Starting phenix.real_space_refine on Mon Jun 23 06:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c67_45241/06_2025/9c67_45241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c67_45241/06_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_45241/06_2025/9c67_45241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c67_45241/06_2025/9c67_45241.map" model { file = "/net/cci-nas-00/data/ceres_data/9c67_45241/06_2025/9c67_45241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c67_45241/06_2025/9c67_45241.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.65, per 1000 atoms: 0.58 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: 7.02 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 3.55 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: 10.42 Time building geometry restraints manager: 8.07 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 600 or resid 701)) selection = (chain 'B' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 600 or resid 701)) selection = (chain 'C' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 502 or resid 515 through 600 or resid 701)) selection = (chain 'D' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 600 or resid 701)) selection = (chain 'E' and (resid 3 through 190 or resid 200 through 250 or resid 300 throug \ h 502 or resid 515 through 600 or resid 701)) selection = (chain 'F' and (resid 3 through 190 or resid 200 through 600 or resid 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 61.140 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.240 ------------------------------------------------------------------------------- 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 : 17.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.046 0.002 TRP E 157 HIS 0.005 0.001 HIS D 396 PHE 0.052 0.001 PHE F 208 TYR 0.031 0.002 TYR D 430 ARG 0.007 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.15802 ( 1177) hydrogen bonds : angle 6.17747 ( 3360) covalent geometry : bond 0.00323 (27362) covalent geometry : angle 0.77142 (37058) *********************** 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 : 3.408 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: 0.3622 time to fit residues: 151.3425 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 : 5.081 ------------------------------------------------------------------------------- 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 284 optimal weight: 9.9990 chunk 255 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 160 optimal weight: 0.0980 chunk 196 optimal weight: 20.0000 chunk 306 optimal weight: 10.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 147 HIS ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN 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 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN E 124 HIS F 92 ASN F 142 GLN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 406 GLN ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.060005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.040982 restraints weight = 146874.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.042524 restraints weight = 95641.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.043565 restraints weight = 72122.458| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27362 Z= 0.234 Angle : 0.703 13.341 37058 Z= 0.358 Chirality : 0.045 0.233 4123 Planarity : 0.005 0.149 4799 Dihedral : 5.068 54.533 3636 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.68 % Favored : 94.08 % Rotamer: Outliers : 4.98 % Allowed : 30.10 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3362 helix: 0.78 (0.13), residues: 1618 sheet: -0.53 (0.26), residues: 398 loop : -1.05 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 157 HIS 0.011 0.001 HIS D 466 PHE 0.025 0.002 PHE F 208 TYR 0.030 0.002 TYR A 463 ARG 0.009 0.001 ARG D 384 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1177) hydrogen bonds : angle 5.22886 ( 3360) covalent geometry : bond 0.00507 (27362) covalent geometry : angle 0.70263 (37058) *********************** 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 372 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 226 time to evaluate : 3.284 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 30 VAL cc_start: 0.9507 (t) cc_final: 0.9282 (m) REVERT: A 58 SER cc_start: 0.5813 (OUTLIER) cc_final: 0.5535 (p) REVERT: A 80 MET cc_start: 0.8938 (mmt) cc_final: 0.8475 (mmt) REVERT: A 164 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8219 (ptmt) REVERT: A 463 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.8001 (t80) REVERT: A 498 TYR cc_start: 0.9547 (OUTLIER) cc_final: 0.8913 (t80) REVERT: A 522 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9152 (mm) REVERT: A 580 MET cc_start: 0.9209 (mmm) cc_final: 0.8985 (mmm) REVERT: B 80 MET cc_start: 0.8992 (mmt) cc_final: 0.8442 (mmt) REVERT: B 137 MET cc_start: 0.9252 (ptp) cc_final: 0.8915 (ptp) REVERT: B 196 MET cc_start: 0.8875 (tpp) cc_final: 0.8638 (tpp) REVERT: B 320 GLN cc_start: 0.9456 (OUTLIER) cc_final: 0.8539 (tp-100) REVERT: B 422 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.4418 (pt0) REVERT: B 496 CYS cc_start: 0.8756 (m) cc_final: 0.7938 (t) REVERT: B 557 SER cc_start: 0.9515 (OUTLIER) cc_final: 0.9303 (t) REVERT: C 89 MET cc_start: 0.7429 (ptt) cc_final: 0.7109 (ptp) REVERT: C 326 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8100 (t0) REVERT: C 365 GLU cc_start: 0.9502 (OUTLIER) cc_final: 0.9131 (pp20) REVERT: C 368 GLN cc_start: 0.9613 (OUTLIER) cc_final: 0.9270 (mm-40) REVERT: C 495 MET cc_start: 0.9046 (ttm) cc_final: 0.8845 (ttm) REVERT: C 580 MET cc_start: 0.9200 (mmm) cc_final: 0.8974 (mmm) REVERT: D 80 MET cc_start: 0.9016 (mmt) cc_final: 0.8763 (mmt) REVERT: D 137 MET cc_start: 0.8710 (mmm) cc_final: 0.8507 (mmm) REVERT: D 208 PHE cc_start: 0.5561 (OUTLIER) cc_final: 0.4688 (m-80) REVERT: D 498 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: D 548 ILE cc_start: 0.9519 (mm) cc_final: 0.9173 (mm) REVERT: D 570 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8720 (mm-30) REVERT: E 14 MET cc_start: 0.7573 (ttt) cc_final: 0.7209 (ttt) REVERT: E 80 MET cc_start: 0.8953 (mmm) cc_final: 0.8532 (mmp) REVERT: E 495 MET cc_start: 0.9168 (ptm) cc_final: 0.8661 (ptm) REVERT: E 498 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.9030 (t80) REVERT: E 580 MET cc_start: 0.9218 (mmm) cc_final: 0.9017 (mmm) REVERT: F 80 MET cc_start: 0.9023 (mmm) cc_final: 0.8609 (mmt) REVERT: F 116 LEU cc_start: 0.9274 (tp) cc_final: 0.9065 (tt) REVERT: F 117 PHE cc_start: 0.8614 (m-80) cc_final: 0.8164 (m-80) REVERT: F 196 MET cc_start: 0.8973 (tpp) cc_final: 0.8626 (tpp) REVERT: F 363 ILE cc_start: 0.9316 (mt) cc_final: 0.9070 (mm) REVERT: F 496 CYS cc_start: 0.8872 (m) cc_final: 0.7935 (t) outliers start: 146 outliers final: 62 residues processed: 345 average time/residue: 0.3215 time to fit residues: 188.8598 Evaluate side-chains 283 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 207 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER 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 211 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 363 ILE 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 463 TYR 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 86 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 381 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 GLU 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 106 MET Chi-restraints excluded: chain C residue 326 ASN 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 482 LEU 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 196 MET 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 416 VAL Chi-restraints excluded: chain D residue 418 LEU 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 272 THR 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 465 LEU 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 19 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 233 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 204 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN C 124 HIS C 370 ASN ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN D 326 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 205 GLN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN ** F 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.056377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.037844 restraints weight = 152102.