Starting phenix.real_space_refine on Thu Jul 31 19:14:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlf_22242/07_2025/6xlf_22242.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlf_22242/07_2025/6xlf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xlf_22242/07_2025/6xlf_22242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlf_22242/07_2025/6xlf_22242.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlf_22242/07_2025/6xlf_22242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlf_22242/07_2025/6xlf_22242.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.59, per 1000 atoms: 0.63 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: 3.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.75 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: 4.72 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4425 1.34 - 1.46: 2933 1.46 - 1.58: 6491 1.58 - 1.69: 10 1.69 - 1.81: 48 Bond restraints: 13907 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.695 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 13902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 18720 3.44 - 6.88: 36 6.88 - 10.33: 5 10.33 - 13.77: 2 13.77 - 17.21: 2 Bond angle restraints: 18765 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.74 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.92 17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" N VAL B 163 " pdb=" CA VAL B 163 " pdb=" C VAL B 163 " ideal model delta sigma weight residual 113.20 109.63 3.57 9.60e-01 1.09e+00 1.38e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.57 10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.62 10.46 3.00e+00 1.11e-01 1.22e+01 ... (remaining 18760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.74: 8046 20.74 - 41.48: 365 41.48 - 62.23: 65 62.23 - 82.97: 18 82.97 - 103.71: 13 Dihedral angle restraints: 8507 sinusoidal: 3588 harmonic: 4919 Sorted by residual: dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -68.56 103.71 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CB GLU B 644 " pdb=" CG GLU B 644 " pdb=" CD GLU B 644 " pdb=" OE1 GLU B 644 " ideal model delta sinusoidal sigma weight residual 0.00 89.41 -89.41 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" O1B ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PB ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sinusoidal sigma weight residual 35.15 -54.07 89.22 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1840 0.057 - 0.114: 230 0.114 - 0.171: 19 0.171 - 0.228: 0 0.228 - 0.285: 2 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE C 154 " pdb=" N ILE C 154 " pdb=" C ILE C 154 " pdb=" CB ILE C 154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2088 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 355 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 224 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO C 225 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 320 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO C 321 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " -0.014 5.00e-02 4.00e+02 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.72: 538 2.72 - 3.32: 15129 3.32 - 3.93: 26520 3.93 - 4.53: 36280 4.53 - 5.14: 56921 Nonbonded interactions: 135388 Sorted by model distance: nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.115 2.170 nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 2.115 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.121 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.132 2.170 nonbonded pdb=" O3G ANP B 801 " pdb="MG MG B 802 " model vdw 2.163 2.170 ... (remaining 135383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 3 through 212 or resid 259 through 675 or resid 801 throug \ h 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.780 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 13908 Z= 0.151 Angle : 0.474 17.210 18765 Z= 0.234 Chirality : 0.040 0.285 2091 Planarity : 0.002 0.029 2395 Dihedral : 12.833 103.711 5305 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.20 % Allowed : 5.51 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.000 TRP D 242 HIS 0.001 0.000 HIS D 309 PHE 0.003 0.000 PHE A 660 TYR 0.003 0.000 TYR A 456 ARG 0.002 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.28201 ( 558) hydrogen bonds : angle 8.92147 ( 1584) covalent geometry : bond 0.00296 (13907) covalent geometry : angle 0.47357 (18765) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 352 time to evaluate : 1.535 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: 0.5897 (ttpt) REVERT: C 162 LYS cc_start: 0.6304 (mttp) cc_final: 0.5858 (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: 0.3255 time to fit residues: 161.3646 Evaluate side-chains 195 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 140 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 119 GLN A 135 GLN A 181 GLN A 380 GLN A 430 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN B 55 GLN B 135 GLN B 276 ASN B 592 GLN 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 = 0.3790 r_free = 0.3790 target = 0.132477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113230 