Starting phenix.real_space_refine on Wed Mar 4 12:52:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlf_22242/03_2026/6xlf_22242.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlf_22242/03_2026/6xlf_22242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xlf_22242/03_2026/6xlf_22242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlf_22242/03_2026/6xlf_22242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlf_22242/03_2026/6xlf_22242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlf_22242/03_2026/6xlf_22242.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 8721 2.51 5 N 2247 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 185 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13653 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4923 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 20, 'TRANS': 588} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4930 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 20, 'TRANS': 589} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2544 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.06, per 1000 atoms: 0.22 Number of scatterers: 13653 At special positions: 0 Unit cell: (105.9, 110.136, 133.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 25 16.00 P 6 15.00 Mg 2 11.99 O 2650 8.00 N 2247 7.00 C 8721 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 432.5 milliseconds 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 40.5% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 4.285A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 50 removed outlier: 4.059A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.550A pdb=" N SER A 126 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.841A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.629A pdb=" N TYR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.535A pdb=" N PHE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.708A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.735A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.577A pdb=" N VAL A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 removed outlier: 4.363A pdb=" N LEU A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.021A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 510 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 3.974A pdb=" N ALA A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 removed outlier: 3.814A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.685A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 627 " --> pdb=" O LYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.563A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.902A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.825A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 50 removed outlier: 4.162A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.777A pdb=" N ILE B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.858A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.527A pdb=" N SER B 126 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.760A pdb=" N TYR B 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 195 removed outlier: 3.764A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.635A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 406 removed outlier: 4.059A pdb=" N VAL B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.676A pdb=" N ASP B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.637A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.784A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 removed outlier: 3.521A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.543A pdb=" N VAL B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 removed outlier: 4.438A pdb=" N LEU B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.557A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 removed outlier: 3.593A pdb=" N LYS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 555 removed outlier: 3.538A pdb=" N ASP B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.558A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 627 removed outlier: 3.693A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 651 removed outlier: 3.521A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.870A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.676A pdb=" N TRP C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 removed outlier: 3.530A pdb=" N GLN C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.711A pdb=" N SER C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU C 122 " --> pdb=" O GLU C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 122' Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.636A pdb=" N ILE C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 150 removed outlier: 3.539A pdb=" N LYS C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.666A pdb=" N ASN C 169 " --> pdb=" O TYR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.774A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 removed outlier: 3.991A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.503A pdb=" N GLU C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.817A