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039232 restraints weight = 99987.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.040168 restraints weight = 76169.372| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 27362 Z= 0.327 Angle : 0.781 15.582 37058 Z= 0.401 Chirality : 0.047 0.222 4123 Planarity : 0.006 0.154 4799 Dihedral : 5.248 53.716 3628 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.01 % Favored : 93.75 % Rotamer: Outliers : 7.00 % Allowed : 28.70 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3362 helix: 0.40 (0.12), residues: 1634 sheet: -1.05 (0.26), residues: 394 loop : -1.28 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 157 HIS 0.008 0.002 HIS F 448 PHE 0.025 0.003 PHE E 586 TYR 0.035 0.003 TYR A 463 ARG 0.006 0.001 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 1177) hydrogen bonds : angle 5.42339 ( 3360) covalent geometry : bond 0.00688 (27362) covalent geometry : angle 0.78097 (37058) *********************** 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 407 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 202 time to evaluate : 3.066 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: 0.9491 (t) cc_final: 0.9210 (m) REVERT: A 58 SER cc_start: 0.6124 (OUTLIER) cc_final: 0.5664 (p) REVERT: A 80 MET cc_start: 0.9069 (mmt) cc_final: 0.8484 (mmt) REVERT: A 94 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9225 (mt) REVERT: A 494 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8560 (mt-10) REVERT: A 498 TYR cc_start: 0.9582 (OUTLIER) cc_final: 0.8421 (t80) REVERT: A 522 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8968 (mm) REVERT: A 559 MET cc_start: 0.9271 (tpt) cc_final: 0.9019 (tpp) REVERT: A 580 MET cc_start: 0.9168 (mmm) cc_final: 0.8906 (mmm) REVERT: A 586 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: B 80 MET cc_start: 0.8928 (mmt) cc_final: 0.8495 (mmt) REVERT: B 104 LYS cc_start: 0.9665 (OUTLIER) cc_final: 0.9418 (mmtm) REVERT: B 196 MET cc_start: 0.8806 (tpp) cc_final: 0.8523 (tpp) REVERT: B 246 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9307 (pt) REVERT: B 320 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.8746 (tp40) REVERT: B 339 TYR cc_start: 0.8198 (m-10) cc_final: 0.7983 (m-10) REVERT: B 495 MET cc_start: 0.9236 (ptm) cc_final: 0.8877 (tmm) REVERT: C 89 MET cc_start: 0.7900 (ptt) cc_final: 0.7493 (ptt) REVERT: C 94 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9342 (mt) REVERT: C 221 TRP cc_start: 0.9512 (OUTLIER) cc_final: 0.9226 (t-100) REVERT: C 365 GLU cc_start: 0.9540 (OUTLIER) cc_final: 0.9165 (pp20) REVERT: C 440 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.8764 (mpt-90) REVERT: C 498 TYR cc_start: 0.9478 (OUTLIER) cc_final: 0.8892 (t80) REVERT: C 512 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8631 (m-10) REVERT: C 559 MET cc_start: 0.9473 (tpt) cc_final: 0.8994 (tpp) REVERT: C 580 MET cc_start: 0.9207 (mmm) cc_final: 0.8931 (mmm) REVERT: D 80 MET cc_start: 0.9228 (mmt) cc_final: 0.8848 (mmt) REVERT: D 137 MET cc_start: 0.8695 (mmm) cc_final: 0.8383 (mmm) REVERT: D 208 PHE cc_start: 0.5672 (OUTLIER) cc_final: 0.4819 (m-80) REVERT: D 498 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8538 (m-80) REVERT: D 570 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8682 (mm-30) REVERT: D 580 MET cc_start: 0.8745 (ttp) cc_final: 0.8480 (ttp) REVERT: E 6 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8478 (mt) REVERT: E 25 GLU cc_start: 0.9474 (OUTLIER) cc_final: 0.9161 (tm-30) REVERT: E 80 MET cc_start: 0.9253 (mmm) cc_final: 0.8934 (mmm) REVERT: E 89 MET cc_start: 0.8573 (tpp) cc_final: 0.8370 (tpp) REVERT: E 463 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8401 (t80) REVERT: E 483 MET cc_start: 0.9253 (mmm) cc_final: 0.8993 (mmm) REVERT: E 495 MET cc_start: 0.9088 (ptm) cc_final: 0.8540 (ptm) REVERT: E 509 MET cc_start: 0.7846 (mmt) cc_final: 0.7608 (tpt) REVERT: E 522 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9174 (mm) REVERT: E 580 MET cc_start: 0.9128 (mmm) cc_final: 0.8881 (mmm) REVERT: F 6 LEU cc_start: 0.9264 (mt) cc_final: 0.8963 (mt) REVERT: F 80 MET cc_start: 0.9256 (mmm) cc_final: 0.8867 (mmm) REVERT: F 87 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9236 (p) REVERT: F 117 PHE cc_start: 0.8824 (m-80) cc_final: 0.8182 (m-80) REVERT: F 135 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8878 (tp30) REVERT: F 151 MET cc_start: 0.8409 (ptp) cc_final: 0.7957 (pmm) REVERT: F 196 MET cc_start: 0.8919 (tpp) cc_final: 0.8327 (tpp) REVERT: F 363 ILE cc_start: 0.9338 (mt) cc_final: 0.9109 (mm) REVERT: F 365 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9217 (tm-30) REVERT: F 405 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8927 (tp40) REVERT: F 408 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.4603 (pm20) REVERT: F 496 CYS cc_start: 0.8520 (m) cc_final: 0.8196 (t) REVERT: F 518 LEU cc_start: 0.9814 (OUTLIER) cc_final: 0.9610 (pp) REVERT: F 559 MET cc_start: 0.8875 (tpt) cc_final: 0.8498 (tpt) outliers start: 205 outliers final: 106 residues processed: 385 average time/residue: 0.3208 time to fit residues: 207.8150 Evaluate side-chains 320 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 187 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 285 HIS 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 363 ILE 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 438 VAL 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 586 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 189 ILE 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 321 SER Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ILE 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 431 TYR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 440 ARG 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 535 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 VAL 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 217 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 434 ASP 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 6 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 185 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 383 SER 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 463 TYR Chi-restraints excluded: chain E residue 522 LEU Chi-restraints excluded: chain E residue 586 PHE 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 87 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 189 ILE 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 315 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 416 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 Chi-restraints excluded: chain F residue 573 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 255 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 304 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 319 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 326 ASN A 406 GLN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN C 124 HIS C 326 ASN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN D 472 HIS E 405 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.058604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039623 restraints weight = 147594.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041187 restraints weight = 94282.