restraints weight = 24484.351| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.28 r_work: 0.3409 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13908 Z= 0.119 Angle : 0.490 5.622 18765 Z= 0.260 Chirality : 0.043 0.148 2091 Planarity : 0.004 0.041 2395 Dihedral : 5.555 80.965 1873 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.53 % Allowed : 11.63 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.18), residues: 1658 helix: -1.37 (0.18), residues: 621 sheet: -1.20 (0.26), residues: 369 loop : -1.64 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 285 HIS 0.005 0.001 HIS D 303 PHE 0.021 0.001 PHE A 104 TYR 0.013 0.001 TYR C 217 ARG 0.005 0.001 ARG B 666 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 558) hydrogen bonds : angle 5.43486 ( 1584) covalent geometry : bond 0.00270 (13907) covalent geometry : angle 0.48979 (18765) Misc. bond : bond 0.00041 ( 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 220 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.559 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS B 211 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7638 (m-30) cc_final: 0.7320 (m-30) REVERT: A 310 GLN cc_start: 0.7468 (pm20) cc_final: 0.6757 (pm20) REVERT: A 585 MET cc_start: 0.8675 (tpt) cc_final: 0.7676 (tpt) REVERT: A 589 MET cc_start: 0.8560 (mmm) cc_final: 0.8288 (mmp) REVERT: A 626 ASP cc_start: 0.7697 (p0) cc_final: 0.7437 (p0) REVERT: B 196 ARG cc_start: 0.8284 (tpt170) cc_final: 0.8082 (tpt170) REVERT: B 314 ARG cc_start: 0.7570 (mtp85) cc_final: 0.7218 (mtp180) REVERT: B 636 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7191 (tttp) REVERT: D 217 TYR cc_start: 0.7306 (t80) cc_final: 0.7025 (t80) REVERT: D 331 ASN cc_start: 0.8824 (m-40) cc_final: 0.8607 (m110) outliers start: 23 outliers final: 9 residues processed: 213 average time/residue: 0.2634 time to fit residues: 81.2115 Evaluate side-chains 174 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 447 VAL 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 C residue 3 VAL Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 156 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 409 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 578 GLN C 303 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102947 restraints weight = 24630.041| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.32 r_work: 0.3251 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13908 Z= 0.168 Angle : 0.537 8.277 18765 Z= 0.280 Chirality : 0.045 0.163 2091 Planarity : 0.004 0.046 2395 Dihedral : 5.727 81.148 1852 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.72 % Allowed : 13.16 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1658 helix: -0.26 (0.21), residues: 614 sheet: -0.99 (0.27), residues: 359 loop : -1.15 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 285 HIS 0.003 0.001 HIS D 303 PHE 0.014 0.002 PHE A 643 TYR 0.015 0.001 TYR A 203 ARG 0.005 0.001 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 558) hydrogen bonds : angle 4.96886 ( 1584) covalent geometry : bond 0.00398 (13907) covalent geometry : angle 0.53673 (18765) Misc. bond : bond 0.00048 ( 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 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.562 Fit side-chains TARDY: cannot create tardy model for: "LYS B 211 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7843 (m-30) cc_final: 0.7540 (m-30) REVERT: A 310 GLN cc_start: 0.7636 (pm20) cc_final: 0.7337 (pm20) REVERT: A 585 MET cc_start: 0.8846 (tpt) cc_final: 0.8016 (tpt) REVERT: B 314 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7293 (mtp180) REVERT: B 349 GLU cc_start: 0.6317 (tp30) cc_final: 0.6079 (mm-30) REVERT: B 636 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7422 (tttp) REVERT: C 275 CYS cc_start: 0.8541 (p) cc_final: 0.8134 (p) outliers start: 41 outliers final: 23 residues processed: 201 average time/residue: 0.2607 time to fit residues: 76.2131 Evaluate side-chains 165 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 384 ILE Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR 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 126 LEU 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 318 THR Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 41 optimal weight: 0.2980 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 145 optimal weight: 0.3980 chunk 149 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104245 restraints weight = 24178.607| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.41 r_work: 0.3240 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3730 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= 0.093 Angle : 0.460 6.745 18765 Z= 0.240 Chirality : 0.042 0.160 2091 Planarity : 0.003 0.045 2395 Dihedral : 5.544 75.203 1852 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.93 % Allowed : 14.68 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1658 helix: 0.18 (0.21), residues: 626 sheet: -0.79 (0.27), residues: 360 loop : -0.93 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 148 HIS 0.002 0.000 HIS B 426 PHE 0.013 