 106 MET cc_start: 0.8419 (ptp) cc_final: 0.8210 (ptp) REVERT: D 137 MET cc_start: 0.8858 (mmm) cc_final: 0.8635 (mmm) REVERT: D 208 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.4727 (m-80) REVERT: D 430 TYR cc_start: 0.8548 (t80) cc_final: 0.8098 (t80) REVERT: D 433 HIS cc_start: 0.8358 (p-80) cc_final: 0.8101 (t70) REVERT: D 460 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.9086 (pt0) REVERT: D 498 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: D 570 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8733 (mm-30) REVERT: D 580 MET cc_start: 0.8505 (ttp) cc_final: 0.8250 (ttp) REVERT: E 25 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9158 (tm-30) REVERT: E 80 MET cc_start: 0.9045 (mmm) cc_final: 0.8614 (mmp) REVERT: E 106 MET cc_start: 0.7515 (mpp) cc_final: 0.7098 (mpp) REVERT: E 135 GLU cc_start: 0.9511 (tp30) cc_final: 0.8951 (tm-30) REVERT: E 483 MET cc_start: 0.9301 (mmm) cc_final: 0.8977 (mmm) REVERT: E 495 MET cc_start: 0.9133 (ptm) cc_final: 0.8618 (ptm) REVERT: E 509 MET cc_start: 0.7866 (mmt) cc_final: 0.7629 (tpt) REVERT: E 522 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9193 (mm) REVERT: E 559 MET cc_start: 0.9249 (tpp) cc_final: 0.8975 (tpp) REVERT: E 580 MET cc_start: 0.9228 (mmm) cc_final: 0.9013 (mmm) REVERT: F 6 LEU cc_start: 0.9197 (mt) cc_final: 0.8907 (mt) REVERT: F 80 MET cc_start: 0.9120 (mmm) cc_final: 0.8622 (mmt) REVERT: F 116 LEU cc_start: 0.9274 (tp) cc_final: 0.9041 (tt) REVERT: F 117 PHE cc_start: 0.8685 (m-80) cc_final: 0.8077 (m-80) REVERT: F 196 MET cc_start: 0.8973 (tpp) cc_final: 0.8623 (tpp) REVERT: F 496 CYS cc_start: 0.8788 (m) cc_final: 0.7906 (t) outliers start: 143 outliers final: 73 residues processed: 337 average time/residue: 0.1343 time to fit residues: 76.8566 Evaluate side-chains 293 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 204 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain E residue 587 ASP Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 326 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 209 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN A 204 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN C 124 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** D 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.060912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.041779 restraints weight = 144355.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.043421 restraints weight = 91885.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.044535 restraints weight = 68216.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.045302 restraints weight = 55736.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.045840 restraints weight = 48523.596| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27362 Z= 0.122 Angle : 0.621 12.244 37058 Z= 0.304 Chirality : 0.043 0.189 4123 Planarity : 0.005 0.148 4799 Dihedral : 4.548 40.000 3625 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.76 % Favored : 95.00 % Rotamer: Outliers : 3.65 % Allowed : 30.75 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: 0.16 (0.15), residues: 3362 helix: 1.15 (0.13), residues: 1605 sheet: -0.51 (0.26), residues: 395 loop : -0.91 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 588 TYR 0.023 0.001 TYR A 463 PHE 0.031 0.001 PHE F 208 TRP 0.014 0.001 TRP E 157 HIS 0.006 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00283 (27362) covalent geometry : angle 0.62102 (37058) hydrogen bonds : bond 0.03425 ( 1177) hydrogen bonds : angle 4.69434 ( 3360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 240 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.9458 (t) cc_final: 0.9205 (m) REVERT: A 58 SER cc_start: 0.6110 (OUTLIER) cc_final: 0.5851 (p) REVERT: A 80 MET cc_start: 0.8939 (mmt) cc_final: 0.8381 (mmt) REVERT: A 164 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8024 (ptmt) REVERT: A 483 MET cc_start: 0.9244 (mmm) cc_final: 0.8966 (mmm) REVERT: A 498 TYR cc_start: 0.9505 (OUTLIER) cc_final: 0.8280 (t80) REVERT: A 522 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9062 (mm) REVERT: A 559 MET cc_start: 0.9224 (tpt) cc_final: 0.8927 (tpp) REVERT: A 580 MET cc_start: 0.9186 (mmm) cc_final: 0.8893 (mmm) REVERT: B 1 MET cc_start: 0.7056 (tmm) cc_final: 0.6655 (tmm) REVERT: B 80 MET cc_start: 0.8945 (mmt) cc_final: 0.8378 (mmt) REVERT: B 161 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8783 (ptp90) REVERT: B 196 MET cc_start: 0.8886 (tpp) cc_final: 0.8537 (tpp) REVERT: B 339 TYR cc_start: 0.7720 (m-10) cc_final: 0.7485 (m-10) REVERT: B 422 GLU cc_start: 0.5254 (OUTLIER) cc_final: 0.3902 (pt0) REVERT: B 431 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: C 135 GLU cc_start: 0.9437 (mp0) cc_final: 0.9051 (pm20) REVERT: C 365 GLU cc_start: 0.9470 (OUTLIER) cc_final: 0.9043 (pp20) REVERT: C 404 MET cc_start: 0.8496 (tmm) cc_final: 0.7945 (tmm) REVERT: C 405 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: C 435 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7795 (t80) REVERT: C 498 TYR cc_start: 0.9387 (OUTLIER) cc_final: 0.8873 (t80) REVERT: C 512 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: C 559 MET cc_start: 0.9412 (tpt) cc_final: 0.8953 (tpp) REVERT: C 580 MET cc_start: 0.9236 (mmm) cc_final: 0.8913 (mmm) REVERT: D 80 MET cc_start: 0.9036 (mmt) cc_final: 0.8640 (mmt) REVERT: D 137 MET cc_start: 0.8740 (mmm) cc_final: 0.8432 (mmm) REVERT: D 208 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.4605 (m-80) REVERT: D 339 TYR cc_start: 0.7871 (m-80) cc_final: 0.7613 (m-80) REVERT: D 384 ARG cc_start: 0.4613 (mtm110) cc_final: 0.4402 (mtm110) REVERT: D 430 TYR cc_start: 0.8545 (t80) cc_final: 0.8060 (t80) REVERT: D 433 HIS cc_start: 0.8293 (p-80) cc_final: 0.8056 (t70) REVERT: D 498 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: D 570 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8632 (mm-30) REVERT: E 80 MET cc_start: 0.9063 (mmm) cc_final: 0.8633 (mmp) REVERT: E 89 MET cc_start: 0.8263 (tpp) cc_final: 0.8038 (tpp) REVERT: E 106 MET cc_start: 0.7526 (mpp) cc_final: 0.7240 (mpp) REVERT: E 135 GLU cc_start: 0.9448 (tp30) cc_final: 0.9237 (tp30) REVERT: E 463 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8357 (t80) REVERT: E 483 MET cc_start: 0.9219 (mmm) cc_final: 0.8879 (mmm) REVERT: E 498 TYR cc_start: 0.9367 (OUTLIER) cc_final: 0.8977 (t80) REVERT: E 580 MET cc_start: 0.9124 (mmm) cc_final: 0.8895 (mmm) REVERT: F 6 LEU cc_start: 0.9144 (mt) cc_final: 0.8817 (mt) REVERT: F 80 MET cc_start: 0.9150 (mmm) cc_final: 0.8700 (mmm) REVERT: F 99 LEU cc_start: 0.8434 (pt) cc_final: 0.7773 (mp) REVERT: F 116 LEU cc_start: 0.9322 (tp) cc_final: 0.9086 (tt) REVERT: F 117 PHE cc_start: 0.8771 (m-80) cc_final: 0.8039 (m-80) REVERT: F 196 MET cc_start: 0.8985 (tpp) cc_final: 0.8574 (tpp) REVERT: F 496 CYS cc_start: 0.8336 (m) cc_final: 0.8102 (t) REVERT: F 580 MET cc_start: 0.9341 (mmp) cc_final: 0.9130 (mmp) outliers start: 107 outliers final: 51 residues processed: 324 average time/residue: 0.1357 time to fit residues: 74.5198 Evaluate side-chains 282 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 215 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 310 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 281 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.060642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.041433 restraints weight = 145831.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.043064 restraints weight = 92991.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.044172 restraints weight = 69218.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.044947 restraints weight = 56663.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045476 restraints weight = 49356.768| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27362 Z= 0.131 Angle : 0.630 13.568 37058 Z= 0.309 Chirality : 0.043 0.211 4123 Planarity : 0.005 0.149 4799 Dihedral : 4.494 39.892 3625 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.00 % Favored : 94.82 % Rotamer: Outliers : 3.99 % Allowed : 30.41 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: 0.17 (0.15), residues: 3362 helix: 1.16 (0.13), residues: 1600 sheet: -0.55 (0.26), residues: 397 loop : -0.89 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 384 TYR 0.025 0.001 TYR A 498 PHE 0.029 0.001 PHE F 208 TRP 0.020 0.001 TRP E 157 HIS 0.004 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00300 (27362) covalent geometry : angle 0.62989 (37058) hydrogen bonds : bond 0.03396 ( 1177) hydrogen bonds : angle 4.67462 ( 3360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 222 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.9485 (t) cc_final: 0.9247 (m) REVERT: A 58 SER cc_start: 0.6404 (OUTLIER) cc_final: 0.6156 (p) REVERT: A 80 MET cc_start: 0.8978 (mmt) cc_final: 0.8396 (mmt) REVERT: A 164 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7911 (ptmt) REVERT: A 470 LEU cc_start: 0.9601 (mp) cc_final: 0.9384 (mp) REVERT: A 483 MET cc_start: 0.9214 (mmm) cc_final: 0.8916 (mmm) REVERT: A 494 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: A 498 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8059 (t80) REVERT: A 522 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9032 (mm) REVERT: A 559 MET cc_start: 0.9285 (tpt) cc_final: 0.8995 (tpp) REVERT: A 580 MET cc_start: 0.9222 (mmm) cc_final: 0.8913 (mmm) REVERT: B 1 MET cc_start: 0.7148 (tmm) cc_final: 0.6829 (tmm) REVERT: B 80 MET cc_start: 0.8961 (mmt) cc_final: 0.8351 (mmt) REVERT: B 161 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8779 (ptp90) REVERT: B 165 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9138 (mmtm) REVERT: B 196 MET cc_start: 0.8906 (tpp) cc_final: 0.8537 (tpp) REVERT: B 339 TYR cc_start: 0.7770 (m-10) cc_final: 0.7455 (m-10) REVERT: B 422 GLU cc_start: 0.5306 (OUTLIER) cc_final: 0.3963 (pt0) REVERT: B 431 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: B 495 MET cc_start: 0.9294 (ptm) cc_final: 0.8817 (tmm) REVERT: C 25 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.9035 (tm-30) REVERT: C 89 MET cc_start: 0.7614 (ptp) cc_final: 0.7335 (ptp) REVERT: C 135 GLU cc_start: 0.9432 (mp0) cc_final: 0.9073 (pm20) REVERT: C 365 GLU cc_start: 0.9473 (OUTLIER) cc_final: 0.9052 (pp20) REVERT: C 404 MET cc_start: 0.8550 (tmm) cc_final: 0.7900 (tmm) REVERT: C 405 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: C 435 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7941 (t80) REVERT: C 498 TYR cc_start: 0.9405 (OUTLIER) cc_final: 0.9015 (t80) REVERT: C 512 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8449 (m-80) REVERT: C 559 MET cc_start: 0.9412 (tpt) cc_final: 0.8991 (tpp) REVERT: C 580 MET cc_start: 0.9298 (mmm) cc_final: 0.8992 (mmm) REVERT: D 80 MET cc_start: 0.9046 (mmt) cc_final: 0.8637 (mmt) REVERT: D 137 MET cc_start: 0.8802 (mmm) cc_final: 0.8458 (mmm) REVERT: D 196 MET cc_start: 0.9145 (mmp) cc_final: 0.8737 (mmp) REVERT: D 208 PHE cc_start: 0.5324 (OUTLIER) cc_final: 0.4469 (m-80) REVERT: D 339 TYR cc_start: 0.8050 (m-80) cc_final: 