Starting phenix.real_space_refine on Tue Nov 18 04:28:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ijz_9682/11_2025/6ijz_9682.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ijz_9682/11_2025/6ijz_9682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ijz_9682/11_2025/6ijz_9682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ijz_9682/11_2025/6ijz_9682.map" model { file = "/net/cci-nas-00/data/ceres_data/6ijz_9682/11_2025/6ijz_9682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ijz_9682/11_2025/6ijz_9682.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7264 2.51 5 N 1778 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10964 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5482 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Restraints were copied for chains: B Time building chain proxies: 4.42, per 1000 atoms: 0.40 Number of scatterers: 10964 At special positions: 0 Unit cell: (95.411, 139.849, 108.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1872 8.00 N 1778 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 427.1 milliseconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 69.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 30 removed outlier: 3.804A pdb=" N VAL A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.656A pdb=" N LYS A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.744A pdb=" N VAL A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Proline residue: A 111 - end of helix removed outlier: 3.891A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 158 through 193 removed outlier: 4.010A pdb=" N HIS A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 164 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 185 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 4.040A pdb=" N LEU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 267 removed outlier: 3.546A pdb=" N GLN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 310 removed outlier: 5.250A pdb=" N ALA A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.562A pdb=" N ALA A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.595A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 382 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.508A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.961A pdb=" N GLU A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 475 removed outlier: 4.215A pdb=" N ARG A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 removed outlier: 3.822A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.609A pdb=" N GLN A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.739A pdb=" N ILE A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 534 through 547 removed outlier: 4.112A pdb=" N MET A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.514A pdb=" N ALA A 558 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 559 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 3.848A pdb=" N ILE A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.948A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 removed outlier: 3.773A pdb=" N GLY A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.838A pdb=" N ALA A 654 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 655 " --> pdb=" O ALA A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 655' Processing helix chain 'A' and resid 659 through 676 removed outlier: 3.852A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 Processing helix chain 'A' and resid 684 through 699 removed outlier: 3.636A pdb=" N ASP A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 3.582A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 30 removed outlier: 3.804A pdb=" N VAL B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.656A pdb=" N LYS B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 93 through 125 removed outlier: 3.744A pdb=" N VAL B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.891A pdb=" N VAL B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 121 " --> pdb=" O TRP B 117 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 158 through 193 removed outlier: 4.009A pdb=" N HIS B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 164 " --> pdb=" O TRP B 160 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 185 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 removed outlier: 4.040A pdb=" N LEU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 267 removed outlier: 3.546A pdb=" N GLN B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 