0.001 PHE B 313 TYR 0.013 0.001 TYR A 203 ARG 0.009 0.000 ARG B 666 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 558) hydrogen bonds : angle 4.66671 ( 1584) covalent geometry : bond 0.00212 (13907) covalent geometry : angle 0.45958 (18765) Misc. bond : bond 0.00014 ( 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 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.572 Fit side-chains 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: 0.7937 (m-30) cc_final: 0.7697 (m-30) REVERT: A 585 MET cc_start: 0.8952 (tpt) cc_final: 0.8255 (tpt) REVERT: B 636 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7495 (tttp) REVERT: B 666 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.7509 (mtm110) REVERT: C 32 GLU cc_start: 0.6214 (pt0) cc_final: 0.5599 (mp0) REVERT: C 275 CYS cc_start: 0.8587 (p) cc_final: 0.8186 (p) REVERT: C 317 TRP cc_start: 0.8843 (t60) cc_final: 0.8430 (t60) REVERT: D 217 TYR cc_start: 0.6950 (t80) cc_final: 0.6607 (t80) outliers start: 29 outliers final: 19 residues processed: 189 average time/residue: 0.2724 time to fit residues: 74.9027 Evaluate side-chains 170 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 423 LEU 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 154 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 152 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.104385 restraints weight = 24285.303| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.36 r_work: 0.3242 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13908 Z= 0.093 Angle : 0.457 6.262 18765 Z= 0.239 Chirality : 0.042 0.157 2091 Planarity : 0.003 0.046 2395 Dihedral : 5.467 75.117 1851 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.39 % Allowed : 14.88 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1658 helix: 0.44 (0.22), residues: 629 sheet: -0.66 (0.28), residues: 361 loop : -0.77 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 285 HIS 0.003 0.000 HIS C 309 PHE 0.012 0.001 PHE A 104 TYR 0.019 0.001 TYR B 203 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.02711 ( 558) hydrogen bonds : angle 4.56212 ( 1584) covalent geometry : bond 0.00214 (13907) covalent geometry : angle 0.45736 (18765) Misc. bond : bond 0.00027 ( 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 205 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.583 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: A 40 ASP cc_start: 0.7926 (m-30) cc_final: 0.7590 (m-30) REVERT: A 585 MET cc_start: 0.8987 (tpt) cc_final: 0.8372 (tpt) REVERT: B 636 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7461 (tttp) REVERT: C 32 GLU cc_start: 0.6375 (pt0) cc_final: 0.5622 (mp0) REVERT: C 275 CYS cc_start: 0.8591 (p) cc_final: 0.8174 (p) REVERT: C 312 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7896 (tppp) REVERT: C 317 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.8590 (t60) REVERT: C 325 GLU cc_start: 0.6842 (pm20) cc_final: 0.6627 (pm20) REVERT: D 217 TYR cc_start: 0.7067 (t80) cc_final: 0.6809 (t80) outliers start: 36 outliers final: 24 residues processed: 196 average time/residue: 0.2504 time to fit residues: 72.5747 Evaluate side-chains 168 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 390 LYS Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 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 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 154 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 317 TRP 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 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 87 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 129 optimal weight: 0.0050 chunk 66 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103067 restraints weight = 24420.028| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.17 r_work: 0.3246 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13908 Z= 0.106 Angle : 0.462 5.888 18765 Z= 0.243 Chirality : 0.042 0.157 2091 Planarity : 0.003 0.045 2395 Dihedral : 5.459 74.766 1851 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.59 % Allowed : 15.08 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1658 helix: 0.56 (0.22), residues: 627 sheet: -0.62 (0.28), residues: 363 loop : -0.69 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 285 HIS 0.003 0.000 HIS C 309 PHE 0.011 0.001 PHE B 104 TYR 0.018 0.001 TYR B 203 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.02728 ( 558) hydrogen bonds : angle 4.48459 ( 1584) covalent geometry : bond 0.00248 (13907) covalent geometry : angle 0.46208 (18765) Misc. bond : bond 0.00031 ( 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 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.578 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: 0.8094 (m-30) cc_final: 0.7802 (m-30) REVERT: A 585 MET cc_start: 0.9140 (tpt) cc_final: 0.8566 (tpt) REVERT: A 636 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7871 (mmmm) REVERT: B 11 GLU cc_start: 0.8484 (tp30) cc_final: 0.8098 (tp30) REVERT: B 636 LYS cc_start: 0.7936 (mmmt) cc_final: 0.7536 (tttp) REVERT: C 275 CYS cc_start: 0.8704 (p) cc_final: 0.8287 (p) REVERT: C 317 TRP cc_start: 