0.7738 (m-10) REVERT: D 384 ARG cc_start: 0.4463 (mtm110) cc_final: 0.4224 (mtm110) REVERT: D 430 TYR cc_start: 0.8607 (t80) cc_final: 0.8153 (t80) REVERT: D 433 HIS cc_start: 0.8325 (p-80) cc_final: 0.8095 (t70) REVERT: D 498 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: D 570 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8600 (mm-30) REVERT: D 580 MET cc_start: 0.8705 (ttp) cc_final: 0.8132 (ttp) REVERT: D 584 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9252 (ttmm) REVERT: E 80 MET cc_start: 0.9052 (mmm) cc_final: 0.8621 (mmp) REVERT: E 106 MET cc_start: 0.7591 (mpp) cc_final: 0.7189 (mpp) REVERT: E 135 GLU cc_start: 0.9461 (tp30) cc_final: 0.9222 (tp30) REVERT: E 178 PHE cc_start: 0.8233 (p90) cc_final: 0.7801 (p90) REVERT: E 463 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8280 (t80) REVERT: E 483 MET cc_start: 0.9190 (mmm) cc_final: 0.8942 (mmm) REVERT: E 498 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.9033 (t80) REVERT: E 580 MET cc_start: 0.9155 (mmm) cc_final: 0.8927 (mmm) REVERT: F 6 LEU cc_start: 0.9167 (mt) cc_final: 0.8855 (mt) REVERT: F 80 MET cc_start: 0.9207 (mmm) cc_final: 0.8759 (mmm) REVERT: F 87 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9083 (p) REVERT: F 117 PHE cc_start: 0.8829 (m-80) cc_final: 0.8271 (m-80) REVERT: F 196 MET cc_start: 0.8959 (tpp) cc_final: 0.8524 (tpp) REVERT: F 496 CYS cc_start: 0.8425 (m) cc_final: 0.8161 (t) REVERT: F 580 MET cc_start: 0.9375 (mmp) cc_final: 0.9150 (mmp) outliers start: 117 outliers final: 58 residues processed: 319 average time/residue: 0.1402 time to fit residues: 75.4553 Evaluate side-chains 286 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 207 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 58 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 321 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 ASN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.059415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040426 restraints weight = 147696.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.042008 restraints weight = 94790.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.043076 restraints weight = 70776.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.043813 restraints weight = 58107.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.044328 restraints weight = 50745.985| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27362 Z= 0.166 Angle : 0.650 13.252 37058 Z= 0.321 Chirality : 0.043 0.222 4123 Planarity : 0.005 0.150 4799 Dihedral : 4.466 39.933 3623 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.65 % Rotamer: Outliers : 4.23 % Allowed : 30.51 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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 (0.15), residues: 3362 helix: 1.09 (0.13), residues: 1618 sheet: -0.65 (0.26), residues: 397 loop : -0.98 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 558 TYR 0.024 0.001 TYR A 463 PHE 0.027 0.001 PHE F 208 TRP 0.018 0.001 TRP E 157 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00370 (27362) covalent geometry : angle 0.64972 (37058) hydrogen bonds : bond 0.03463 ( 1177) hydrogen bonds : angle 4.70217 ( 3360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 218 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7548 (ttt) cc_final: 0.7208 (ttt) REVERT: A 30 VAL cc_start: 0.9477 (t) cc_final: 0.9226 (m) REVERT: A 58 SER cc_start: 0.6543 (OUTLIER) cc_final: 0.6287 (p) REVERT: A 80 MET cc_start: 0.9051 (mmt) cc_final: 0.8427 (mmt) REVERT: A 106 MET cc_start: 0.7392 (mpp) cc_final: 0.6875 (mpp) REVERT: A 164 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8019 (ptmt) REVERT: A 470 LEU cc_start: 0.9620 (mp) cc_final: 0.9410 (mp) REVERT: A 494 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: A 498 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 522 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9027 (mm) REVERT: A 559 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9037 (tpp) REVERT: A 580 MET cc_start: 0.9229 (mmm) cc_final: 0.8851 (mmm) REVERT: A 586 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: B 1 MET cc_start: 0.7171 (tmm) cc_final: 0.6842 (tmm) REVERT: B 80 MET cc_start: 0.8979 (mmt) cc_final: 0.8358 (mmt) REVERT: B 104 LYS cc_start: 0.9665 (OUTLIER) cc_final: 0.9387 (mmtm) REVERT: B 151 MET cc_start: 0.8329 (mmt) cc_final: 0.8120 (mmm) REVERT: B 165 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9164 (mmtm) REVERT: B 196 MET cc_start: 0.8837 (tpp) cc_final: 0.8501 (tpp) REVERT: B 320 GLN cc_start: 0.9452 (OUTLIER) cc_final: 0.8644 (tp-100) REVERT: B 339 TYR cc_start: 0.7780 (m-10) cc_final: 0.7409 (m-80) REVERT: B 422 GLU cc_start: 0.5420 (OUTLIER) cc_final: 0.4083 (pt0) REVERT: B 431 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: C 25 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.9045 (tm-30) REVERT: C 30 VAL cc_start: 0.9016 (t) cc_final: 0.8750 (m) REVERT: C 135 GLU cc_start: 0.9409 (mp0) cc_final: 0.9197 (pm20) REVERT: C 365 GLU cc_start: 0.9486 (OUTLIER) cc_final: 0.9132 (pp20) REVERT: C 368 GLN cc_start: 0.9652 (OUTLIER) cc_final: 0.9276 (mm-40) REVERT: C 404 MET cc_start: 0.8607 (tmm) cc_final: 0.7930 (tmm) REVERT: C 405 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: C 435 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7935 (t80) REVERT: C 498 TYR cc_start: 0.9500 (OUTLIER) cc_final: 0.8971 (t80) REVERT: C 512 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8508 (m-10) REVERT: C 559 MET cc_start: 0.9426 (tpt) cc_final: 0.9017 (tpp) REVERT: C 580 MET cc_start: 0.9326 (mmm) cc_final: 0.8994 (mmm) REVERT: D 80 MET cc_start: 0.9040 (mmt) cc_final: 0.8566 (mmt) REVERT: D 137 MET cc_start: 0.8898 (mmm) cc_final: 0.8564 (mmm) REVERT: D 208 PHE cc_start: 0.5429 (OUTLIER) cc_final: 0.4585 (m-80) REVERT: D 384 ARG cc_start: 0.4587 (mtm110) cc_final: 0.4290 (mtm110) REVERT: D 430 TYR cc_start: 0.8645 (t80) cc_final: 0.8202 (t80) REVERT: D 433 HIS cc_start: 0.8283 (p-80) cc_final: 0.7999 (t70) REVERT: D 498 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: D 580 MET cc_start: 0.8748 (ttp) cc_final: 0.8265 (ttp) REVERT: D 584 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9214 (ttmm) REVERT: E 14 MET cc_start: 0.7518 (ttt) cc_final: 0.7137 (ttt) REVERT: E 25 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9144 (tm-30) REVERT: E 80 MET cc_start: 0.9110 (mmm) cc_final: 0.8707 (mmp) REVERT: E 89 MET cc_start: 0.8309 (tpp) cc_final: 0.8072 (tpp) REVERT: E 106 MET cc_start: 0.7778 (mpp) cc_final: 0.7326 (mpp) REVERT: E 135 GLU cc_start: 0.9520 (tp30) cc_final: 0.9291 (tp30) REVERT: E 463 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8265 (t80) REVERT: E 483 MET cc_start: 0.9192 (mmm) cc_final: 0.8939 (mmm) REVERT: E 498 TYR cc_start: 0.9384 (OUTLIER) cc_final: 0.9086 (t80) REVERT: E 573 PHE cc_start: 0.9482 (OUTLIER) cc_final: 0.9180 (m-80) REVERT: E 580 MET cc_start: 0.9175 (mmm) cc_final: 0.8937 (mmm) REVERT: F 6 LEU cc_start: 0.9172 (mt) cc_final: 0.8878 (mt) REVERT: F 80 MET cc_start: 0.9239 (mmm) cc_final: 0.8635 (mmt) REVERT: F 87 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9153 (p) REVERT: F 89 MET cc_start: 0.8638 (mmm) cc_final: 0.8041 (mmm) REVERT: F 117 PHE cc_start: 0.8912 (m-80) cc_final: 0.8438 (m-80) REVERT: F 164 LYS cc_start: 0.9631 (mtmt) cc_final: 0.9271 (mptt) REVERT: F 196 MET cc_start: 0.8972 (tpp) cc_final: 0.8520 (tpp) REVERT: F 496 CYS cc_start: 0.8467 (m) cc_final: 0.8190 (t) REVERT: F 580 MET cc_start: 0.9407 (mmp) cc_final: 0.9193 (mmp) outliers start: 124 outliers final: 70 residues processed: 320 average time/residue: 0.1465 time to fit residues: 78.0142 Evaluate side-chains 306 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 209 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 310 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 331 optimal weight: 0.0770 chunk 235 optimal weight: 6.9990 chunk 296 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.060402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.041271 restraints weight = 144892.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042892 restraints weight = 92702.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.043992 restraints weight = 69093.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.044751 restraints weight = 56617.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.045275 restraints weight = 49374.650| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27362 Z= 0.117 Angle : 0.648 12.918 37058 Z= 0.313 Chirality : 0.043 0.255 4123 Planarity : 0.005 0.147 4799 Dihedral : 4.434 38.174 3623 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.88 % Favored : 94.94 % Rotamer: Outliers : 3.96 % Allowed : 31.16 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: 0.17 (0.15), residues: 3362 helix: 1.16 (0.13), residues: 1608 sheet: -0.53 (0.26), residues: 395 loop : -0.91 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 468 TYR 0.021 0.001 TYR A 463 PHE 0.033 0.001 PHE F 359 TRP 0.018 0.001 TRP E 157 HIS 0.004 0.001 HIS E 466 Details of bonding type rmsd covalent geometry : bond 0.00272 (27362) covalent geometry : angle 0.64826 (37058) hydrogen bonds : bond 0.03305 ( 1177) hydrogen bonds : angle 4.56636 ( 3360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 233 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7511 (ttt) cc_final: 0.7138 (ttt) REVERT: A 30 VAL cc_start: 0.9479 (t) cc_final: 0.9227 (m) REVERT: A 58 SER cc_start: 0.6433 (OUTLIER) cc_final: 0.6178 (p) REVERT: A 80 MET cc_start: 0.9059 (mmt) cc_final: 0.8418 (mmt) REVERT: A 106 MET cc_start: 0.7372 (mpp) cc_final: 0.6871 (mpp) REVERT: A 164 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8049 (ptmt) REVERT: A 494 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: A 498 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8048 (t80) REVERT: A 522 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8986 (mm) REVERT: A 559 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.9024 (tpp) REVERT: A 580 MET cc_start: 0.9231 (mmm) cc_final: 0.8859 (mmm) REVERT: A 586 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: B 1 MET cc_start: 0.7254 (tmm) cc_final: 0.6936 (tmm) REVERT: B 80 MET cc_start: 0.8970 (mmt) cc_final: 0.8332 (mmt) REVERT: B 104 LYS cc_start: 0.9646 (OUTLIER) cc_final: 0.9359 (mmtm) REVERT: B 132 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8276 (tpm170) REVERT: B 151 MET cc_start: 0.8299 (mmt) cc_final: 0.7940 (mmm) REVERT: B 196 MET cc_start: 0.8843 (tpp) cc_final: 0.8470 (tpp) REVERT: B 305 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.4486 (mm) REVERT: B 339 TYR cc_start: 0.7701 (m-10) cc_final: 0.7373 (m-10) REVERT: B 422 GLU cc_start: 0.5299 (OUTLIER) cc_final: 0.3942 (pt0) REVERT: B 431 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6478 (m-80) REVERT: C 25 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8980 (tm-30) REVERT: C 30 VAL cc_start: 0.8982 (t) cc_final: 0.8684 (m) REVERT: C 135 GLU cc_start: 0.9426 (mp0) cc_final: 0.9181 (pm20) REVERT: C 165 LYS cc_start: 0.9659 (mtmm) cc_final: 0.9444 (ptpp) REVERT: C 365 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9051 (pp20) REVERT: C 404 MET cc_start: 0.8514 (tmm) cc_final: 0.7873 (tmm) REVERT: C 405 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: C 435 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7930 (t80) REVERT: C 512 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8461 (m-10) REVERT: C 559 MET cc_start: 0.9391 (tpt) cc_final: 0.9012 (tpp) REVERT: C 580 MET cc_start: 0.9310 (mmm) cc_final: 0.9050 (mmm) REVERT: D 80 MET cc_start: 0.9051 (mmt) cc_final: 0.8576 (mmt) REVERT: D 93 GLU cc_start: 0.8778 (pm20) cc_final: 0.8433 (pm20) REVERT: D 106 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8310 (ptp) REVERT: D 137 MET cc_start: 0.8893 (mmm) cc_final: 0.8562 (mmm) REVERT: D 208 PHE cc_start: 0.5035 (OUTLIER) cc_final: 0.4241 (m-80) REVERT: D 339 TYR cc_start: 0.8025 (m-80) cc_final: 0.7644 (m-10) REVERT: D 384 ARG cc_start: 0.4649 (mtm110) cc_final: 0.4331 (mtm110) REVERT: D 430 TYR cc_start: 0.8609 (t80) cc_final: 0.8180 (t80) REVERT: D 433 HIS cc_start: 0.8227 (p-80) cc_final: 0.7950 (t70) REVERT: D 580 MET cc_start: 0.8766 (ttp) cc_final: 0.8374 (ttp) REVERT: D 584 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9223 (ttmm) REVERT: E 6 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8400 (mt) REVERT: E 80 MET cc_start: 0.9080 (mmm) cc_final: 0.8658 (mmp) REVERT: E 89 MET cc_start: 0.8373 (tpp) cc_final: 0.8102 (tpp) REVERT: E 106 MET cc_start: 0.7793 (mpp) cc_final: 0.7440 (mpp) REVERT: E 135 GLU cc_start: 0.9505 (tp30) cc_final: 0.9284 (tp30) REVERT: E 294 MET cc_start: 0.9787 (mmm) cc_final: 0.9581 (mmm) REVERT: E 397 LEU cc_start: 0.9610 (mt) cc_final: 0.9094 (pp) REVERT: E 463 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8108 (t80) REVERT: E 483 MET cc_start: 0.9163 (mmm) cc_final: 0.8906 (mmm) REVERT: E 573 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9219 (m-80) REVERT: E 580 MET cc_start: 0.9151 (mmm) cc_final: 0.8915 (mmm) REVERT: F 14 MET cc_start: 0.9189 (mmm) cc_final: 0.8803 (mmp) REVERT: F 80 MET cc_start: 0.9231 (mmm) cc_final: 0.8597 (mmt) REVERT: F 87 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9143 (p) REVERT: F 89 MET cc_start: 0.8697 (mmm) cc_final: 0.8179 (mmm) REVERT: F 106 MET cc_start: 0.8115 (ptp) cc_final: 0.7829 (ptp) REVERT: F 117 PHE cc_start: 0.8952 (m-80) cc_final: 0.8384 (m-80) REVERT: F 196 MET cc_start: 0.8966 (tpp) cc_final: 0.8519 (tpp) REVERT: F 496 CYS cc_start: 0.8528 (m) cc_final: 0.8196 (t) REVERT: F 580 MET cc_start: 0.9374 (mmp) cc_final: 0.9167 (mmp) outliers start: 116 outliers final: 65 residues processed: 325 average time/residue: 0.1661 time to fit residues: 88.7198 Evaluate side-chains 307 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 218 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 498 TYR Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 304 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 229 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 336 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 12 optimal weight: 0.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.060404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.041384 restraints weight = 145165.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043012 restraints weight = 92170.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.044114 restraints weight = 68474.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.044879 restraints weight = 55997.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.045382 restraints weight = 48725.123| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 27362 Z= 0.118 Angle : 0.659 13.057 37058 Z= 0.317 Chirality : 0.043 0.305 4123 Planarity : 0.004 0.147 4799 Dihedral : 4.389 36.180 3623 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.82 % Favored : 95.03 % Rotamer: Outliers : 3.72 % Allowed : 31.60 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: 0.19 (0.15), residues: 3362 helix: 1.15 (0.13), residues: 1609 sheet: -0.44 (0.26), residues: 397 loop : -0.89 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 468 TYR 0.019 0.001 TYR A 463 PHE 0.029 0.001 PHE F 208 TRP 0.016 0.001 TRP E 157 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00275 (27362) covalent geometry : angle 0.65920 (37058) hydrogen bonds : bond 0.03257 ( 1177) hydrogen bonds : angle 4.55184 ( 3360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 230 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.9492 (t) cc_final: 0.9246 (m) REVERT: A 58 SER cc_start: 0.6428 (OUTLIER) cc_final: 0.6177 (p) REVERT: A 106 MET cc_start: 0.7277 (mpp) cc_final: 0.6597 (mpp) REVERT: A 164 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8106 (ptmt) REVERT: A 498 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8037 (t80) REVERT: A 522 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8963 (mm) REVERT: A 559 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.9061 (tpp) REVERT: A 580 MET cc_start: 0.9266 (mmm) cc_final: 0.8886 (mmm) REVERT: A 586 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: B 1 MET cc_start: 0.7406 (tmm) cc_final: 0.7106 (tmm) REVERT: B 80 MET cc_start: 0.8971 (mmt) cc_final: 0.8335 (mmt) REVERT: B 104 LYS cc_start: 0.9637 (OUTLIER) cc_final: 0.9350 (mmtm) REVERT: B 151 MET cc_start: 0.8396 (mmt) cc_final: 0.7932 (mmm) REVERT: B 196 MET cc_start: 0.8882 (tpp) cc_final: 0.8546 (tpp) REVERT: B 305 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.4557 (mm) REVERT: B 320 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.8637 (tp-100) REVERT: B 339 TYR cc_start: 0.7788 (m-10) cc_final: 0.7509 (m-10) REVERT: B 422 GLU cc_start: 0.5299 (OUTLIER) cc_final: 0.3948 (pt0) REVERT: B 431 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: C 25 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.9009 (tm-30) REVERT: C 30 VAL cc_start: 0.8961 (t) cc_final: 0.8657 (m) REVERT: C 135 GLU cc_start: 0.9425 (mp0) cc_final: 0.9185 (pm20) REVERT: C 165 LYS cc_start: 0.9662 (mtmm) cc_final: 0.9104 (ptpp) REVERT: C 365 GLU cc_start: 0.9466 (OUTLIER) cc_final: 0.9041 (pp20) REVERT: C 404 MET cc_start: 0.8467 (tmm) cc_final: 0.7834 (tmm) REVERT: C 405 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: C 435 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7920 (t80) REVERT: C 483 MET cc_start: 0.9082 (mmm) cc_final: 0.8817 (mmm) REVERT: C 512 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8520 (m-10) REVERT: C 559 MET cc_start: 0.9384 (tpt) cc_final: 0.9025 (tpp) REVERT: C 580 MET cc_start: 0.9325 (mmm) cc_final: 0.8952 (mmm) REVERT: D 80 MET cc_start: 0.9111 (mmt) cc_final: 0.8381 (mmt) REVERT: D 93 GLU cc_start: 0.8779 (pm20) cc_final: 0.8468 (pm20) REVERT: D 137 MET cc_start: 0.8905 (mmm) cc_final: 0.8582 (mmm) REVERT: D 208 PHE cc_start: 0.4945 (OUTLIER) cc_final: 0.4161 (m-80) REVERT: D 339 TYR cc_start: 0.8046 (m-80) cc_final: 0.7637 (m-10) REVERT: D 384 ARG cc_start: 0.4650 (mtm110) cc_final: 0.3638 (mtm-85) REVERT: D 430 TYR cc_start: 0.8624 (t80) cc_final: 0.8169 (t80) REVERT: D 433 HIS cc_start: 0.8220 (p-80) cc_final: 0.7907 (t-90) REVERT: D 580 MET cc_start: 0.8794 (ttp) cc_final: 0.8391 (ttp) REVERT: D 584 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9226 (ttmm) REVERT: E 6 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8424 (mt) REVERT: E 80 MET cc_start: 0.9052 (mmm) cc_final: 0.8626 (mmp) REVERT: E 89 MET cc_start: 0.8442 (tpp) cc_final: 0.8191 (tpp) REVERT: E 106 MET cc_start: 0.7737 (mpp) cc_final: 0.7410 (mpp) REVERT: E 135 GLU cc_start: 0.9504 (tp30) cc_final: 0.9277 (tp30) REVERT: E 463 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8079 (t80) REVERT: E 483 MET cc_start: 0.9147 (mmm) cc_final: 0.8891 (mmm) REVERT: E 559 MET cc_start: 0.9090 (tpt) cc_final: 0.8843 (tpp) REVERT: E 580 MET cc_start: 0.9166 (mmm) cc_final: 0.8938 (mmm) REVERT: F 6 LEU cc_start: 0.9138 (mt) cc_final: 0.8857 (mp) REVERT: F 80 MET cc_start: 0.9227 (mmm) cc_final: 0.8565 (mmt) REVERT: F 87 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.9087 (p) REVERT: F 117 PHE cc_start: 0.8958 (m-80) cc_final: 0.8381 (m-80) REVERT: F 196 MET cc_start: 0.8997 (tpp) cc_final: 0.8559 (tpp) REVERT: F 496 CYS cc_start: 0.8548 (m) cc_final: 0.8142 (t) REVERT: F 580 MET cc_start: 0.9382 (mmp) cc_final: 0.9172 (mmp) outliers start: 109 outliers final: 68 residues processed: 316 average time/residue: 0.1445 time to fit residues: 77.1637 Evaluate side-chains 308 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 219 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 498 TYR Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 196 optimal weight: 9.9990 chunk 305 optimal weight: 0.4980 chunk 319 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 321 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.060167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041117 restraints weight = 145985.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.042722 restraints weight = 93255.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043830 restraints weight = 69537.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044589 restraints weight = 56875.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045120 restraints weight = 49534.282| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 27362 Z= 0.127 Angle : 0.685 13.680 37058 Z= 0.330 Chirality : 0.043 0.296 4123 Planarity : 0.004 0.148 4799 Dihedral : 4.406 37.976 3623 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.94 % Favored : 94.91 % Rotamer: Outliers : 3.41 % Allowed : 31.91 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: 0.16 (0.15), residues: 3362 helix: 1.15 (0.13), residues: 1603 sheet: -0.50 (0.26), residues: 397 loop : -0.90 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 468 TYR 0.019 0.001 TYR A 463 PHE 0.028 0.001 PHE F 208 TRP 0.015 0.001 TRP E 157 HIS 0.003 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00295 (27362) covalent geometry : angle 0.68504 (37058) hydrogen bonds : bond 0.03277 ( 1177) hydrogen bonds : angle 4.58715 ( 3360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 221 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.9475 (t) cc_final: 0.9209 (m) REVERT: A 58 SER cc_start: 0.6473 (OUTLIER) cc_final: 0.6218 (p) REVERT: A 106 MET cc_start: 0.7281 (mpp) cc_final: 0.6577 (mpp) REVERT: A 164 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8003 (ptpt) REVERT: A 483 MET cc_start: 0.9209 (mmm) cc_final: 0.8906 (mmm) REVERT: A 498 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8107 (t80) REVERT: A 522 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 559 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.9064 (tpp) REVERT: A 580 MET cc_start: 0.9242 (mmm) cc_final: 0.8977 (mmm) REVERT: A 586 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: B 1 MET cc_start: 0.7445 (tmm) cc_final: 0.7147 (tmm) REVERT: B 80 MET cc_start: 0.8965 (mmt) cc_final: 0.8318 (mmt) REVERT: B 104 LYS cc_start: 0.9633 (OUTLIER) cc_final: 0.9352 (mmtm) REVERT: B 137 MET cc_start: 0.9190 (ptp) cc_final: 0.8932 (mtt) REVERT: B 151 MET cc_start: 0.8531 (mmt) cc_final: 0.8102 (mmm) REVERT: B 196 MET cc_start: 0.8912 (tpp) cc_final: 0.8590 (tpp) REVERT: B 305 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.4586 (mm) REVERT: B 320 GLN cc_start: 0.9424 (OUTLIER) cc_final: 0.8633 (tp-100) REVERT: B 339 TYR cc_start: 0.7783 (m-10) cc_final: 0.7501 (m-10) REVERT: B 422 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.4098 (pt0) REVERT: B 431 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: C 25 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8984 (tm-30) REVERT: C 135 GLU cc_start: 0.9433 (mp0) cc_final: 0.9186 (pm20) REVERT: C 221 TRP cc_start: 0.9404 (OUTLIER) cc_final: 0.9133 (t-100) REVERT: C 365 GLU cc_start: 0.9464 (OUTLIER) cc_final: 0.9043 (pp20) REVERT: C 389 ASP cc_start: 0.7745 (t0) cc_final: 0.7269 (t0) REVERT: C 404 MET cc_start: 0.8492 (tmm) cc_final: 0.7869 (tmm) REVERT: C 405 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: C 498 TYR cc_start: 0.9498 (OUTLIER) cc_final: 0.9007 (t80) REVERT: C 512 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8534 (m-10) REVERT: C 559 MET cc_start: 0.9371 (tpt) cc_final: 0.9006 (tpp) REVERT: C 580 MET cc_start: 0.9331 (mmm) cc_final: 0.8951 (mmm) REVERT: D 80 MET cc_start: 0.9124 (mmt) cc_final: 0.8390 (mmt) REVERT: D 93 GLU cc_start: 0.8782 (pm20) cc_final: 0.8489 (pm20) REVERT: D 137 MET cc_start: 0.8886 (mmm) cc_final: 0.8568 (mmm) REVERT: D 208 PHE cc_start: 0.4962 (OUTLIER) cc_final: 0.4155 (m-80) REVERT: D 339 TYR cc_start: 0.8102 (m-80) cc_final: 0.7690 (m-10) REVERT: D 384 ARG cc_start: 0.4892 (mtm110) cc_final: 0.3859 (mtm-85) REVERT: D 430 TYR cc_start: 0.8689 (t80) cc_final: 0.8221 (t80) REVERT: D 433 HIS cc_start: 0.8251 (p-80) cc_final: 0.7917 (t-90) REVERT: D 580 MET cc_start: 0.8763 (ttp) cc_final: 0.8320 (ttp) REVERT: D 584 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.9258 (ttmm) REVERT: E 6 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8468 (mt) REVERT: E 80 MET cc_start: 0.9041 (mmm) cc_final: 0.8593 (mmp) REVERT: E 89 MET cc_start: 0.8473 (tpp) cc_final: 0.8238 (tpp) REVERT: E 106 MET cc_start: 0.7853 (mpp) cc_final: 0.7490 (mpp) REVERT: E 135 GLU cc_start: 0.9517 (tp30) cc_final: 0.9281 (tp30) REVERT: E 463 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8046 (t80) REVERT: E 483 MET cc_start: 0.9146 (mmm) cc_final: 0.8889 (mmm) REVERT: E 498 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.9086 (t80) REVERT: E 559 MET cc_start: 0.9089 (tpt) cc_final: 0.8770 (tpp) REVERT: E 580 MET cc_start: 0.9149 (mmm) cc_final: 0.8921 (mmm) REVERT: F 6 LEU cc_start: 0.9129 (mt) cc_final: 0.8842 (mp) REVERT: F 14 MET cc_start: 0.9148 (mmm) cc_final: 0.8773 (mmt) REVERT: F 80 MET cc_start: 0.9233 (mmm) cc_final: 0.8729 (mmm) REVERT: F 87 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9158 (p) REVERT: F 89 MET cc_start: 0.8511 (mmm) cc_final: 0.8299 (mmm) REVERT: F 106 MET cc_start: 0.8064 (ptp) cc_final: 0.7777 (ptp) REVERT: F 117 PHE cc_start: 0.8957 (m-80) cc_final: 0.8393 (m-80) REVERT: F 151 MET cc_start: 0.7757 (mtt) cc_final: 0.7524 (mmt) REVERT: F 196 MET cc_start: 0.8989 (tpp) cc_final: 0.8543 (tpp) REVERT: F 496 CYS cc_start: 0.8461 (m) cc_final: 0.8131 (t) REVERT: F 580 MET cc_start: 0.9391 (mmp) cc_final: 0.9178 (mmp) outliers start: 100 outliers final: 68 residues processed: 303 average time/residue: 0.1613 time to fit residues: 81.9169 Evaluate side-chains 304 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 213 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 498 TYR Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 10 optimal weight: 4.9990 chunk 327 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 225 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 326 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.060364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.041405 restraints weight = 145715.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.043013 restraints weight = 93149.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.044104 restraints weight = 69335.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.044864 restraints weight = 56743.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.045384 restraints weight = 49400.708| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 27362 Z= 0.116 Angle : 0.688 13.849 37058 Z= 0.330 Chirality : 0.043 0.311 4123 Planarity : 0.004 0.147 4799 Dihedral : 4.365 37.127 3623 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.88 % Favored : 94.97 % Rotamer: Outliers : 3.07 % Allowed : 32.32 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.18 (0.15), residues: 3362 helix: 1.16 (0.13), residues: 1602 sheet: -0.46 (0.26), residues: 386 loop : -0.89 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 162 TYR 0.018 0.001 TYR A 463 PHE 0.029 0.001 PHE F 208 TRP 0.015 0.001 TRP E 157 HIS 0.006 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00272 (27362) covalent geometry : angle 0.68804 (37058) hydrogen bonds : bond 0.03270 ( 1177) hydrogen bonds : angle 4.54613 ( 3360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 230 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7246 (mpp) cc_final: 0.6522 (mpp) REVERT: A 164 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8049 (ptpt) REVERT: A 483 MET cc_start: 0.9190 (mmm) cc_final: 0.8886 (mmm) REVERT: A 498 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8107 (t80) REVERT: A 522 