Starting phenix.real_space_refine on Sat Sep 12 04:34:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xlf_22242/09_2026/6xlf_22242.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlf_22242/09_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_22242/09_2026/6xlf_22242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlf_22242/09_2026/6xlf_22242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlf_22242/09_2026/6xlf_22242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlf_22242/09_2026/6xlf_22242.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xlf_22242/09_2026/6xlf_22242.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xlf_22242/09_2026/6xlf_22242.cif" } 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-2.2.1-6174/lib/python3.11/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: 3.09, per 1000 atoms: 0.23 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: 1.04 Conformation dependent library (CDL) restraints added in 543.1 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: 0.47 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: 2.41 Time building geometry restraints manager: 1.42 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: 8006 20.74 - 41.48: 351 41.48 - 62.23: 65 62.23 - 82.97: 17 82.97 - 103.71: 12 Dihedral angle restraints: 8451 sinusoidal: 3532 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 8448 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: 1.090 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.310 Find NCS groups from input model: 0.350 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 12.703 103.711 5249 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/Z covalent geometry : bond 0.00296 / 0.15 (13907) covalent geometry : angle 0.47357 / 0.23 (18765) hydrogen bonds : bond 0.28201 / 18.62 ( 558) hydrogen bonds : angle 8.92147 / 6.22 ( 1584) Misc. bond : bond 0.00011 / 0.01 ( 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 : 0.396 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: 0.1472 time to fit residues: 74.3581 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 : 0.545 ------------------------------------------------------------------------------- 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... 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 = 0.3668 r_free = 0.3668 target = 0.123748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.102877 restraints weight = 24725.040| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.24 r_work: 0.3261 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13908 Z= 0.227 Angle : 0.592 5.788 18765 Z= 0.314 Chirality : 0.046 0.177 2091 Planarity : 0.004 0.044 2395 Dihedral : 5.353 82.323 1817 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.66 % Allowed : 11.43 % Favored : 85.91 % 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: -2.25 (0.19), residues: 1658 helix: -1.36 (0.18), residues: 620 sheet: -1.28 (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 0.014 0.002 TYR C 217 PHE 0.023 0.002 PHE A 104 TRP 0.019 0.002 TRP D 285 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (13907) covalent geometry : angle 0.59237 / 0.31 (18765) hydrogen bonds : bond 0.03922 / 2.56 ( 558) hydrogen bonds : angle 5.34738 / 3.75 ( 1584) Misc. bond : bond 0.00018 / 0.01 ( 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 222 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.563 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS B 211 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7929 (m-30) cc_final: 0.7643 (m-30) REVERT: A 179 ASP cc_start: 0.8275 (m-30) cc_final: 0.8008 (t0) REVERT: A 310 GLN cc_start: 0.7840 (pm20) cc_final: 0.7248 (pm20) REVERT: A 532 GLU cc_start: 0.7659 (tt0) cc_final: 0.7424 (tt0) REVERT: A 585 MET cc_start: 0.8911 (tpt) cc_final: 0.7881 (tpt) REVERT: A 589 MET cc_start: 0.8883 (mmm) cc_final: 0.8635 (mmp) REVERT: B 55 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7361 (mm-40) REVERT: B 426 HIS cc_start: 0.8847 (t70) cc_final: 0.8625 (t-170) REVERT: B 636 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7324 (tttp) REVERT: C 275 CYS cc_start: 0.8696 (p) cc_final: 0.8376 (p) REVERT: D 228 GLU cc_start: 0.7789 (mp0) cc_final: 0.7458 (mp0) outliers start: 40 outliers final: 22 residues processed: 213 average time/residue: 0.1293 time to fit residues: 39.9919 Evaluate side-chains 171 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 379 LEU 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 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: 0.7980 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.126183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105596 restraints weight = 24931.135| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.39 r_work: 0.3282 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13908 Z= 0.109 Angle : 0.468 