pdb=" N ILE C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.511A pdb=" N GLU D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 removed outlier: 4.182A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.618A pdb=" N VAL D 328 " --> pdb=" O GLU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.699A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.525A pdb=" N GLU A 4 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR B 210 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.666A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 removed outlier: 4.145A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR A 210 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN C 207 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.738A pdb=" N ALA A 315 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 307 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 339 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 452 removed outlier: 3.947A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.330A pdb=" N LYS A 560 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE A 611 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 562 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.617A pdb=" N PHE B 313 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.808A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.358A pdb=" N LYS B 560 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 611 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL B 562 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 15 Processing sheet with id=AB3, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.995A pdb=" N LYS C 43 " --> pdb=" O HIS C 78 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS C 78 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS C 45 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLU C 76 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL C 47 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU C 74 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 213 through 218 removed outlier: 5.299A pdb=" N THR C 214 " --> pdb=" O GLY C 319 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.746A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 213 through 218 removed outlier: 7.097A pdb=" N ILE D 216 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR D 318 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU D 218 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS D 316 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS D 280 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS D 275 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL D 282 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 272 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 222 572 hydrogen bonds defined for protein. 1584 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: 2.30 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4425 1.34 - 1.46: 2933 1.46 - 1.58: 6491 1.58 - 1.69: 10 1.69 - 1.81: 48 Bond restraints: 13907 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.695 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 13902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 18720 3.44 - 6.88: 36 6.88 - 10.33: 5 10.33 - 13.77: 2 13.77 - 17.21: 2 Bond angle restraints: 18765 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.74 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.92 17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" N VAL B 163 " pdb=" CA VAL B 163 " pdb=" C VAL B 163 " ideal model delta sigma weight residual 113.20 109.63 3.57 9.60e-01 1.09e+00 1.38e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.57 10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.62 10.46 3.00e+00 1.11e-01 1.22e+01 ... (remaining 18760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.74: 8046 20.74 - 41.48: 365 41.48 - 62.23: 65 62.23 - 82.97: 18 82.97 - 103.71: 13 Dihedral angle restraints: 8507 sinusoidal: 3588 harmonic: 4919 Sorted by residual: dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -68.56 103.71 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CB GLU B 644 " pdb=" CG GLU B 644 " pdb=" CD GLU B 644 " pdb=" OE1 GLU B 644 " ideal model delta sinusoidal sigma weight residual 0.00 89.41 -89.41 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" O1B ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PB ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sinusoidal sigma weight residual 35.15 -54.07 89.22 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1840 0.057 - 0.114: 230 0.114 - 0.171: 19 0.171 - 0.228: 0 0.228 - 0.285: 2 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE C 154 " pdb=" N ILE C 154 " pdb=" C ILE C 154 " pdb=" CB ILE C 154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2088 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 355 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 224 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO C 225 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 320 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO C 321 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " -0.014 