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.042240 restraints weight = 70465.916| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 27362 Z= 0.138 Angle : 0.650 13.058 37058 Z= 0.321 Chirality : 0.043 0.184 4123 Planarity : 0.005 0.151 4799 Dihedral : 4.936 56.191 3628 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.94 % Favored : 94.88 % Rotamer: Outliers : 4.40 % Allowed : 31.37 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3362 helix: 0.96 (0.13), residues: 1628 sheet: -0.87 (0.26), residues: 397 loop : -1.06 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 157 HIS 0.006 0.001 HIS E 466 PHE 0.031 0.001 PHE F 208 TYR 0.028 0.002 TYR A 463 ARG 0.006 0.000 ARG E 588 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 1177) hydrogen bonds : angle 4.84247 ( 3360) covalent geometry : bond 0.00315 (27362) covalent geometry : angle 0.64994 (37058) *********************** 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 355 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 226 time to evaluate : 3.285 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 30 VAL cc_start: 0.9482 (t) cc_final: 0.9181 (m) REVERT: A 80 MET cc_start: 0.9029 (mmt) cc_final: 0.8452 (mmt) REVERT: A 106 MET cc_start: 0.7300 (mpp) cc_final: 0.6870 (mpp) REVERT: A 498 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7834 (t80) REVERT: A 559 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8985 (tpp) REVERT: A 580 MET cc_start: 0.9192 (mmm) cc_final: 0.8930 (mmm) REVERT: B 1 MET cc_start: 0.7223 (tmm) cc_final: 0.6834 (tmm) REVERT: B 80 MET cc_start: 0.8995 (mmt) cc_final: 0.8452 (mmt) REVERT: B 106 MET cc_start: 0.8560 (ptp) cc_final: 0.8315 (ptp) REVERT: B 132 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8416 (tpm170) REVERT: B 165 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9230 (mmtp) REVERT: B 196 MET cc_start: 0.8760 (tpp) cc_final: 0.8410 (tpp) REVERT: B 339 TYR cc_start: 0.7997 (m-10) cc_final: 0.7657 (m-10) REVERT: B 422 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.3967 (pt0) REVERT: B 431 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6585 (m-80) REVERT: B 472 HIS cc_start: 0.8495 (m-70) cc_final: 0.8151 (m-70) REVERT: B 495 MET cc_start: 0.9168 (ptm) cc_final: 0.8911 (tmm) REVERT: C 30 VAL cc_start: 0.9037 (t) cc_final: 0.8751 (m) REVERT: C 89 MET cc_start: 0.7816 (ptt) cc_final: 0.7321 (ptp) REVERT: C 94 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9321 (mp) REVERT: C 221 TRP cc_start: 0.9413 (OUTLIER) cc_final: 0.9190 (t-100) REVERT: C 365 GLU cc_start: 0.9534 (OUTLIER) cc_final: 0.9112 (pp20) REVERT: C 404 MET cc_start: 0.8570 (tmm) cc_final: 0.7928 (tmm) REVERT: C 440 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8900 (mpt-90) REVERT: C 498 TYR cc_start: 0.9478 (OUTLIER) cc_final: 0.8951 (t80) REVERT: C 512 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8654 (m-10) REVERT: C 543 SER cc_start: 0.9415 (OUTLIER) cc_final: 0.9069 (p) REVERT: C 559 MET cc_start: 0.9435 (tpt) cc_final: 0.9028 (tpp) REVERT: C 580 MET cc_start: 0.9238 (mmm) cc_final: 0.8920 (mmm) REVERT: D 80 MET cc_start: 0.9178 (mmt) cc_final: 0.8772 (mmt) REVERT: D 137 MET cc_start: 0.8698 (mmm) cc_final: 0.8316 (mmm) REVERT: D 205 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8600 (pp30) REVERT: D 208 PHE cc_start: 0.5541 (OUTLIER) cc_final: 0.4733 (m-80) REVERT: D 339 TYR cc_start: 0.8170 (m-10) cc_final: 0.7969 (m-10) REVERT: D 496 CYS cc_start: 0.8506 (m) cc_final: 0.8240 (t) REVERT: D 498 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8650 (m-80) REVERT: D 570 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8662 (mm-30) REVERT: D 580 MET cc_start: 0.8586 (ttp) cc_final: 0.8221 (ttp) REVERT: D 584 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9167 (ttmm) REVERT: E 6 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8466 (mt) REVERT: E 80 MET cc_start: 0.9226 (mmm) cc_final: 0.8912 (mmm) REVERT: E 463 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8197 (t80) REVERT: E 483 MET cc_start: 0.9181 (mmm) cc_final: 0.8930 (mmm) REVERT: E 494 GLU cc_start: 0.8197 (pm20) cc_final: 0.7681 (pm20) REVERT: E 495 MET cc_start: 0.9044 (ptm) cc_final: 0.8590 (ptm) REVERT: E 498 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.8859 (t80) REVERT: E 580 MET cc_start: 0.9125 (mmm) cc_final: 0.8890 (mmm) REVERT: F 80 MET cc_start: 0.9265 (mmm) cc_final: 0.8819 (mmm) REVERT: F 87 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9189 (p) REVERT: F 93 GLU cc_start: 0.8446 (tp30) cc_final: 0.8237 (tp30) REVERT: F 117 PHE cc_start: 0.8792 (m-80) cc_final: 0.8140 (m-80) REVERT: F 151 MET cc_start: 0.8257 (ptp) cc_final: 0.7873 (pmm) REVERT: F 196 MET cc_start: 0.8938 (tpp) cc_final: 0.8522 (tpp) REVERT: F 496 CYS cc_start: 0.8508 (m) cc_final: 0.8210 (t) REVERT: F 518 LEU cc_start: 0.9778 (OUTLIER) cc_final: 0.9559 (pp) REVERT: F 580 MET cc_start: 0.9382 (mmp) cc_final: 0.9155 (mmp) outliers start: 129 outliers final: 60 residues processed: 336 average time/residue: 0.3469 time to fit residues: 193.7674 Evaluate side-chains 289 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 207 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 352 LEU 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 498 TYR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 211 LEU 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 321 SER Chi-restraints excluded: chain B residue 378 LEU 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 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 482 LEU 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 543 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 385 LYS 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 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 255 LEU Chi-restraints excluded: chain E residue 256 LEU 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 E residue 586 PHE Chi-restraints excluded: chain E residue 600 ASN 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 315 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 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 293 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 321 optimal weight: 0.0670 chunk 92 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 39 optimal weight: 0.1980 overall best weight: 2.4524 ------------------------------------------------------------------------------- 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 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 534 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.057778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.038895 restraints weight = 150948.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040421 restraints weight = 96615.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.041443 restraints weight = 72510.477| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27362 Z= 0.170 Angle : 0.654 14.401 37058 Z= 0.325 Chirality : 0.044 0.228 4123 Planarity : 0.005 0.151 4799 Dihedral : 4.788 41.755 3628 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 5.39 % Allowed : 30.61 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3362 helix: 0.96 (0.13), residues: 1639 sheet: -0.94 (0.26), residues: 401 loop : -1.13 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 157 HIS 0.005 0.001 HIS A 576 PHE 0.027 0.001 PHE F 208 TYR 0.026 0.002 TYR A 463 ARG 0.005 0.000 ARG D 384 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 1177) hydrogen bonds : angle 4.83016 ( 3360) covalent geometry : bond 0.00379 (27362) covalent geometry : angle 0.65436 (37058) *********************** 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 368 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 210 time to evaluate : 3.050 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 VAL cc_start: 0.9552 (t) cc_final: 0.9299 (m) REVERT: A 58 SER cc_start: 0.6471 (OUTLIER) cc_final: 0.6193 (p) REVERT: A 80 MET cc_start: 0.9117 (mmt) cc_final: 0.8491 (mmt) REVERT: A 204 ASN cc_start: 0.5955 (t160) cc_final: 0.5386 (t0) REVERT: A 470 LEU cc_start: 0.9640 (mp) cc_final: 0.9389 (mp) REVERT: A 483 MET cc_start: 0.9238 (mmm) cc_final: 0.9026 (mmm) REVERT: A 494 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: A 498 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.7885 (t80) REVERT: A 522 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8956 (mm) REVERT: A 559 MET cc_start: 0.9349 (tpt) cc_final: 0.9072 (tpp) REVERT: A 586 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: B 1 MET cc_start: 0.7291 (tmm) cc_final: 0.6971 (tmm) REVERT: B 80 MET cc_start: 0.9038 (mmt) cc_final: 0.8472 (mmt) REVERT: B 132 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8390 (tpm170) REVERT: B 164 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9228 (ptpp) REVERT: B 196 MET cc_start: 0.8858 (tpp) cc_final: 0.8516 (tpp) REVERT: B 339 TYR cc_start: 0.8029 (m-10) cc_final: 0.7669 (m-10) REVERT: B 422 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4135 (pt0) REVERT: B 431 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: B 472 HIS cc_start: 0.8478 (m-70) cc_final: 0.8124 (m-70) REVERT: C 25 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.9122 (tm-30) REVERT: C 30 VAL cc_start: 0.9126 (t) cc_final: 0.8829 (m) REVERT: C 89 MET cc_start: 0.7972 (ptt) cc_final: 0.7585 (ptt) REVERT: C 221 TRP cc_start: 0.9477 (OUTLIER) cc_final: 0.9185 (t-100) REVERT: C 365 GLU cc_start: 0.9528 (OUTLIER) cc_final: 0.9115 (pp20) REVERT: C 404 MET cc_start: 0.8627 (tmm) cc_final: 0.7953 (tmm) REVERT: C 405 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: C 512 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8680 (m-10) REVERT: C 543 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.9113 (p) REVERT: C 559 MET cc_start: 0.9435 (tpt) cc_final: 0.9040 (tpp) REVERT: C 580 MET cc_start: 0.9298 (mmm) cc_final: 0.8974 (mmm) REVERT: D 80 MET cc_start: 0.9204 (mmt) cc_final: 0.8765 (mmt) REVERT: D 137 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8399 (mmm) REVERT: D 196 MET cc_start: 0.9156 (mmp) cc_final: 0.8786 (mmp) REVERT: D 208 PHE cc_start: 0.5592 (OUTLIER) cc_final: 0.4685 (m-80) REVERT: D 339 TYR cc_start: 0.8128 (m-10) cc_final: 0.7912 (m-10) REVERT: D 384 ARG cc_start: 0.4560 (mtm110) cc_final: 0.4319 (mtm110) REVERT: D 472 HIS cc_start: 0.8433 (m90) cc_final: 0.8058 (m170) REVERT: D 498 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8674 (m-80) REVERT: D 580 MET cc_start: 0.8645 (ttp) cc_final: 0.8261 (ttp) REVERT: D 584 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9137 (ttmm) REVERT: E 80 MET cc_start: 0.9235 (mmm) cc_final: 0.8879 (mmm) REVERT: E 89 MET cc_start: 0.8392 (tpp) cc_final: 0.8169 (tpp) REVERT: E 106 MET cc_start: 0.7721 (mpp) cc_final: 0.7229 (mpp) REVERT: E 255 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9156 (mp) REVERT: E 463 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8084 (t80) REVERT: E 483 MET cc_start: 0.9158 (mmm) cc_final: 0.8886 (mmm) REVERT: E 498 TYR cc_start: 0.9296 (OUTLIER) cc_final: 0.8874 (t80) REVERT: E 573 PHE cc_start: 0.9565 (OUTLIER) cc_final: 0.9027 (m-80) REVERT: E 580 MET cc_start: 0.9153 (mmm) cc_final: 0.8910 (mmm) REVERT: F 6 LEU cc_start: 0.9187 (mt) cc_final: 0.8946 (mp) REVERT: F 80 MET cc_start: 0.9313 (mmm) cc_final: 0.8862 (mmm) REVERT: F 87 THR cc_start: 0.9436 (OUTLIER) cc_final: 0.9198 (p) REVERT: F 89 MET cc_start: 0.8787 (mmm) cc_final: 0.8244 (mmm) REVERT: F 117 PHE cc_start: 0.8931 (m-80) cc_final: 0.8261 (m-80) REVERT: F 151 MET cc_start: 0.8310 (ptp) cc_final: 0.7941 (pmm) REVERT: F 196 MET cc_start: 0.8913 (tpp) cc_final: 0.8489 (tpp) REVERT: F 363 ILE cc_start: 0.9243 (mt) cc_final: 0.8996 (mm) REVERT: F 496 CYS cc_start: 0.8600 (m) cc_final: 0.8309 (t) REVERT: F 580 MET cc_start: 0.9433 (mmp) cc_final: 0.9218 (mmp) outliers start: 158 outliers final: 79 residues processed: 348 average time/residue: 0.3485 time to fit residues: 201.2296 Evaluate side-chains 305 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 202 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 323 VAL 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 573 PHE Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 189 ILE 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 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 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 482 LEU 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 535 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 137 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 321 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 494 GLU 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 103 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 433 HIS 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 E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 1 MET 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 315 VAL 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 436 LYS Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 498 TYR 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 315 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 199 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 283 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 285 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN C 326 ASN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.058358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039570 restraints weight = 147460.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.041122 restraints weight = 93916.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.042168 restraints weight = 70116.309| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 27362 Z= 0.130 Angle : 0.653 14.359 37058 Z= 0.318 Chirality : 0.043 0.232 4123 Planarity : 0.005 0.150 4799 Dihedral : 4.675 40.837 3625 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.88 % Favored : 94.94 % Rotamer: Outliers : 4.85 % Allowed : 30.78 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3362 helix: 1.04 (0.13), residues: 1633 sheet: -0.84 (0.26), residues: 397 loop : -1.04 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 157 HIS 0.004 0.001 HIS A 576 PHE 0.030 0.001 PHE F 208 TYR 0.024 0.001 TYR A 463 ARG 0.004 0.000 ARG E 588 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 1177) hydrogen bonds : angle 4.67316 ( 3360) covalent geometry : bond 0.00300 (27362) covalent geometry : angle 0.65288 (37058) *********************** 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 360 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 218 time to evaluate : 3.109 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: A 58 SER cc_start: 0.6757 (OUTLIER) cc_final: 0.6507 (p) REVERT: A 80 MET cc_start: 0.9123 (mmt) cc_final: 0.8482 (mmt) REVERT: A 106 MET cc_start: 0.7286 (mpp) cc_final: 0.6731 (mpp) REVERT: A 204 ASN cc_start: 0.5685 (t160) cc_final: 0.5305 (t0) REVERT: A 498 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7925 (t80) REVERT: A 522 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9044 (mm) REVERT: A 559 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9051 (tpp) REVERT: A 586 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: B 1 MET cc_start: 0.7453 (tmm) cc_final: 0.7164 (tmm) REVERT: B 80 MET cc_start: 0.9015 (mmt) cc_final: 0.8421 (mmt) REVERT: B 132 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7905 (mmm160) REVERT: B 151 MET cc_start: 0.8530 (mmm) cc_final: 0.8293 (mmm) REVERT: B 196 MET cc_start: 0.8859 (tpp) cc_final: 0.8495 (tpp) REVERT: B 305 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.4872 (mm) REVERT: B 339 TYR cc_start: 0.7990 (m-10) cc_final: 0.7644 (m-10) REVERT: B 422 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.4061 (pt0) REVERT: B 431 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: C 25 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.9103 (tm-30) REVERT: C 30 VAL cc_start: 0.9108 (t) cc_final: 0.8803 (m) REVERT: C 89 MET cc_start: 0.7923 (ptt) cc_final: 0.7537 (ptt) REVERT: C 221 TRP cc_start: 0.9437 (OUTLIER) cc_final: 0.9156 (t-100) REVERT: C 365 GLU cc_start: 0.9512 (OUTLIER) cc_final: 0.9087 (pp20) REVERT: C 404 MET cc_start: 0.8501 (tmm) cc_final: 0.7951 (tmm) REVERT: C 435 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8117 (t80) REVERT: C 440 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8816 (mpt-90) REVERT: C 512 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8691 (m-10) REVERT: C 543 SER cc_start: 0.9443 (OUTLIER) cc_final: 0.9135 (p) REVERT: C 559 MET cc_start: 0.9404 (tpt) cc_final: 0.9016 (tpp) REVERT: C 580 MET cc_start: 0.9317 (mmm) cc_final: 0.8983 (mmm) REVERT: D 80 MET cc_start: 0.9186 (mmt) cc_final: 0.8744 (mmt) REVERT: D 106 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8169 (ptp) REVERT: D 137 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8452 (mmm) REVERT: D 208 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.4649 (m-80) REVERT: D 339 TYR cc_start: 0.8150 (m-10) cc_final: 0.7939 (m-10) REVERT: D 384 ARG cc_start: 0.4513 (mtm110) cc_final: 0.4238 (mtm110) REVERT: D 472 HIS cc_start: 0.8372 (m90) cc_final: 0.8011 (m170) REVERT: D 498 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8634 (m-80) REVERT: D 580 MET cc_start: 0.8639 (ttp) cc_final: 0.8225 (ttp) REVERT: D 584 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9127 (ttmm) REVERT: E 80 MET cc_start: 0.9226 (mmm) cc_final: 0.8871 (mmm) REVERT: E 89 MET cc_start: 0.8433 (tpp) cc_final: 0.8223 (tpp) REVERT: E 463 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.8034 (t80) REVERT: E 483 MET cc_start: 0.9134 (mmm) cc_final: 0.8863 (mmm) REVERT: E 498 TYR cc_start: 0.9292 (OUTLIER) cc_final: 0.8925 (t80) REVERT: E 548 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9260 (tp) REVERT: E 559 MET cc_start: 0.9229 (tpt) cc_final: 0.9016 (tpp) REVERT: E 573 PHE cc_start: 0.9544 (OUTLIER) cc_final: 0.9095 (m-80) REVERT: E 580 MET cc_start: 0.9141 (mmm) cc_final: 0.8901 (mmm) REVERT: F 14 MET cc_start: 0.9108 (mmm) cc_final: 0.8731 (mmp) REVERT: F 80 MET cc_start: 0.9302 (mmm) cc_final: 0.8838 (mmm) REVERT: F 87 THR cc_start: 0.9427 (OUTLIER) cc_final: 0.9209 (p) REVERT: F 88 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8600 (ttmt) REVERT: F 117 PHE cc_start: 0.8933 (m-80) cc_final: 0.8253 (m-80) REVERT: F 151 MET cc_start: 0.8254 (ptp) cc_final: 0.7907 (pmm) REVERT: F 196 MET cc_start: 0.8961 (tpp) cc_final: 0.8513 (tpp) REVERT: F 363 ILE cc_start: 0.9234 (mt) cc_final: 0.9013 (mm) REVERT: F 520 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9175 (mppt) REVERT: F 580 MET cc_start: 0.9420 (mmp) cc_final: 0.9190 (mmp) outliers start: 142 outliers final: 75 residues processed: 340 average time/residue: 0.3482 time to fit residues: 196.1227 Evaluate side-chains 306 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 203 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 466 HIS 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 132 ARG Chi-restraints excluded: chain B residue 161 ARG 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 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 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS 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 440 ARG 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 535 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 369 LYS 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 E residue 548 ILE 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 88 LYS 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 315 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 520 LYS Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 549 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 125 optimal weight: 0.0040 chunk 59 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.058989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.040166 restraints weight = 146141.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.041760 restraints weight = 92640.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042835 restraints weight = 68764.762| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2945 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 : 0.664 14.452 37058 Z= 0.319 Chirality : 0.044 0.326 4123 Planarity : 0.005 0.151 4799 Dihedral : 4.595 39.785 3625 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.79 % Favored : 95.06 % Rotamer: Outliers : 4.27 % Allowed : 31.16 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3362 helix: 1.08 (0.13), residues: 1622 sheet: -0.73 (0.26), residues: 401 loop : -0.96 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 157 HIS 0.004 0.001 HIS E 466 PHE 0.031 0.001 PHE F 208 TYR 0.021 0.001 TYR A 463 ARG 0.004 0.000 ARG E 588 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 1177) hydrogen bonds : angle 4.57707 ( 3360) covalent geometry : bond 0.00275 (27362) covalent geometry : angle 0.66383 (37058) *********************** 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 344 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 219 time to evaluate : 2.969 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: A 14 MET cc_start: 0.7577 (ttm) cc_final: 0.7253 (ttt) REVERT: A 80 MET cc_start: 0.9132 (mmt) cc_final: 0.8487 (mmt) REVERT: A 106 MET cc_start: 0.7237 (mpp) cc_final: 0.6702 (mpp) REVERT: A 204 ASN cc_start: 0.5575 (t160) cc_final: 0.5259 (t0) REVERT: A 498 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7909 (t80) REVERT: A 522 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8964 (mm) REVERT: A 559 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.9008 (tpp) REVERT: A 582 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9508 (tt) REVERT: A 586 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: B 1 MET cc_start: 0.7367 (tmm) cc_final: 0.7093 (tmm) REVERT: B 80 MET cc_start: 0.8997 (mmt) cc_final: 0.8385 (mmt) REVERT: B 151 MET cc_start: 0.8621 (mmm) cc_final: 0.8194 (mmm) REVERT: B 196 MET cc_start: 0.8914 (tpp) cc_final: 0.8570 (tpp) REVERT: B 305 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.4816 (mm) REVERT: B 339 TYR cc_start: 0.7987 (m-10) cc_final: 0.7675 (m-10) REVERT: B 422 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4002 (pt0) REVERT: B 431 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: C 25 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.9058 (tm-30) REVERT: C 89 MET cc_start: 0.7941 (ptt) cc_final: 0.7547 (ptt) REVERT: C 221 TRP cc_start: 0.9414 (OUTLIER) cc_final: 0.9136 (t-100) REVERT: C 365 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.9077 (pp20) REVERT: C 404 MET cc_start: 0.8396 (tmm) cc_final: 0.7764 (tmm) REVERT: C 405 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: C 435 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8121 (t80) REVERT: C 512 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8752 (m-10) REVERT: C 559 MET cc_start: 0.9349 (tpt) cc_final: 0.9093 (tpp) REVERT: C 580 MET cc_start: 0.9302 (mmm) cc_final: 0.9022 (mmm) REVERT: D 80 MET cc_start: 0.9114 (mmt) cc_final: 0.8638 (mmt) REVERT: D 106 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8209 (ptp) REVERT: D 137 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8263 (mmm) REVERT: D 196 MET cc_start: 0.9092 (mmp) cc_final: 0.8683 (mmp) REVERT: D 208 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4308 (m-80) REVERT: D 339 TYR cc_start: 0.8202 (m-10) cc_final: 0.7971 (m-10) REVERT: D 384 ARG cc_start: 0.4664 (mtm110) cc_final: 0.3892 (mtm-85) REVERT: D 472 HIS cc_start: 0.8333 (m90) cc_final: 0.7955 (m170) REVERT: D 580 MET cc_start: 0.8644 (ttp) cc_final: 0.8233 (ttp) REVERT: D 584 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9123 (ttmm) REVERT: E 80 MET cc_start: 0.9183 (mmm) cc_final: 0.8974 (mmm) REVERT: E 89 MET cc_start: 0.8457 (tpp) cc_final: 0.8224 (tpp) REVERT: E 106 MET cc_start: 0.7695 (mpp) cc_final: 0.7021 (mpp) REVERT: E 255 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9130 (mt) REVERT: E 463 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8024 (t80) REVERT: E 483 MET cc_start: 0.9108 (mmm) cc_final: 0.8829 (mmm) REVERT: E 498 TYR cc_start: 0.9334 (OUTLIER) cc_final: 0.8930 (t80) REVERT: E 548 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9233 (tp) REVERT: E 573 PHE cc_start: 0.9516 (OUTLIER) cc_final: 0.9126 (m-80) REVERT: E 580 MET cc_start: 0.9176 (mmm) cc_final: 0.8957 (mmm) REVERT: F 14 MET cc_start: 0.9090 (mmm) cc_final: 0.8877 (mmm) REVERT: F 80 MET cc_start: 0.9306 (mmm) cc_final: 0.8827 (mmm) REVERT: F 87 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9169 (p) REVERT: F 88 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8696 (ttmt) REVERT: F 93 GLU cc_start: 0.8497 (tp30) cc_final: 0.8267 (tp30) REVERT: F 117 PHE cc_start: 0.8939 (m-80) cc_final: 0.8415 (m-80) REVERT: F 151 MET cc_start: 0.8389 (ptp) cc_final: 0.7974 (pmm) REVERT: F 196 MET cc_start: 0.9001 (tpp) cc_final: 0.8573 (tpp) REVERT: F 520 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9162 (mppt) REVERT: F 580 MET cc_start: 0.9446 (mmp) cc_final: 0.9214 (mmp) outliers start: 125 outliers final: 66 residues processed: 327 average time/residue: 0.3512 time to fit residues: 189.0042 Evaluate side-chains 294 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 202 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 318 LEU 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 582 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 103 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 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 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU 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 221 TRP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS 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 528 VAL Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 494 GLU 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 103 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 381 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 E residue 548 ILE Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 1 MET 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 88 LYS 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 315 VAL Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 520 LYS Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 549 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 336 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 331 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 210 optimal weight: 0.0980 overall best weight: 4.0188 ------------------------------------------------------------------------------- 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 111 GLN ** 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** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 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 = 0.3525 r_free = 0.3525 target = 0.056152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037653 restraints weight = 154914.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.039115 restraints weight = 99409.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.040097 restraints weight = 74709.591| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 27362 Z= 0.250 Angle : 0.732 17.444 37058 Z= 0.368 Chirality : 0.045 0.306 4123 Planarity : 0.005 0.153 4799 Dihedral : 4.801 41.132 3625 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 4.74 % Allowed : 30.96 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3362 helix: 0.76 (0.13), residues: 1642 sheet: -0.89 (0.26), residues: 392 loop : -1.17 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 157 HIS 0.006 0.001 HIS A 245 PHE 0.024 0.002 PHE F 208 TYR 0.032 0.002 TYR C 463 ARG 0.015 0.001 ARG F 384 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 1177) hydrogen bonds : angle 4.93461 ( 3360) covalent geometry : bond 0.00536 (27362) covalent geometry : angle 0.73156 (37058) *********************** 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 337 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 198 time to evaluate : 3.052 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 14 MET cc_start: 0.7695 (ttm) cc_final: 0.7316 (ttt) REVERT: A 62 CYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8267 (t) REVERT: A 80 MET cc_start: 0.9215 (mmt) cc_final: 0.8759 (mmt) REVERT: A 106 MET cc_start: 0.7453 (mpp) cc_final: 0.6793 (mpp) REVERT: A 204 ASN cc_start: 0.5934 (t160) cc_final: 0.5621 (t0) REVERT: A 483 MET cc_start: 0.9196 (mmm) cc_final: 0.8884 (mmm) REVERT: A 498 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8043 (t80) REVERT: A 559 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9045 (tpp) REVERT: A 586 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: B 1 MET cc_start: 0.7306 (tmm) cc_final: 0.6972 (tmm) REVERT: B 80 MET cc_start: 0.9068 (mmt) cc_final: 0.8487 (mmt) REVERT: B 137 MET cc_start: 0.9219 (mtt) cc_final: 0.8655 (mpp) REVERT: B 151 MET cc_start: 0.8770 (mmm) cc_final: 0.8256 (mmm) REVERT: B 196 MET cc_start: 0.8891 (tpp) cc_final: 0.8513 (tpp) REVERT: B 305 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.5088 (mm) REVERT: B 339 TYR cc_start: 0.8061 (m-10) cc_final: 0.7780 (m-10) REVERT: B 422 GLU cc_start: 0.5657 (OUTLIER) cc_final: 0.4332 (pt0) REVERT: B 431 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: C 21 HIS cc_start: 0.9188 (m-70) cc_final: 0.8742 (m-70) REVERT: C 89 MET cc_start: 0.8291 (ptt) cc_final: 0.7980 (ptt) REVERT: C 221 TRP cc_start: 0.9523 (OUTLIER) cc_final: 0.9222 (t-100) REVERT: C 365 GLU cc_start: 0.9519 (OUTLIER) cc_final: 0.9113 (pp20) REVERT: C 404 MET cc_start: 0.8746 (tmm) cc_final: 0.8144 (tmm) REVERT: C 405 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: C 512 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8751 (m-10) REVERT: C 543 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.9205 (p) REVERT: C 559 MET cc_start: 0.9431 (tpt) cc_final: 0.8985 (tpp) REVERT: C 580 MET cc_start: 0.9257 (mmm) cc_final: 0.8945 (mmm) REVERT: D 80 MET cc_start: 0.9237 (mmt) cc_final: 0.8731 (mmt) REVERT: D 137 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8300 (mmm) REVERT: D 196 MET cc_start: 0.9252 (mmp) cc_final: 0.8846 (mmp) REVERT: D 208 PHE cc_start: 0.5737 (OUTLIER) cc_final: 0.4800 (m-80) REVERT: D 339 TYR cc_start: 0.8152 (m-10) cc_final: 0.7890 (m-10) REVERT: D 472 HIS cc_start: 0.8366 (m90) cc_final: 0.8016 (m-70) REVERT: D 498 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: D 580 MET cc_start: 0.8655 (ttp) cc_final: 0.8289 (ttp) REVERT: D 584 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9131 (ttmm) REVERT: E 6 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8711 (mt) REVERT: E 80 MET cc_start: 0.9283 (mmm) cc_final: 0.8914 (mmm) REVERT: E 106 MET cc_start: 0.7636 (mpp) cc_final: 0.6962 (mpp) REVERT: E 255 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9117 (mp) REVERT: E 463 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8042 (t80) REVERT: E 548 ILE cc_start: 0.9562 (OUTLIER) cc_final: 0.9318 (tp) REVERT: E 573 PHE cc_start: 0.9603 (OUTLIER) cc_final: 0.9272 (m-80) REVERT: E 580 MET cc_start: 0.9164 (mmm) cc_final: 0.8932 (mmm) REVERT: F 6 LEU cc_start: 0.9118 (mp) cc_final: 0.8819 (tp) REVERT: F 14 MET cc_start: 0.9030 (mmm) cc_final: 0.8804 (mmm) REVERT: F 80 MET cc_start: 0.9376 (mmm) cc_final: 0.8893 (mmm) REVERT: F 87 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9233 (p) REVERT: F 151 MET cc_start: 0.8480 (ptp) cc_final: 0.8204 (pmm) REVERT: F 194 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8752 (mmmm) REVERT: F 196 MET cc_start: 0.8954 (tpp) cc_final: 0.8578 (tpp) REVERT: F 520 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9221 (mppt) REVERT: F 586 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8246 (m-80) outliers start: 139 outliers final: 90 residues processed: 316 average time/residue: 0.3394 time to fit residues: 178.3221 Evaluate side-chains 307 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 192 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 466 HIS 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 573 PHE Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 217 ILE 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 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 