5.249 18765 Z= 0.246 Chirality : 0.043 0.159 2091 Planarity : 0.003 0.045 2395 Dihedral : 4.746 77.362 1801 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.06 % Allowed : 14.09 % Favored : 83.85 % 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: -1.29 (0.20), residues: 1658 helix: -0.28 (0.21), residues: 614 sheet: -0.94 (0.27), residues: 360 loop : -1.19 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 666 TYR 0.017 0.001 TYR C 230 PHE 0.014 0.001 PHE B 104 TRP 0.010 0.001 TRP D 285 HIS 0.002 0.001 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13907) covalent geometry : angle 0.46780 / 0.25 (18765) hydrogen bonds : bond 0.03274 / 2.15 ( 558) hydrogen bonds : angle 4.87980 / 3.41 ( 1584) Misc. bond : bond 0.00029 / 0.02 ( 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 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.510 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: 0.7835 (m-30) cc_final: 0.7526 (m-30) REVERT: A 310 GLN cc_start: 0.7610 (pm20) cc_final: 0.7312 (pm20) REVERT: A 532 GLU cc_start: 0.7536 (tt0) cc_final: 0.7319 (tt0) REVERT: A 585 MET cc_start: 0.8803 (tpt) cc_final: 0.7986 (tpt) REVERT: A 639 THR cc_start: 0.8940 (m) cc_final: 0.8604 (p) REVERT: B 636 LYS cc_start: 0.7767 (mmmt) cc_final: 0.7453 (tttp) REVERT: B 666 ARG cc_start: 0.7724 (mtp-110) cc_final: 0.7497 (mtm110) REVERT: C 325 GLU cc_start: 0.7494 (pp20) cc_final: 0.7165 (pm20) REVERT: D 217 TYR cc_start: 0.7021 (t80) cc_final: 0.6678 (t80) outliers start: 31 outliers final: 21 residues processed: 193 average time/residue: 0.1265 time to fit residues: 35.3714 Evaluate side-chains 165 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 412 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 16 MET 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 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 239 ILE Chi-restraints excluded: chain D residue 240 LEU 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: 5.9990 chunk 39 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103609 restraints weight = 24426.806| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.32 r_work: 0.3227 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3779 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= 0.101 Angle : 0.456 7.700 18765 Z= 0.239 Chirality : 0.042 0.159 2091 Planarity : 0.003 0.044 2395 Dihedral : 4.584 76.153 1796 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.39 % Allowed : 14.02 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1658 helix: 0.18 (0.22), residues: 623 sheet: -0.78 (0.27), residues: 361 loop : -0.95 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 59 TYR 0.018 0.001 TYR C 230 PHE 0.013 0.001 PHE B 104 TRP 0.009 0.001 TRP C 317 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (13907) covalent geometry : angle 0.45646 / 0.24 (18765) hydrogen bonds : bond 0.02858 / 1.87 ( 558) hydrogen bonds : angle 4.65129 / 3.25 ( 1584) Misc. bond : bond 0.00027 / 0.02 ( 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 200 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.527 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: 0.7926 (m-30) cc_final: 0.7582 (m-30) REVERT: A 585 MET cc_start: 0.8930 (tpt) cc_final: 0.8120 (tpt) REVERT: A 636 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7562 (ttmm) REVERT: A 639 THR cc_start: 0.8920 (m) cc_final: 0.8601 (p) REVERT: B 610 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7975 (pt0) REVERT: B 636 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7488 (tttp) REVERT: C 32 GLU cc_start: 0.6183 (pt0) cc_final: 0.5613 (mp0) REVERT: C 217 TYR cc_start: 0.7864 (t80) cc_final: 0.7481 (t80) REVERT: C 275 CYS cc_start: 0.8573 (p) cc_final: 0.8240 (p) REVERT: C 314 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7551 (mm110) REVERT: D 217 TYR cc_start: 0.7097 (t80) cc_final: 0.6877 (t80) REVERT: D 294 PHE cc_start: 0.8102 (m-80) cc_final: 0.7740 (m-80) outliers start: 36 outliers final: 23 residues processed: 191 average time/residue: 0.1220 time to fit residues: 34.5471 Evaluate side-chains 172 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain B residue 16 MET 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 610 GLU Chi-restraints excluded: chain C residue 44 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: 0.0370 chunk 75 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099734 restraints weight = 24537.382| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.37 r_work: 0.3172 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13908 Z= 0.157 Angle : 0.503 6.482 18765 Z= 0.264 Chirality : 0.044 0.159 2091 Planarity : 0.003 0.046 2395 Dihedral : 4.777 79.356 1795 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.99 % Allowed : 14.55 % Favored : 82.46 % 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: -0.70 (0.21), residues: 