5.00e-02 4.00e+02 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.72: 538 2.72 - 3.32: 15129 3.32 - 3.93: 26520 3.93 - 4.53: 36280 4.53 - 5.14: 56921 Nonbonded interactions: 135388 Sorted by model distance: nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.115 2.170 nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 2.115 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.121 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.132 2.170 nonbonded pdb=" O3G ANP B 801 " pdb="MG MG B 802 " model vdw 2.163 2.170 ... (remaining 135383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 3 through 212 or resid 259 through 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.360 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 0.144 13908 Z= 0.151 Angle : 0.474 17.210 18765 Z= 0.234 Chirality : 0.040 0.285 2091 Planarity : 0.002 0.029 2395 Dihedral : 12.833 103.711 5305 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.20 % Allowed : 5.51 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.16), residues: 1658 helix: -3.56 (0.11), residues: 604 sheet: -1.50 (0.26), residues: 349 loop : -2.42 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 32 TYR 0.003 0.000 TYR A 456 PHE 0.003 0.000 PHE A 660 TRP 0.005 0.000 TRP D 242 HIS 0.001 0.000 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00296 (13907) covalent geometry : angle 0.47357 (18765) hydrogen bonds : bond 0.28201 ( 558) hydrogen bonds : angle 8.92147 ( 1584) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 352 time to evaluate : 0.395 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS B 211 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 LYS cc_start: 0.6151 (mttt) cc_final: 0.5898 (ttpt) REVERT: C 162 LYS cc_start: 0.6304 (mttp) cc_final: 0.5857 (mmtp) REVERT: C 329 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.7213 (ttm-80) REVERT: D 217 TYR cc_start: 0.6840 (t80) cc_final: 0.6551 (t80) outliers start: 18 outliers final: 11 residues processed: 366 average time/residue: 0.1455 time to fit residues: 72.5525 Evaluate side-chains 194 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 278 ASP Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 119 GLN A 135 GLN A 181 GLN A 380 GLN A 409 GLN A 430 GLN A 584 ASN B 55 GLN B 135 GLN B 276 ASN C 267 ASN D 284 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102950 restraints weight = 24733.291| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.24 r_work: 0.3264 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13908 Z= 0.222 Angle : 0.591 5.761 18765 Z= 0.311 Chirality : 0.046 0.168 2091 Planarity : 0.004 0.044 2395 Dihedral : 6.101 81.599 1873 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.59 % Allowed : 11.36 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1658 helix: -1.32 (0.18), residues: 620 sheet: -1.26 (0.26), residues: 373 loop : -1.54 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 133 TYR 0.015 0.002 TYR C 217 PHE 0.024 0.002 PHE A 104 TRP 0.018 0.002 TRP D 285 HIS 0.005 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00519 (13907) covalent geometry : angle 0.59114 (18765) hydrogen bonds : bond 0.03908 ( 558) hydrogen bonds : angle 5.32867 ( 1584) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7742 (m-30) cc_final: 0.7426 (m-30) REVERT: A 310 GLN cc_start: 0.7682 (pm20) cc_final: 0.7114 (pm20) REVERT: A 585 MET cc_start: 0.8815 (tpt) cc_final: 0.7853 (tpt) REVERT: A 589 MET cc_start: 0.8647 (mmm) cc_final: 0.8383 (mmp) REVERT: B 55 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7259 (mm-40) REVERT: B 314 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7393 (mtp180) REVERT: B 636 LYS cc_start: 0.7716 (mmmt) cc_final: 0.7283 (tttp) REVERT: D 228 GLU cc_start: 0.7576 (mp0) cc_final: 0.7277 (mp0) outliers start: 39 outliers final: 21 residues processed: 209 average time/residue: 0.1271 time to fit residues: 38.1476 Evaluate side-chains 168 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS C 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105593 restraints weight = 24649.791| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.34 r_work: 0.3294 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13908 Z= 0.103 Angle : 0.464 5.206 18765 Z= 0.244 Chirality : 0.042 0.159 2091 Planarity : 0.003 0.045 2395 Dihedral : 5.571 78.047 1853 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.93 % Allowed : 14.02 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1658 helix: -0.27 (0.21), residues: 617 sheet: -0.96 (0.27), residues: 361 loop : -1.20 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 666 TYR 0.016 0.001 TYR C 230 PHE 0.014 0.001 PHE B 313 TRP 0.010 0.001 TRP D 285 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00237 (13907) covalent geometry : angle 0.46365 (18765) hydrogen bonds : bond 0.03224 ( 558) hydrogen bonds : angle 4.85428 ( 1584) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7849 (m-30) cc_final: 0.7530 (m-30) REVERT: A 310 GLN cc_start: 0.7583 (pm20) cc_final: 0.7256 (pm20) REVERT: A 585 MET cc_start: 0.8802 (tpt) cc_final: 0.7968 (tpt) REVERT: A 639 THR cc_start: 0.8944 (m) cc_final: 0.8611 (p) REVERT: B 636 LYS cc_start: 0.7758 (mmmt) cc_final: 0.7435 (tttp) REVERT: B 666 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.7494 (mtm110) REVERT: C 275 CYS cc_start: 0.8530 (p) cc_final: 0.8158 (p) REVERT: D 217 TYR cc_start: 0.6952 (t80) cc_final: 0.6600 (t80) outliers start: 29 outliers final: 18 residues processed: 195 average time/residue: 0.1186 time to fit residues: 33.3320 Evaluate side-chains 164 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.121278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100177 restraints weight = 24517.280| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.41 r_work: 0.3190 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13908 Z= 0.147 Angle : 0.496 7.728 18765 Z= 0.260 Chirality : 0.043 0.164 2091 Planarity : 0.003 0.046 2395 Dihedral : 5.588 78.123 1852 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.79 % Allowed : 14.22 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.21), residues: 1658 helix: 0.16 (0.22), residues: 618 sheet: -0.96 (0.27), residues: 370 loop : -0.90 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 314 TYR 0.017 0.001 TYR A 203 PHE 0.013 0.001 PHE B 104 TRP 0.009 0.001 TRP C 317 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00346 (13907) covalent geometry : angle 0.49623 (18765) hydrogen bonds : bond 0.03098 ( 558) hydrogen bonds : angle 4.78002 ( 1584) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7969 (m-30) cc_final: 0.7625 (m-30) REVERT: A 585 MET cc_start: 0.9000 (tpt) cc_final: 0.8214 (tpt) REVERT: B 314 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7267 (mtp180) REVERT: B 636 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7556 (tttp) REVERT: B 665 ASN cc_start: 0.8398 (m-40) cc_final: 0.8166 (m-40) REVERT: C 275 CYS cc_start: 0.8658 (p) cc_final: 0.8284 (p) REVERT: D 294 PHE cc_start: 0.8227 (m-80) cc_final: 0.7878 (m-80) outliers start: 42 outliers final: 31 residues processed: 190 average time/residue: 0.1164 time to fit residues: 32.7587 Evaluate side-chains 172 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.0170 chunk 75 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098148 restraints weight = 24640.273| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.15 r_work: 0.3168 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13908 Z= 0.173 Angle : 0.514 6.256 18765 Z= 0.270 Chirality : 0.044 0.158 2091 Planarity : 0.003 0.045 2395 Dihedral : 5.728 77.631 1852 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.06 % Allowed : 14.82 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1658 helix: 0.29 (0.22), residues: 620 sheet: -0.84 (0.28), residues: 362 loop : -0.90 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 32 TYR 0.011 0.001 TYR C 230 PHE 0.016 0.001 PHE A 104 TRP 0.010 0.001 TRP C 317 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00413 (13907) covalent geometry : angle 0.51421 (18765) hydrogen bonds : bond 0.03174 ( 558) hydrogen bonds : angle 4.80146 ( 1584) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.482 Fit side-chains REVERT: A 40 ASP cc_start: 0.8080 (m-30) cc_final: 0.7813 (m-30) REVERT: A 585 MET cc_start: 0.9124 (tpt) cc_final: 0.8445 (tpt) REVERT: A 636 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8033 (ttmm) REVERT: B 314 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7609 (mtp180) REVERT: B 349 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6346 (mm-30) REVERT: B 636 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7715 (tttp) REVERT: B 665 ASN cc_start: 0.8506 (m-40) cc_final: 0.8288 (m-40) REVERT: C 275 CYS cc_start: 0.8787 (p) cc_final: 0.8416 (p) REVERT: C 312 LYS cc_start: 0.8393 (tttt) cc_final: 0.8175 (ttpt) REVERT: D 284 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8769 (m170) outliers start: 46 outliers final: 31 residues processed: 190 average time/residue: 0.1123 time to fit residues: 31.6937 Evaluate side-chains 174 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 100 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS C 94 ASN D 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097030 restraints weight = 24717.132| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.21 r_work: 0.3149 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13908 Z= 0.201 Angle : 0.545 8.897 18765 Z= 0.284 Chirality : 0.045 0.160 2091 Planarity : 0.003 0.046 2395 Dihedral : 5.809 75.658 1852 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.86 % Allowed : 16.28 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1658 helix: 0.29 (0.21), residues: 615 sheet: -0.86 (0.28), residues: 353 loop : -0.89 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 32 TYR 0.011 0.001 TYR C 230 PHE 0.015 0.001 PHE A 104 TRP 0.014 0.001 TRP B 581 HIS 0.008 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00481 (13907) covalent geometry : angle 0.54494 (18765) hydrogen bonds : bond 0.03284 ( 558) hydrogen bonds : angle 4.83838 ( 1584) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8135 (m-30) cc_final: 0.7927 (m-30) REVERT: A 585 MET cc_start: 0.9151 (tpt) cc_final: 0.8459 (tpt) REVERT: A 636 