431 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 221 TRP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 385 LYS 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 C residue 535 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 573 PHE 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 137 MET Chi-restraints excluded: chain D residue 178 PHE 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 322 LEU Chi-restraints excluded: chain D residue 347 SER 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 433 HIS Chi-restraints excluded: chain D residue 434 ASP 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 182 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 1 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 87 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 472 HIS Chi-restraints excluded: chain F residue 498 TYR Chi-restraints excluded: chain F residue 520 LYS Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 112 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 225 optimal weight: 20.0000 chunk 179 optimal weight: 8.9990 chunk 331 optimal weight: 0.0770 chunk 27 optimal weight: 0.0050 chunk 124 optimal weight: 10.0000 chunk 243 optimal weight: 0.0470 chunk 254 optimal weight: 2.9990 chunk 164 optimal weight: 0.0870 chunk 306 optimal weight: 2.9990 overall best weight: 0.6430 ------------------------------------------------------------------------------- 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 371 GLN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.058204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039410 restraints weight = 148678.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.040988 restraints weight = 93986.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.042047 restraints weight = 69883.960| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3407 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= 0.122 Angle : 0.705 15.971 37058 Z= 0.336 Chirality : 0.044 0.316 4123 Planarity : 0.005 0.151 4799 Dihedral : 4.684 41.061 3625 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.88 % Favored : 94.97 % Rotamer: Outliers : 3.52 % Allowed : 32.08 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3362 helix: 1.02 (0.13), residues: 1616 sheet: -0.71 (0.27), residues: 395 loop : -0.95 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 157 HIS 0.004 0.001 HIS E 466 PHE 0.031 0.001 PHE F 208 TYR 0.024 0.001 TYR A 463 ARG 0.009 0.001 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 1177) hydrogen bonds : angle 4.63206 ( 3360) covalent geometry : bond 0.00285 (27362) covalent geometry : angle 0.70453 (37058) *********************** 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 317 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 214 time to evaluate : 3.044 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: A 14 MET cc_start: 0.7555 (ttm) cc_final: 0.7112 (ttt) REVERT: A 62 CYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8151 (t) REVERT: A 80 MET cc_start: 0.9171 (mmt) cc_final: 0.8734 (mmt) REVERT: A 106 MET cc_start: 0.7286 (mpp) cc_final: 0.6430 (mpp) REVERT: A 204 ASN cc_start: 0.5971 (t160) cc_final: 0.5684 (t0) REVERT: A 483 MET cc_start: 0.9171 (mmm) cc_final: 0.8837 (mmm) REVERT: A 498 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 559 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8997 (tpp) REVERT: A 586 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 1 MET cc_start: 0.7455 (tmm) cc_final: 0.7158 (tmm) REVERT: B 80 MET cc_start: 0.9026 (mmt) cc_final: 0.8422 (mmt) REVERT: B 151 MET cc_start: 0.8722 (mmm) cc_final: 0.8303 (mmm) REVERT: B 196 MET cc_start: 0.8837 (tpp) cc_final: 0.8454 (tpp) REVERT: B 305 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.4879 (mm) REVERT: B 339 TYR cc_start: 0.8039 (m-10) cc_final: 0.7680 (m-10) REVERT: B 422 GLU cc_start: 0.5407 (OUTLIER) cc_final: 0.4085 (pt0) REVERT: B 431 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: C 21 HIS cc_start: 0.9126 (m-70) cc_final: 0.8832 (m90) REVERT: C 89 MET cc_start: 0.8070 (ptt) cc_final: 0.7720 (ptt) REVERT: C 221 TRP cc_start: 0.9416 (OUTLIER) cc_final: 0.9153 (t-100) REVERT: C 365 GLU cc_start: 0.9509 (OUTLIER) cc_final: 0.9085 (pp20) REVERT: C 404 MET cc_start: 0.8489 (tmm) cc_final: 0.7937 (tmm) REVERT: C 435 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8177 (t80) REVERT: C 483 MET cc_start: 0.9106 (mmm) cc_final: 0.8833 (mmm) REVERT: C 512 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8767 (m-10) REVERT: C 559 MET cc_start: 0.9378 (tpt) cc_final: 0.8993 (tpp) REVERT: C 580 MET cc_start: 0.9240 (mmm) cc_final: 0.8901 (mmm) REVERT: D 80 MET cc_start: 0.9221 (mmt) cc_final: 0.8698 (mmt) REVERT: D 137 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8372 (mmm) REVERT: D 196 MET cc_start: 0.9129 (mmp) cc_final: 0.8746 (mmp) REVERT: D 339 TYR cc_start: 0.8217 (m-10) cc_final: 0.7994 (m-10) REVERT: D 472 HIS cc_start: 0.8371 (m90) cc_final: 0.7993 (m-70) REVERT: D 580 MET cc_start: 0.8688 (ttp) cc_final: 0.8301 (ttp) REVERT: D 584 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9110 (ttmm) REVERT: E 80 MET cc_start: 0.9265 (mmm) cc_final: 0.9035 (mmm) REVERT: E 106 MET cc_start: 0.7611 (mpp) cc_final: 0.6974 (mpp) REVERT: E 255 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9105 (mt) REVERT: E 463 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7992 (t80) REVERT: E 483 MET cc_start: 0.9089 (mmm) cc_final: 0.8803 (mmm) REVERT: E 548 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9091 (tp) REVERT: E 552 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9307 (mm) REVERT: E 559 MET cc_start: 0.9176 (tpt) cc_final: 0.8933 (tpp) REVERT: E 573 PHE cc_start: 0.9526 (OUTLIER) cc_final: 0.9255 (m-80) REVERT: E 580 MET cc_start: 0.9163 (mmm) cc_final: 0.8945 (mmm) REVERT: F 80 MET cc_start: 0.9331 (mmm) cc_final: 0.8836 (mmm) REVERT: F 87 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9175 (p) REVERT: F 194 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8783 (mmmm) REVERT: F 520 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.9141 (mppt) REVERT: F 580 MET cc_start: 0.9324 (mmp) cc_final: 0.9120 (mmp) outliers start: 103 outliers final: 67 residues processed: 299 average time/residue: 0.3239 time to fit residues: 164.0421 Evaluate side-chains 292 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 204 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 431 TYR 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 475 ASN 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 65 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 305 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 431 TYR Chi-restraints excluded: chain B residue 518 LEU 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 221 TRP Chi-restraints excluded: chain C residue 322 LEU 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 405 GLN 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 528 VAL Chi-restraints excluded: chain C residue 535 ILE 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 137 MET Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 219 GLN 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 44 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 463 TYR Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 1 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 87 THR Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 520 LYS Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 116 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 326 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 475 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** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.057559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038854 restraints weight = 149806.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.040388 restraints weight = 95335.