1658 helix: 0.33 (0.22), residues: 620 sheet: -0.83 (0.28), residues: 358 loop : -0.87 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.017 0.001 TYR A 203 PHE 0.014 0.001 PHE A 104 TRP 0.010 0.001 TRP C 317 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13907) covalent geometry : angle 0.50324 / 0.26 (18765) hydrogen bonds : bond 0.03111 / 2.03 ( 558) hydrogen bonds : angle 4.74088 / 3.32 ( 1584) Misc. bond : bond 0.00045 / 0.03 ( 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: 45 poor density : 155 time to evaluate : 0.550 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 40 ASP cc_start: 0.7972 (m-30) cc_final: 0.7750 (m-30) REVERT: A 533 LYS cc_start: 0.7114 (mtmm) cc_final: 0.6816 (mppt) REVERT: A 585 MET cc_start: 0.9001 (tpt) cc_final: 0.8331 (tpt) REVERT: B 349 GLU cc_start: 0.6428 (mm-30) cc_final: 0.6192 (mm-30) REVERT: B 636 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7563 (tttp) REVERT: B 665 ASN cc_start: 0.8471 (m-40) cc_final: 0.8269 (m-40) REVERT: C 275 CYS cc_start: 0.8708 (p) cc_final: 0.8381 (p) REVERT: D 294 PHE cc_start: 0.8344 (m-80) cc_final: 0.7981 (m-80) outliers start: 45 outliers final: 29 residues processed: 187 average time/residue: 0.1198 time to fit residues: 33.4699 Evaluate side-chains 173 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 16 MET 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 3 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 578 GLN C 94 ASN C 303 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099469 restraints weight = 24524.512| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.14 r_work: 0.3194 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4368 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= 0.141 Angle : 0.489 8.013 18765 Z= 0.255 Chirality : 0.044 0.158 2091 Planarity : 0.003 0.045 2395 Dihedral : 4.768 77.656 1795 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.66 % Allowed : 15.75 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.21), residues: 1658 helix: 0.45 (0.22), residues: 623 sheet: -0.79 (0.28), residues: 363 loop : -0.85 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.015 0.001 TYR A 203 PHE 0.013 0.001 PHE A 104 TRP 0.008 0.001 TRP D 285 HIS 0.002 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13907) covalent geometry : angle 0.48924 / 0.26 (18765) hydrogen bonds : bond 0.02982 / 1.94 ( 558) hydrogen bonds : angle 4.67594 / 3.28 ( 1584) Misc. bond : bond 0.00034 / 0.02 ( 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 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.554 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.9117 (tpt) cc_final: 0.8513 (tpt) REVERT: A 636 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7888 (ttmm) REVERT: B 349 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6270 (mm-30) REVERT: B 636 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7652 (tttp) REVERT: B 665 ASN cc_start: 0.8476 (m-40) cc_final: 0.8247 (m-40) REVERT: C 275 CYS cc_start: 0.8765 (p) cc_final: 0.8411 (p) REVERT: C 325 GLU cc_start: 0.7639 (pm20) cc_final: 0.7285 (pm20) REVERT: D 219 GLU cc_start: 0.8746 (tt0) cc_final: 0.8086 (mp0) REVERT: D 271 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: D 294 PHE cc_start: 0.8298 (m-80) cc_final: 0.7923 (m-80) outliers start: 40 outliers final: 33 residues processed: 184 average time/residue: 0.1222 time to fit residues: 33.2836 Evaluate side-chains 176 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 84 MET 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 578 GLN Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 3 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 271 GLU 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: 1.9990 chunk 97 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 160 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100711 restraints weight = 24424.491| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.16 r_work: 0.3208 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13908 Z= 0.108 Angle : 0.469 8.091 18765 Z= 0.246 Chirality : 0.043 0.159 2091 Planarity : 0.003 0.044 2395 Dihedral : 4.682 77.308 1795 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.59 % Allowed : 16.15 % Favored : 81.26 % 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: -0.46 (0.21), residues: 1658 helix: 0.57 (0.22), residues: 622 sheet: -0.72 (0.28), residues: 364 loop : -0.76 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.013 0.001 TYR A 203 PHE 0.011 0.001 PHE A 104 TRP 0.009 0.001 TRP B 581 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13907) covalent geometry : angle 0.46948 / 0.25 (18765) hydrogen bonds : bond 0.02811 / 1.83 ( 558) hydrogen bonds : angle 4.58001 / 3.22 ( 1584) Misc. bond : bond 0.00025 / 0.02 ( 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 