0.8959 (OUTLIER) cc_final: 0.8678 (t60) outliers start: 39 outliers final: 27 residues processed: 178 average time/residue: 0.2452 time to fit residues: 65.0290 Evaluate side-chains 170 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 390 LYS 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 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 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 408 GLU 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 317 TRP 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 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 68 optimal weight: 0.0980 chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103350 restraints weight = 24383.123| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.17 r_work: 0.3249 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13908 Z= 0.098 Angle : 0.466 7.631 18765 Z= 0.242 Chirality : 0.042 0.157 2091 Planarity : 0.003 0.044 2395 Dihedral : 5.408 73.794 1851 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.39 % Allowed : 15.75 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1658 helix: 0.63 (0.22), residues: 629 sheet: -0.55 (0.28), residues: 363 loop : -0.62 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.003 0.000 HIS C 309 PHE 0.010 0.001 PHE B 104 TYR 0.016 0.001 TYR B 203 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 558) hydrogen bonds : angle 4.41387 ( 1584) covalent geometry : bond 0.00229 (13907) covalent geometry : angle 0.46557 (18765) Misc. bond : bond 0.00032 ( 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 186 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.585 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: A 40 ASP cc_start: 0.8110 (m-30) cc_final: 0.7810 (m-30) REVERT: A 585 MET cc_start: 0.9110 (tpt) cc_final: 0.8512 (tpt) REVERT: B 11 GLU cc_start: 0.8474 (tp30) cc_final: 0.8084 (tp30) REVERT: B 349 GLU cc_start: 0.6351 (mm-30) cc_final: 0.6149 (mm-30) REVERT: B 636 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7539 (tttp) REVERT: C 275 CYS cc_start: 0.8666 (p) cc_final: 0.8232 (p) REVERT: C 317 TRP cc_start: 0.8932 (OUTLIER) cc_final: 0.8676 (t60) outliers start: 36 outliers final: 28 residues processed: 177 average time/residue: 0.2575 time to fit residues: 68.7287 Evaluate side-chains 171 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 390 LYS 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 B residue 101 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 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 460 MET 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 317 TRP 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 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 17 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.0050 chunk 128 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 163 optimal weight: 0.0980 chunk 22 optimal weight: 0.0060 overall best weight: 0.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104987 restraints weight = 24374.035| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.20 r_work: 0.3269 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13908 Z= 0.087 Angle : 0.466 7.265 18765 Z= 0.241 Chirality : 0.042 0.158 2091 Planarity : 0.003 0.043 2395 Dihedral : 5.341 72.837 1851 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.13 % Allowed : 16.08 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1658 helix: 0.68 (0.22), residues: 628 sheet: -0.46 (0.28), residues: 362 loop : -0.56 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.006 0.001 HIS C 303 PHE 0.010 0.001 PHE B 104 TYR 0.014 0.001 TYR B 203 ARG 0.008 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 558) hydrogen bonds : angle 4.34605 ( 1584) covalent geometry : bond 0.00199 (13907) covalent geometry : angle 0.46579 (18765) Misc. bond : bond 0.00016 ( 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 183 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.615 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: A 40 ASP cc_start: 0.8140 (m-30) cc_final: 0.7769 (m-30) REVERT: A 312 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: A 585 MET cc_start: 0.9086 (tpt) cc_final: 0.8508 (tpt) REVERT: B 11 GLU cc_start: 0.8460 (tp30) cc_final: 0.8089 (tp30) REVERT: B 349 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5989 (mm-30) REVERT: B 636 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7382 (tttp) REVERT: C 134 LYS cc_start: 0.6484 (mttt) cc_final: 0.6066 (ptmt) REVERT: C 275 CYS cc_start: 0.8639 (p) cc_final: 0.8199 (p) outliers start: 32 outliers final: 26 residues processed: 173 average time/residue: 0.2341 time to fit residues: 61.9449 Evaluate side-chains 167 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 390 LYS 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 157 THR Chi-restraints excluded: chain B residue 159 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 408 GLU Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 578 GLN Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 126 LEU 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 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 