310 removed outlier: 5.250A pdb=" N ALA B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.561A pdb=" N ALA B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 389 removed outlier: 3.596A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 382 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 387 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.508A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 420 through 428 Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.961A pdb=" N GLU B 452 " --> pdb=" O MET B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 removed outlier: 4.215A pdb=" N ARG B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.822A pdb=" N ALA B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.608A pdb=" N GLN B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 512 removed outlier: 3.739A pdb=" N ILE B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'B' and resid 534 through 547 removed outlier: 4.112A pdb=" N MET B 540 " --> pdb=" O LYS B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.514A pdb=" N ALA B 558 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 559 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 583 removed outlier: 3.848A pdb=" N ILE B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.947A pdb=" N ILE B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 removed outlier: 3.773A pdb=" N GLY B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 removed outlier: 3.837A pdb=" N ALA B 654 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 655 " --> pdb=" O ALA B 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 651 through 655' Processing helix chain 'B' and resid 659 through 676 removed outlier: 3.852A pdb=" N VAL B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 674 " --> pdb=" O HIS B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 684 through 699 removed outlier: 3.636A pdb=" N ASP B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 709 removed outlier: 3.581A pdb=" N GLN B 709 " --> pdb=" O LYS B 705 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205 removed outlier: 4.859A pdb=" N VAL A 239 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 203 through 205 removed outlier: 4.860A pdb=" N VAL B 239 " --> pdb=" O MET B 320 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1653 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: 1.61 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3027 1.33 - 1.45: 2070 1.45 - 1.57: 6083 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11272 Sorted by residual: bond pdb=" CB TRP A 624 " pdb=" CG TRP A 624 " ideal model delta sigma weight residual 1.498 1.404 0.094 3.10e-02 1.04e+03 9.10e+00 bond pdb=" CB TRP B 624 " pdb=" CG TRP B 624 " ideal model delta sigma weight residual 1.498 1.405 0.093 3.10e-02 1.04e+03 9.04e+00 bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.54e+00 bond pdb=" CB PRO A 111 " pdb=" CG PRO A 111 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.54e+00 bond pdb=" CB TRP B 172 " pdb=" CG TRP B 172 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.15e+00 ... (remaining 11267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 14665 2.32 - 4.64: 541 4.64 - 6.97: 96 6.97 - 9.29: 40 9.29 - 11.61: 6 Bond angle restraints: 15348 Sorted by residual: angle pdb=" C SER B 619 " pdb=" N ALA B 620 " pdb=" CA ALA B 620 " ideal model delta sigma weight residual 121.70 133.31 -11.61 1.80e+00 3.09e-01 4.16e+01 angle pdb=" C SER A 619 " pdb=" N ALA A 620 " pdb=" CA ALA A 620 " ideal model delta sigma weight residual 121.70 133.31 -11.61 1.80e+00 3.09e-01 4.16e+01 angle pdb=" C VAL A 206 " pdb=" N ARG A 207 " pdb=" CA ARG A 207 " ideal model delta sigma weight residual 121.54 130.94 -9.40 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C VAL B 206 " pdb=" N ARG B 207 " pdb=" CA ARG B 207 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" CA TRP B 624 " pdb=" CB TRP B 624 " pdb=" CG TRP B 624 " ideal model delta sigma weight residual 113.60 104.68 8.92 1.90e+00 2.77e-01 2.20e+01 ... (remaining 15343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.25: 5910 12.25 - 24.50: 580 24.50 - 36.75: 120 36.75 - 49.00: 32 49.00 - 61.25: 4 Dihedral angle restraints: 6646 sinusoidal: 2596 harmonic: 4050 Sorted by residual: dihedral pdb=" CA GLN B 135 " pdb=" C GLN B 135 " pdb=" N LEU B 136 " pdb=" CA LEU B 136 " ideal model delta harmonic sigma weight residual -180.00 -131.79 -48.21 