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.519 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.9097 (tpt) cc_final: 0.8532 (tpt) REVERT: A 636 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7916 (ttmm) REVERT: B 349 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6317 (mm-30) REVERT: B 636 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7648 (tttp) REVERT: B 665 ASN cc_start: 0.8447 (m-40) cc_final: 0.8197 (m-40) REVERT: C 275 CYS cc_start: 0.8727 (p) cc_final: 0.8370 (p) REVERT: C 325 GLU cc_start: 0.7589 (pm20) cc_final: 0.7127 (pm20) REVERT: D 219 GLU cc_start: 0.8618 (tt0) cc_final: 0.8040 (mp0) REVERT: D 271 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: D 294 PHE cc_start: 0.8242 (m-80) cc_final: 0.7887 (m-80) outliers start: 39 outliers final: 32 residues processed: 178 average time/residue: 0.1159 time to fit residues: 31.1495 Evaluate side-chains 175 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 84 MET 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 408 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 3 VAL 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 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 271 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 155 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.0270 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 463 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097950 restraints weight = 24610.672| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.23 r_work: 0.3145 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4736 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= 0.200 Angle : 0.540 8.262 18765 Z= 0.282 Chirality : 0.045 0.166 2091 Planarity : 0.004 0.060 2395 Dihedral : 4.961 76.097 1795 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.46 % Allowed : 16.74 % Favored : 80.80 % 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: -0.60 (0.21), residues: 1658 helix: 0.43 (0.22), residues: 622 sheet: -0.79 (0.28), residues: 352 loop : -0.82 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 136 TYR 0.015 0.002 TYR C 217 PHE 0.012 0.001 PHE B 104 TRP 0.013 0.002 TRP B 581 HIS 0.002 0.001 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (13907) covalent geometry : angle 0.53971 / 0.28 (18765) hydrogen bonds : bond 0.03213 / 2.10 ( 558) hydrogen bonds : angle 4.77927 / 3.36 ( 1584) Misc. bond : bond 0.00051 / 0.03 ( 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: 37 poor density : 148 time to evaluate : 0.550 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.9151 (tpt) cc_final: 0.8581 (tpt) REVERT: A 636 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8009 (ttmm) REVERT: B 349 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6995 (mm-30) REVERT: B 636 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7658 (tttp) REVERT: C 127 ILE cc_start: 0.5134 (OUTLIER) cc_final: 0.4874 (mp) REVERT: C 275 CYS cc_start: 0.8760 (p) cc_final: 0.8385 (p) REVERT: D 219 GLU cc_start: 0.8751 (tt0) cc_final: 0.8505 (tt0) REVERT: D 271 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7512 (tm-30) outliers start: 37 outliers final: 32 residues processed: 177 average time/residue: 0.1176 time to fit residues: 31.3200 Evaluate side-chains 171 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 84 MET 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 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 127 ILE 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 271 GLU 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: 0.6980 chunk 41 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 578 GLN D 212 ASN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099636 restraints weight = 24643.881| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.21 r_work: 0.3192 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4715 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= 0.118 Angle : 0.488 8.347 18765 Z= 0.255 Chirality : 0.043 0.159 2091 Planarity : 0.003 0.046 2395 Dihedral : 4.795 75.901 1795 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.52 % Allowed : 16.68 % Favored : 80.80 % 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: -0.50 (0.21), residues: 1658 helix: 0.55 (0.22), residues: 623 sheet: -0.79 (0.28), residues: 361 loop : -0.77 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.015 0.001 TYR C 217 PHE 0.011 0.001 PHE B 104 TRP 0.011 0.001 TRP B 581 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13907) covalent geometry : angle 0.48789 / 0.26 (18765) hydrogen bonds : bond 0.02866 / 1.87 ( 558) hydrogen bonds : angle 4.61616 / 3.24 ( 1584) Misc. bond : bond 0.00028 / 0.02 ( 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 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.538 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.9118 (tpt) cc_final: 