45 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102376 restraints weight = 24183.738| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.19 r_work: 0.3227 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13908 Z= 0.127 Angle : 0.502 10.307 18765 Z= 0.259 Chirality : 0.043 0.161 2091 Planarity : 0.003 0.044 2395 Dihedral : 5.430 72.431 1851 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.93 % Allowed : 16.54 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1658 helix: 0.64 (0.22), residues: 629 sheet: -0.45 (0.28), residues: 364 loop : -0.58 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 581 HIS 0.010 0.001 HIS C 303 PHE 0.024 0.001 PHE B 579 TYR 0.014 0.001 TYR A 203 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.02804 ( 558) hydrogen bonds : angle 4.42474 ( 1584) covalent geometry : bond 0.00303 (13907) covalent geometry : angle 0.50248 (18765) Misc. bond : bond 0.00044 ( 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 170 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.710 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: 0.8133 (m-30) cc_final: 0.7876 (m-30) REVERT: A 585 MET cc_start: 0.9101 (tpt) cc_final: 0.8418 (tpt) REVERT: B 11 GLU cc_start: 0.8502 (tp30) cc_final: 0.8119 (tp30) REVERT: B 636 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7413 (tttp) REVERT: C 134 LYS cc_start: 0.6549 (mttt) cc_final: 0.6121 (ptmt) REVERT: C 275 CYS cc_start: 0.8669 (p) cc_final: 0.8224 (p) outliers start: 29 outliers final: 27 residues processed: 162 average time/residue: 0.2407 time to fit residues: 59.4263 Evaluate side-chains 169 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 390 LYS 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 157 THR Chi-restraints excluded: chain B residue 159 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 460 MET 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 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 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 71 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099993 restraints weight = 24373.665| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.15 r_work: 0.3197 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13908 Z= 0.162 Angle : 0.543 11.706 18765 Z= 0.280 Chirality : 0.044 0.183 2091 Planarity : 0.003 0.045 2395 Dihedral : 5.577 72.679 1851 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.06 % Allowed : 16.74 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1658 helix: 0.59 (0.22), residues: 628 sheet: -0.51 (0.28), residues: 363 loop : -0.59 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 285 HIS 0.008 0.001 HIS C 303 PHE 0.019 0.001 PHE A 643 TYR 0.021 0.001 TYR B 565 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 558) hydrogen bonds : angle 4.53522 ( 1584) covalent geometry : bond 0.00391 (13907) covalent geometry : angle 0.54307 (18765) Misc. bond : bond 0.00063 ( 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 173 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.733 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: 0.8279 (m-30) cc_final: 0.7969 (m-30) REVERT: A 585 MET cc_start: 0.9081 (tpt) cc_final: 0.8387 (tpt) REVERT: B 11 GLU cc_start: 0.8580 (tp30) cc_final: 0.8243 (tp30) REVERT: B 636 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7541 (tttp) REVERT: C 275 CYS cc_start: 0.8662 (p) cc_final: 0.8246 (p) outliers start: 31 outliers final: 28 residues processed: 164 average time/residue: 0.2450 time to fit residues: 60.8306 Evaluate side-chains 163 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 390 LYS 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 157 THR Chi-restraints excluded: chain B residue 159 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 460 MET 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 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 65 optimal weight: 0.0020 chunk 123 optimal weight: 5.9990 chunk 160 optimal weight: 0.2980 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 157 optimal weight: 0.0040 chunk 79 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104133 restraints weight = 24687.947| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.15 r_work: 0.3263 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13908 Z= 0.093 Angle : 0.488 9.369 18765 Z= 0.253 Chirality : 0.042 0.163 2091 Planarity : 0.003 0.045 2395 Dihedral : 5.418 71.326 1851 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.53 % Allowed : 17.14 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1658 helix: 0.71 (0.22), residues: 631 sheet: -0.43 (0.28), residues: 355 loop : -0.50 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 148 HIS 0.004 0.001 HIS C 303 PHE 0.017 0.001 PHE A 643 TYR 0.010 0.001 TYR A 203 ARG 0.007 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.02656 ( 558) hydrogen bonds : angle 4.35482 ( 1584) covalent geometry : bond 0.00212 (13907) covalent geometry : angle 0.48803 (18765) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6654.30 seconds wall clock time: 114 minutes 56.29 seconds (6896.29 seconds total)