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLN A 135 " pdb=" C GLN A 135 " pdb=" N LEU A 136 " pdb=" CA LEU A 136 " ideal model delta harmonic sigma weight residual -180.00 -131.83 -48.17 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA LYS A 134 " pdb=" C LYS A 134 " pdb=" N GLN A 135 " pdb=" CA GLN A 135 " ideal model delta harmonic sigma weight residual 180.00 148.87 31.13 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 6643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1371 0.073 - 0.146: 326 0.146 - 0.218: 34 0.218 - 0.291: 11 0.291 - 0.364: 2 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL B 206 " pdb=" CA VAL B 206 " pdb=" CG1 VAL B 206 " pdb=" CG2 VAL B 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA TYR A 613 " pdb=" N TYR A 613 " pdb=" C TYR A 613 " pdb=" CB TYR A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1741 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 233 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C TYR B 233 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR B 233 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 234 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 233 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C TYR A 233 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR A 233 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 234 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 612 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" C VAL A 612 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL A 612 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 613 " 0.018 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 52 2.58 - 3.16: 8901 3.16 - 3.74: 16886 3.74 - 4.32: 22900 4.32 - 4.90: 37417 Nonbonded interactions: 86156 Sorted by model distance: nonbonded pdb=" O VAL B 612 " pdb=" CD1 TYR B 613 " model vdw 2.000 3.340 nonbonded pdb=" O VAL A 612 " pdb=" CD1 TYR A 613 " model vdw 2.001 3.340 nonbonded pdb=" OG SER A 216 " pdb=" OE1 GLU A 219 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 216 " pdb=" OE1 GLU B 219 " model vdw 2.242 3.040 nonbonded pdb=" O PHE B 420 " pdb=" OG SER B 423 " model vdw 2.314 3.040 ... (remaining 86151 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.008 0.094 11272 Z= 0.323 Angle : 1.110 11.610 15348 Z= 0.589 Chirality : 0.064 0.364 1744 Planarity : 0.009 0.068 1914 Dihedral : 10.644 61.249 4010 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.93 % Favored : 88.77 % Rotamer: Outliers : 0.69 % Allowed : 3.45 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 2.78 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.03 (0.17), residues: 1354 helix: -2.86 (0.13), residues: 860 sheet: -3.31 (1.09), residues: 20 loop : -4.03 (0.23), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 630 TYR 0.048 0.003 TYR A 181 PHE 0.029 0.003 PHE A 21 TRP 0.043 0.004 TRP A 525 HIS 0.009 0.002 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00764 (11272) covalent geometry : angle 1.10977 (15348) hydrogen bonds : bond 0.15687 ( 557) hydrogen bonds : angle 6.99577 ( 1653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 376 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7405 (m110) REVERT: A 165 MET cc_start: 0.8984 (mmm) cc_final: 0.8551 (mpp) REVERT: A 370 SER cc_start: 0.9131 (p) cc_final: 0.8818 (t) REVERT: A 397 GLN cc_start: 0.8925 (mp10) cc_final: 0.8443 (mp10) REVERT: A 415 ILE cc_start: 0.7030 (mm) cc_final: 0.6711 (mm) REVERT: A 428 PHE cc_start: 0.9116 (t80) cc_final: 0.8820 (t80) REVERT: A 446 MET cc_start: 0.8927 (tpt) cc_final: 0.8697 (tpp) REVERT: A 512 LYS cc_start: 0.9126 (tttp) cc_final: 0.8792 (ttmm) REVERT: A 521 MET cc_start: 0.7940 (mmt) cc_final: 0.7468 (mmt) REVERT: A 574 GLN cc_start: 0.8580 (mt0) cc_final: 0.8362 (mt0) REVERT: A 581 LEU cc_start: 0.8919 (mt) cc_final: 0.8698 (mt) REVERT: A 589 MET cc_start: 0.8154 (mmm) cc_final: 0.7795 (mmm) REVERT: A 612 VAL cc_start: 0.8839 (t) cc_final: 0.8499 (p) REVERT: A 682 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7957 (mtm-85) REVERT: A 709 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 712 TYR cc_start: 0.8591 (m-80) cc_final: 0.8236 (m-80) REVERT: B 14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7390 (m110) REVERT: B 165 MET cc_start: 0.8986 (mmm) cc_final: 0.8565 (mpp) REVERT: B 303 LYS cc_start: 0.7984 (mttt) cc_final: 0.7779 (mttt) REVERT: B 378 MET cc_start: 0.8575 (mmt) cc_final: 0.8103 (mmt) REVERT: B 397 GLN