0.8510 (tpt) REVERT: A 636 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7934 (ttmm) REVERT: B 636 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7581 (tttp) REVERT: C 127 ILE cc_start: 0.5143 (OUTLIER) cc_final: 0.4867 (mp) REVERT: C 275 CYS cc_start: 0.8770 (p) cc_final: 0.8389 (p) REVERT: D 219 GLU cc_start: 0.8708 (tt0) cc_final: 0.8062 (mp0) REVERT: D 271 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7420 (tm-30) outliers start: 38 outliers final: 33 residues processed: 174 average time/residue: 0.1076 time to fit residues: 28.5984 Evaluate side-chains 175 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 84 MET 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 408 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 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 212 ASN Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 271 GLU 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: 2.9990 chunk 127 optimal weight: 0.9990 chunk 152 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 GLN D 212 ASN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101089 restraints weight = 24498.070| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.12 r_work: 0.3217 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4724 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= 0.103 Angle : 0.482 8.389 18765 Z= 0.253 Chirality : 0.043 0.160 2091 Planarity : 0.003 0.045 2395 Dihedral : 4.732 76.514 1795 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.59 % Allowed : 16.48 % Favored : 80.93 % 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: -0.38 (0.21), residues: 1658 helix: 0.63 (0.22), residues: 620 sheet: -0.69 (0.28), residues: 353 loop : -0.69 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 314 TYR 0.011 0.001 TYR C 230 PHE 0.010 0.001 PHE B 313 TRP 0.013 0.001 TRP B 581 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (13907) covalent geometry : angle 0.48223 / 0.25 (18765) hydrogen bonds : bond 0.02742 / 1.78 ( 558) hydrogen bonds : angle 4.54946 / 3.19 ( 1584) Misc. bond : bond 0.00021 / 0.01 ( 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 189 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.669 Fit side-chains TARDY: cannot create tardy model for: "LYS A 211 " (corrupted residue). Skipping it. REVERT: A 585 MET cc_start: 0.9094 (tpt) cc_final: 0.8456 (tpt) REVERT: A 636 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7929 (ttmm) REVERT: B 636 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7599 (tttp) REVERT: C 103 GLU cc_start: 0.8719 (mp0) cc_final: 0.8486 (mp0) REVERT: C 127 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4891 (mp) REVERT: C 275 CYS cc_start: 0.8746 (p) cc_final: 0.8356 (p) REVERT: C 325 GLU cc_start: 0.7562 (pm20) cc_final: 0.7155 (pm20) REVERT: D 219 GLU cc_start: 0.8738 (tt0) cc_final: 0.8091 (mp0) REVERT: D 271 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7494 (tm-30) outliers start: 39 outliers final: 32 residues processed: 177 average time/residue: 0.1130 time to fit residues: 30.3845 Evaluate side-chains 173 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 636 LYS Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 84 MET 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 408 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 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 212 ASN Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 271 GLU 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: 0.9990 chunk 27 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 212 ASN ** D 284 HIS ** 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 = 0.3651 r_free = 0.3651 target = 0.122591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102058 restraints weight = 24754.103| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.23 r_work: 0.3247 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4738 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= 0.107 Angle : 0.490 8.191 18765 Z= 0.255 Chirality : 0.043 0.159 2091 Planarity : 0.003 0.045 2395 Dihedral : 4.680 73.210 1795 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.33 % Allowed : 17.01 % Favored : 80.66 % 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: -0.35 (0.21), residues: 1658 helix: 0.61 (0.22), residues: 626 sheet: -0.63 (0.28), residues: 361 loop : -0.65 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 314 TYR 0.015 0.001 TYR B 203 PHE 0.011 0.001 PHE A 104 TRP 0.010 0.001 TRP C 317 HIS 0.002 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13907) covalent geometry : angle 0.49008 / 0.26 (18765) hydrogen bonds : bond 0.02778 / 1.79 ( 558) hydrogen bonds : angle 4.52328 / 3.17 ( 1584) Misc. bond : bond 0.00024 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.14 seconds wall clock time: 56 minutes 21.75 seconds (3381.75 seconds total)