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7980 (ttmm) REVERT: B 314 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7615 (mtp180) REVERT: B 349 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6981 (mm-30) REVERT: B 636 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7647 (tttp) REVERT: C 130 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5704 (pm20) REVERT: C 275 CYS cc_start: 0.8791 (p) cc_final: 0.8409 (p) REVERT: D 284 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8772 (m170) outliers start: 43 outliers final: 32 residues processed: 186 average time/residue: 0.1106 time to fit residues: 30.1340 Evaluate side-chains 178 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 71 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 578 GLN ** C 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 = 0.3623 r_free = 0.3623 target = 0.121579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100997 restraints weight = 24486.709| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.20 r_work: 0.3208 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13908 Z= 0.105 Angle : 0.474 7.689 18765 Z= 0.248 Chirality : 0.043 0.157 2091 Planarity : 0.003 0.044 2395 Dihedral : 5.571 75.305 1851 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.59 % Allowed : 16.94 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1658 helix: 0.47 (0.22), residues: 623 sheet: -0.80 (0.28), residues: 355 loop : -0.78 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.012 0.001 TYR C 230 PHE 0.012 0.001 PHE A 104 TRP 0.010 0.001 TRP B 581 HIS 0.010 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00246 (13907) covalent geometry : angle 0.47418 (18765) hydrogen bonds : bond 0.02831 ( 558) hydrogen bonds : angle 4.60093 ( 1584) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.418 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8146 (m-30) cc_final: 0.7785 (m-30) REVERT: A 585 MET cc_start: 0.9104 (tpt) cc_final: 0.8575 (tpt) REVERT: B 314 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7551 (mtp180) REVERT: B 636 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7570 (tttp) REVERT: C 130 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5882 (pm20) REVERT: C 275 CYS cc_start: 0.8766 (p) cc_final: 0.8383 (p) REVERT: C 317 TRP cc_start: 0.8920 (t60) cc_final: 0.8426 (t60) REVERT: D 217 TYR cc_start: 0.7604 (t80) cc_final: 0.7217 (t80) REVERT: D 284 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.8715 (m170) outliers start: 39 outliers final: 31 residues processed: 198 average time/residue: 0.1072 time to fit residues: 31.0719 Evaluate side-chains 175 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 578 GLN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 155 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102024 restraints weight = 24391.625| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.93 r_work: 0.3213 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13908 Z= 0.120 Angle : 0.491 8.217 18765 Z= 0.257 Chirality : 0.043 0.160 2091 Planarity : 0.003 0.044 2395 Dihedral : 5.575 76.225 1851 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.59 % Allowed : 17.34 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1658 helix: 0.55 (0.22), residues: 623 sheet: -0.73 (0.28), residues: 351 loop : -0.81 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.018 0.001 TYR C 217 PHE 0.011 0.001 PHE B 104 TRP 0.011 0.001 TRP B 581 HIS 0.009 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00283 (13907) covalent geometry : angle 0.49093 (18765) hydrogen bonds : bond 0.02860 ( 558) hydrogen bonds : angle 4.58422 ( 1584) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.531 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8149 (m-30) cc_final: 0.7863 (m-30) REVERT: A 585 MET cc_start: 0.9071 (tpt) cc_final: 0.8485 (tpt) REVERT: A 636 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8004 (ttmm) REVERT: B 314 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7558 (mtp180) REVERT: B 636 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7611 (tttp) REVERT: C 127 ILE cc_start: 0.4972 (OUTLIER) cc_final: 0.4703 (mp) REVERT: C 130 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5901 (pm20) REVERT: C 275 CYS cc_start: 0.8716 (p) cc_final: 0.8304 (p) REVERT: C 317 TRP cc_start: 0.8899 (t60) cc_final: 0.8423 (t60) REVERT: D 217 TYR cc_start: 0.7572 (t80) cc_final: 0.7265 (t80) REVERT: D 284 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.8695 (m170) outliers start: 39 outliers final: 31 residues processed: 178 average time/residue: 0.1039 time to fit residues: 28.0842 Evaluate side-chains 180 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 578 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.120707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099932 restraints weight = 24863.621| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.22 r_work: 0.3215 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13908 Z= 0.145 Angle : 0.509 8.163 18765 Z= 0.267 Chirality : 0.044 0.161 2091 Planarity : 0.003 0.044 2395 Dihedral : 5.589 71.366 1851 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.72 % Allowed : 17.54 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1658 helix: 0.55 (0.22), residues: 621 sheet: -0.71 (0.28), residues: 351 loop : -0.77 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.010 0.001 TYR C 230 PHE 0.013 0.001 PHE C 302 TRP 0.010 0.001 TRP B 581 HIS 0.007 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00345 (13907) covalent geometry : angle 0.50903 (18765) hydrogen bonds : bond 0.02975 ( 558) hydrogen bonds : angle 4.62441 ( 1584) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.577 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8211 (m-30) cc_final: 0.7890 (m-30) REVERT: A 585 MET cc_start: 0.8956 (tpt) cc_final: 0.8265 (tpt) REVERT: A 636 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8012 (ttmm) REVERT: B 11 GLU cc_start: 0.8322 (tp30) cc_final: 0.8118 (tp30) REVERT: B 314 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7674 (mtp180) REVERT: B 383 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8429 (mmtp) REVERT: B 636 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7655 (tttp) REVERT: C 127 ILE cc_start: 0.5120 (OUTLIER) cc_final: 0.4832 (mp) REVERT: C 130 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5798 (pm20) REVERT: C 275 CYS cc_start: 0.8708 (p) cc_final: 0.8299 (p) REVERT: C 317 TRP cc_start: 0.8929 (t60) cc_final: 0.8460 (t60) REVERT: D 217 TYR cc_start: 0.7609 (t80) cc_final: 0.7177 (t80) REVERT: D 284 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.7617 (m-70) outliers start: 41 outliers final: 33 residues processed: 178 average time/residue: 0.1067 time to fit residues: 28.7649 Evaluate side-chains 175 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 578 GLN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 117 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 578 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101317 restraints weight = 24573.627| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.21 r_work: 0.3238 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13908 Z= 0.111 Angle : 0.488 8.337 18765 Z= 0.255 Chirality : 0.043 0.161 2091 Planarity : 0.003 0.043 2395 Dihedral : 5.505 71.210 1851 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.59 % Allowed : 17.61 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1658 helix: 0.63 (0.22), residues: 622 sheet: -0.62 (0.28), residues: 351 loop : -0.75 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.011 0.001 TYR C 230 PHE 0.011 0.001 PHE B 104 TRP 0.009 0.001 TRP C 242 HIS 0.007 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00259 (13907) covalent geometry : angle 0.48784 (18765) hydrogen bonds : bond 0.02793 ( 558) hydrogen bonds : angle 4.52857 ( 1584) Misc. bond : bond 0.00027 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.401 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 585 MET cc_start: 0.8925 (tpt) cc_final: 0.8265 (tpt) REVERT: A 636 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7993 (ttmm) REVERT: B 11 GLU cc_start: 0.8273 (tp30) cc_final: 0.7965 (tp30) REVERT: B 314 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7627 (mtp180) REVERT: B 383 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8396 (mmtp) REVERT: B 636 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7657 (tttp) REVERT: C 127 ILE cc_start: 0.5143 (OUTLIER) cc_final: 0.4843 (mp) REVERT: C 130 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5809 (pm20) REVERT: C 275 CYS cc_start: 0.8671 (p) cc_final: 0.8263 (p) REVERT: C 317 TRP cc_start: 0.8896 (t60) cc_final: 0.8397 (t60) REVERT: D 217 TYR cc_start: 0.7558 (t80) cc_final: 0.7192 (t80) REVERT: D 284 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.7611 (m-70) outliers start: 39 outliers final: 33 residues processed: 177 average time/residue: 0.1100 time to fit residues: 29.0489 Evaluate side-chains 173 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 578 GLN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 2 optimal weight: 0.0670 chunk 27 optimal weight: 0.0040 chunk 158 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.7732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102099 restraints weight = 24678.070| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.21 r_work: 0.3251 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13908 Z= 0.102 Angle : 0.480 6.880 18765 Z= 0.252 Chirality : 0.043 0.160 2091 Planarity : 0.003 0.043 2395 Dihedral : 5.444 70.879 1851 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.52 % Allowed : 18.14 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1658 helix: 0.60 (0.22), residues: 626 sheet: -0.53 (0.28), residues: 351 loop : -0.71 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.010 0.001 TYR C 230 PHE 0.012 0.001 PHE A 104 TRP 0.009 0.001 TRP B 581 HIS 0.006 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00237 (13907) covalent geometry : angle 0.48049 (18765) hydrogen bonds : bond 0.02735 ( 558) hydrogen bonds : angle 4.47256 ( 1584) Misc. bond : bond 0.00023 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3054.56 seconds wall clock time: 53 minutes 5.41 seconds (3185.41 seconds total)