cc_start: 0.8824 (mp10) cc_final: 0.8383 (mp10) REVERT: B 446 MET cc_start: 0.8921 (tpt) cc_final: 0.8698 (tpt) REVERT: B 448 MET cc_start: 0.8808 (ttt) cc_final: 0.8244 (ttt) REVERT: B 459 SER cc_start: 0.8685 (m) cc_final: 0.8211 (t) REVERT: B 521 MET cc_start: 0.7893 (mmt) cc_final: 0.7396 (mmt) REVERT: B 589 MET cc_start: 0.8254 (mmm) cc_final: 0.7968 (mmm) REVERT: B 645 LEU cc_start: 0.8316 (mt) cc_final: 0.8105 (mm) REVERT: B 690 MET cc_start: 0.8038 (ttm) cc_final: 0.7739 (ttm) REVERT: B 709 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8441 (tm-30) REVERT: B 712 TYR cc_start: 0.8704 (m-80) cc_final: 0.8406 (m-80) outliers start: 8 outliers final: 6 residues processed: 379 average time/residue: 0.1028 time to fit residues: 55.7939 Evaluate side-chains 268 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 262 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 232 HIS A 340 GLN A 489 GLN A 542 HIS A 607 HIS A 608 GLN B 151 ASN B 232 HIS B 340 GLN B 489 GLN B 495 ASN B 567 ASN B 607 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113909 restraints weight = 18584.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117144 restraints weight = 9920.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119178 restraints weight = 6736.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120313 restraints weight = 5322.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121158 restraints weight = 4656.055| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11272 Z= 0.164 Angle : 0.729 8.023 15348 Z= 0.382 Chirality : 0.046 0.171 1744 Planarity : 0.006 0.058 1914 Dihedral : 7.321 49.908 1478 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 3.53 % Allowed : 10.52 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.20), residues: 1354 helix: -1.48 (0.16), residues: 870 sheet: -3.33 (1.05), residues: 30 loop : -3.82 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 698 TYR 0.023 0.002 TYR A 181 PHE 0.018 0.001 PHE B 428 TRP 0.027 0.002 TRP B 624 HIS 0.006 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00380 (11272) covalent geometry : angle 0.72861 (15348) hydrogen bonds : bond 0.04101 ( 557) hydrogen bonds : angle 4.51561 ( 1653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 311 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7975 (m-40) cc_final: 0.7561 (m110) REVERT: A 36 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7825 (mmt180) REVERT: A 257 ASN cc_start: 0.8784 (m-40) cc_final: 0.8491 (m110) REVERT: A 307 LYS cc_start: 0.8606 (mttt) cc_final: 0.8030 (mttt) REVERT: A 370 SER cc_start: 0.8927 (p) cc_final: 0.8621 (t) REVERT: A 415 ILE cc_start: 0.6725 (mm) cc_final: 0.6479 (mm) REVERT: A 436 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8729 (mm) REVERT: A 446 MET cc_start: 0.9120 (tpt) cc_final: 0.8671 (tpp) REVERT: A 488 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 512 LYS cc_start: 0.9106 (tttp) cc_final: 0.8890 (ttmm) REVERT: A 613 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: A 712 TYR cc_start: 0.8518 (m-80) cc_final: 0.8145 (m-80) REVERT: B 36 ARG cc_start: 0.8220 (tpp-160) cc_final: 0.7965 (mmt-90) REVERT: B 103 TRP cc_start: 0.7856 (t-100) cc_final: 0.7552 (t-100) REVERT: B 182 GLU cc_start: 0.8167 (tt0) cc_final: 0.7912 (tt0) REVERT: B 204 VAL cc_start: 0.9574 (t) cc_final: 0.9332 (m) REVERT: B 257 ASN cc_start: 0.8741 (m-40) cc_final: 0.8468 (m110) REVERT: B 307 LYS cc_start: 0.8521 (mttt) cc_final: 0.7661 (mttt) REVERT: B 422 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8201 (ttpt) REVERT: B 446 MET cc_start: 0.9065 (tpt) cc_final: 0.8599 (tpp) REVERT: B 459 SER cc_start: 0.8576 (m) cc_final: 0.8229 (t) REVERT: B 712 TYR cc_start: 0.8580 (m-80) cc_final: 0.8195 (m-80) outliers start: 41 outliers final: 28 residues processed: 334 average time/residue: 0.0986 time to fit residues: 47.6016 Evaluate side-chains 297 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 670 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 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 151 ASN A 340 GLN A 567 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 340 GLN B 567 ASN B 710 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113482 restraints weight = 18665.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116716 restraints weight = 9897.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118782 restraints weight = 6667.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120060 restraints weight = 5229.