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8977 (mm) REVERT: A 559 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9063 (tpp) REVERT: A 580 MET cc_start: 0.9236 (mmm) cc_final: 0.9016 (mmm) REVERT: A 586 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: B 1 MET cc_start: 0.7394 (tmm) cc_final: 0.7109 (tmm) REVERT: B 80 MET cc_start: 0.8951 (mmt) cc_final: 0.8303 (mmt) REVERT: B 104 LYS cc_start: 0.9604 (OUTLIER) cc_final: 0.9349 (mmtm) REVERT: B 137 MET cc_start: 0.9190 (ptp) cc_final: 0.8962 (mtt) REVERT: B 151 MET cc_start: 0.8413 (mmt) cc_final: 0.7968 (mmm) REVERT: B 196 MET cc_start: 0.8877 (tpp) cc_final: 0.8546 (tpp) REVERT: B 339 TYR cc_start: 0.7769 (m-10) cc_final: 0.7435 (m-10) REVERT: B 422 GLU cc_start: 0.5530 (OUTLIER) cc_final: 0.4173 (pt0) REVERT: B 431 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: C 25 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8950 (tm-30) REVERT: C 135 GLU cc_start: 0.9431 (mp0) cc_final: 0.9174 (pm20) REVERT: C 221 TRP cc_start: 0.9381 (OUTLIER) cc_final: 0.9097 (t-100) REVERT: C 365 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9062 (pp20) REVERT: C 389 ASP cc_start: 0.7835 (t0) cc_final: 0.7370 (t0) REVERT: C 404 MET cc_start: 0.8426 (tmm) cc_final: 0.7846 (tmm) REVERT: C 405 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: C 498 TYR cc_start: 0.9486 (OUTLIER) cc_final: 0.9031 (t80) REVERT: C 512 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: C 580 MET cc_start: 0.9328 (mmm) cc_final: 0.8942 (mmm) REVERT: D 80 MET cc_start: 0.9113 (mmt) cc_final: 0.8381 (mmt) REVERT: D 137 MET cc_start: 0.8946 (mmm) cc_final: 0.8649 (mmm) REVERT: D 208 PHE cc_start: 0.4810 (OUTLIER) cc_final: 0.4041 (m-80) REVERT: D 339 TYR cc_start: 0.8109 (m-80) cc_final: 0.7702 (m-10) REVERT: D 384 ARG cc_start: 0.4933 (mtm110) cc_final: 0.3888 (mtm-85) REVERT: D 430 TYR cc_start: 0.8661 (t80) cc_final: 0.8192 (t80) REVERT: D 433 HIS cc_start: 0.8243 (p-80) cc_final: 0.7883 (t-90) REVERT: D 580 MET cc_start: 0.8782 (ttp) cc_final: 0.8319 (ttp) REVERT: D 584 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9173 (ttmm) REVERT: E 6 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8477 (mt) REVERT: E 80 MET cc_start: 0.9011 (mmm) cc_final: 0.8563 (mmp) REVERT: E 89 MET cc_start: 0.8429 (tpp) cc_final: 0.8195 (tpp) REVERT: E 106 MET cc_start: 0.7857 (mpp) cc_final: 0.7499 (mpp) REVERT: E 135 GLU cc_start: 0.9505 (tp30) cc_final: 0.9268 (tp30) REVERT: E 463 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8045 (t80) REVERT: E 483 MET cc_start: 0.9121 (mmm) cc_final: 0.8872 (mmm) REVERT: E 498 TYR cc_start: 0.9429 (OUTLIER) cc_final: 0.9112 (t80) REVERT: E 559 MET cc_start: 0.9058 (tpt) cc_final: 0.8757 (tpp) REVERT: E 580 MET cc_start: 0.9144 (mmm) cc_final: 0.8916 (mmm) REVERT: F 6 LEU cc_start: 0.9109 (mt) cc_final: 0.8810 (mp) REVERT: F 14 MET cc_start: 0.9093 (mmm) cc_final: 0.8688 (mmt) REVERT: F 80 MET cc_start: 0.9242 (mmm) cc_final: 0.8762 (mmm) REVERT: F 89 MET cc_start: 0.8567 (mmm) cc_final: 0.8236 (mmm) REVERT: F 93 GLU cc_start: 0.8286 (tp30) cc_final: 0.8007 (tp30) REVERT: F 106 MET cc_start: 0.8035 (ptp) cc_final: 0.7742 (ptp) REVERT: F 117 PHE cc_start: 0.8960 (m-80) cc_final: 0.8416 (m-80) REVERT: F 151 MET cc_start: 0.7831 (mtt) cc_final: 0.7596 (mmt) REVERT: F 196 MET cc_start: 0.9009 (tpp) cc_final: 0.8577 (tpp) REVERT: F 496 CYS cc_start: 0.8514 (m) cc_final: 0.8133 (t) REVERT: F 580 MET cc_start: 0.9379 (mmp) cc_final: 0.9175 (mmp) outliers start: 90 outliers final: 64 residues processed: 303 average time/residue: 0.1659 time to fit residues: 84.4131 Evaluate side-chains 298 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 215 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 439 HIS Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 498 TYR Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 498 TYR Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 573 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 309 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 321 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 301 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.058844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.040024 restraints weight = 147425.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.041564 restraints weight = 94597.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042623 restraints weight = 70835.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.043353 restraints weight = 58190.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.043836 restraints weight = 50846.236| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27362 Z= 0.168 Angle : 0.708 15.429 37058 Z= 0.346 Chirality : 0.043 0.279 4123 Planarity : 0.005 0.148 4799 Dihedral : 4.421 37.810 3623 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.18 % Favored : 94.68 % Rotamer: Outliers : 3.28 % Allowed : 32.32 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.13 (0.15), residues: 3362 helix: 1.11 (0.13), residues: 1607 sheet: -0.53 (0.26), residues: 391 loop : -0.92 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 468 TYR 0.023 0.001 TYR C 463 PHE 0.026 0.001 PHE F 208 TRP 0.016 0.001 TRP E 157 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00379 (27362) covalent geometry : angle 0.70753 (37058) hydrogen bonds : bond 0.03462 ( 1177) hydrogen bonds : angle 4.66293 ( 3360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5056.28 seconds wall clock time: 88 minutes 26.81 seconds (5306.81 seconds total)