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041427 restraints weight = 71208.351| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 27362 Z= 0.144 Angle : 0.690 16.893 37058 Z= 0.335 Chirality : 0.044 0.315 4123 Planarity : 0.005 0.152 4799 Dihedral : 4.649 40.886 3625 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.09 % Favored : 94.77 % Rotamer: Outliers : 3.48 % Allowed : 32.25 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3362 helix: 1.00 (0.13), residues: 1621 sheet: -0.70 (0.27), residues: 386 loop : -0.93 (0.18), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 157 HIS 0.003 0.001 HIS A 466 PHE 0.028 0.001 PHE F 208 TYR 0.024 0.001 TYR A 463 ARG 0.009 0.000 ARG D 384 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 1177) hydrogen bonds : angle 4.64938 ( 3360) covalent geometry : bond 0.00334 (27362) covalent geometry : angle 0.69021 (37058) ********************** 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 312 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 210 time to evaluate : 3.186 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: A 14 MET cc_start: 0.7583 (ttm) cc_final: 0.7137 (ttt) REVERT: A 62 CYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8191 (t) REVERT: A 80 MET cc_start: 0.9208 (mmt) cc_final: 0.8772 (mmt) REVERT: A 106 MET cc_start: 0.7335 (mpp) cc_final: 0.6448 (mpp) REVERT: A 204 ASN cc_start: 0.5948 (t160) cc_final: 0.5663 (t0) REVERT: A 483 MET cc_start: 0.9145 (mmm) cc_final: 0.8934 (mmm) REVERT: A 498 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 559 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9004 (tpp) REVERT: A 582 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9529 (tt) REVERT: A 586 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: B 1 MET cc_start: 0.7467 (tmm) cc_final: 0.7168 (tmm) REVERT: B 80 MET cc_start: 0.9032 (mmt) cc_final: 0.8424 (mmt) REVERT: B 151 MET cc_start: 0.8794 (mmm) cc_final: 0.8258 (mmm) REVERT: B 196 MET cc_start: 0.8859 (tpp) cc_final: 0.8490 (tpp) REVERT: B 305 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.4942 (mm) REVERT: B 339 TYR cc_start: 0.8087 (m-10) cc_final: 0.7727 (m-10) REVERT: B 422 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.4152 (pt0) REVERT: B 431 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: C 21 HIS cc_start: 0.9150 (m-70) cc_final: 0.8863 (m90) REVERT: C 89 MET cc_start: 0.8201 (ptt) cc_final: 0.7889 (ptt) REVERT: C 106 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7463 (ptp) REVERT: C 221 TRP cc_start: 0.9459 (OUTLIER) cc_final: 0.9172 (t-100) REVERT: C 365 GLU cc_start: 0.9506 (OUTLIER) cc_final: 0.9077 (pp20) REVERT: C 404 MET cc_start: 0.8539 (tmm) cc_final: 0.7884 (tmm) REVERT: C 405 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: C 435 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8164 (t80) REVERT: C 483 MET cc_start: 0.9068 (mmm) cc_final: 0.8777 (mmm) REVERT: C 512 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8803 (m-10) REVERT: C 559 MET cc_start: 0.9392 (tpt) cc_final: 0.9006 (tpp) REVERT: C 580 MET cc_start: 0.9209 (mmm) cc_final: 0.8874 (mmm) REVERT: D 80 MET cc_start: 0.9241 (mmt) cc_final: 0.8718 (mmt) REVERT: D 137 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8365 (mmm) REVERT: D 196 MET cc_start: 0.9165 (mmp) cc_final: 0.8784 (mmp) REVERT: D 339 TYR cc_start: 0.8223 (m-10) cc_final: 0.7994 (m-10) REVERT: D 472 HIS cc_start: 0.8380 (m90) cc_final: 0.7999 (m-70) REVERT: D 580 MET cc_start: 0.8682 (ttp) cc_final: 0.8294 (ttp) REVERT: D 584 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9114 (ttmm) REVERT: E 80 MET cc_start: 0.9246 (mmm) cc_final: 0.9007 (mmm) REVERT: E 106 MET cc_start: 0.7631 (mpp) cc_final: 0.7011 (mpp) REVERT: E 255 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9109 (mt) REVERT: E 463 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8003 (t80) REVERT: E 495 MET cc_start: 0.8663 (ptm) cc_final: 0.7653 (ppp) REVERT: E 498 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.8937 (t80) REVERT: E 548 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9104 (tp) REVERT: E 552 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9305 (mm) REVERT: E 559 MET cc_start: 0.9133 (tpt) cc_final: 0.8831 (tpp) REVERT: E 573 PHE cc_start: 0.9549 (OUTLIER) cc_final: 0.9318 (m-80) REVERT: E 580 MET cc_start: 0.9163 (mmm) cc_final: 0.8934 (mmm) REVERT: F 6 LEU cc_start: 0.9047 (mp) cc_final: 0.8800 (mp) REVERT: F 14 MET cc_start: 0.8965 (mmm) cc_final: 0.8530 (mmt) REVERT: F 80 MET cc_start: 0.9330 (mmm) cc_final: 0.8834 (mmm) REVERT: F 87 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9153 (p) REVERT: F 88 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8664 (mtmt) REVERT: F 194 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8782 (mmmm) REVERT: F 520 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9178 (mppt) REVERT: F 580 MET cc_start: 0.9372 (mmp) cc_final: 0.9157 (mmp) REVERT: F 586 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8195 (m-80) outliers start: 102 outliers final: 67 residues processed: 294 average time/residue: 0.3998 time to fit residues: 195.5061 Evaluate side-chains 299 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 205 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 466 HIS 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 582 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 305 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 431 TYR Chi-restraints excluded: chain B residue 518 LEU 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 322 LEU 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 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 528 VAL Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 569 ILE 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 137 MET Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 494 GLU 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 103 ILE Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 381 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 E residue 548 ILE Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 586 PHE Chi-restraints excluded: chain F residue 1 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 87 THR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 208 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 356 ASN Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 399 LEU Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 520 LYS Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 586 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 238 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 115 optimal weight: 0.0870 chunk 225 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 257 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- 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 475 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.058282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039561 restraints weight = 148158.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.041121 restraints weight = 93654.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.042191 restraints weight = 69742.514| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 27362 Z= 0.120 Angle : 0.697 16.587 37058 Z= 0.333 Chirality : 0.044 0.302 4123 Planarity : 0.005 0.150 4799 Dihedral : 4.576 40.673 3625 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.76 % Favored : 95.09 % Rotamer: Outliers : 3.14 % Allowed : 32.66 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3362 helix: 1.05 (0.13), residues: 1618 sheet: -0.62 (0.27), residues: 399 loop : -0.92 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 157 HIS 0.003 0.001 HIS E 466 PHE 0.030 0.001 PHE F 208 TYR 0.021 0.001 TYR A 463 ARG 0.008 0.000 ARG F 468 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1177) hydrogen bonds : angle 4.53867 ( 3360) covalent geometry : bond 0.00284 (27362) covalent geometry : angle 0.69655 (37058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10056.28 seconds wall clock time: 176 minutes 53.88 seconds (10613.88 seconds total)