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120817 restraints weight = 4523.583| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.136 Angle : 0.663 8.213 15348 Z= 0.347 Chirality : 0.044 0.172 1744 Planarity : 0.005 0.059 1914 Dihedral : 6.826 53.613 1478 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.31 % Favored : 90.55 % Rotamer: Outliers : 3.62 % Allowed : 14.83 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.22), residues: 1354 helix: -0.77 (0.17), residues: 894 sheet: -3.09 (1.11), residues: 30 loop : -3.67 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 198 TYR 0.017 0.002 TYR B 181 PHE 0.020 0.001 PHE B 428 TRP 0.021 0.001 TRP A 525 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00312 (11272) covalent geometry : angle 0.66262 (15348) hydrogen bonds : bond 0.03479 ( 557) hydrogen bonds : angle 4.05550 ( 1653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8223 (tpp-160) cc_final: 0.7702 (tpp-160) REVERT: A 78 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 200 ASP cc_start: 0.8039 (t0) cc_final: 0.7820 (t0) REVERT: A 257 ASN cc_start: 0.8707 (m-40) cc_final: 0.8456 (m110) REVERT: A 303 LYS cc_start: 0.9085 (tptp) cc_final: 0.8845 (tptp) REVERT: A 415 ILE cc_start: 0.6527 (mm) cc_final: 0.6121 (mm) REVERT: A 421 MET cc_start: 0.8419 (mmt) cc_final: 0.8068 (mmt) REVERT: A 446 MET cc_start: 0.9125 (tpt) cc_final: 0.8623 (tpp) REVERT: A 459 SER cc_start: 0.8602 (m) cc_final: 0.8263 (t) REVERT: A 525 TRP cc_start: 0.7766 (t-100) cc_final: 0.7434 (t-100) REVERT: A 531 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: A 570 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8693 (tm-30) REVERT: A 613 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: A 712 TYR cc_start: 0.8561 (m-80) cc_final: 0.8199 (m-80) REVERT: B 78 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 103 TRP cc_start: 0.7831 (t-100) cc_final: 0.7599 (t-100) REVERT: B 182 GLU cc_start: 0.8144 (tt0) cc_final: 0.7872 (tt0) REVERT: B 303 LYS cc_start: 0.9028 (tptp) cc_final: 0.8787 (tptp) REVERT: B 415 ILE cc_start: 0.6390 (mm) cc_final: 0.5932 (mm) REVERT: B 421 MET cc_start: 0.8049 (tpp) cc_final: 0.7672 (mmt) REVERT: B 422 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8204 (ttpt) REVERT: B 446 MET cc_start: 0.9097 (tpt) cc_final: 0.8630 (tpp) REVERT: B 459 SER cc_start: 0.8632 (m) cc_final: 0.8227 (t) REVERT: B 505 ILE cc_start: 0.8499 (tt) cc_final: 0.8279 (tt) REVERT: B 531 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: B 613 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.7092 (m-10) REVERT: B 702 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6062 (mm) REVERT: B 712 TYR cc_start: 0.8600 (m-80) cc_final: 0.8235 (m-80) outliers start: 42 outliers final: 24 residues processed: 306 average time/residue: 0.0992 time to fit residues: 44.3885 Evaluate side-chains 285 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 670 HIS Chi-restraints excluded: chain B residue 702 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 567 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113633 restraints weight = 18680.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116881 restraints weight = 9920.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118903 restraints weight = 6673.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120124 restraints weight = 5250.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120918 restraints weight = 4547.390| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11272 Z= 0.130 Angle : 0.651 7.971 15348 Z= 0.335 Chirality : 0.044 0.164 1744 Planarity : 0.005 0.046 1914 Dihedral : 6.576 56.233 1478 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.62 % Allowed : 16.29 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.23), residues: 1354 helix: -0.28 (0.17), residues: 892 sheet: -2.93 (1.10), residues: 30 loop : -3.39 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 198 TYR 0.015 0.002 TYR A 468 PHE 0.023 0.001 PHE A 428 TRP 0.022 0.001 TRP A 525 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00301 (11272) covalent geometry : angle 0.65126 (15348) hydrogen bonds : bond 0.03195 ( 557) hydrogen bonds : angle 3.88659 ( 1653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.7473 (mmm160) REVERT: A 78 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 190 GLN cc_start: 0.8270 (tp40) cc_final: 0.7974 (tp40) REVERT: A 257 ASN cc_start: 0.8681 (m-40) cc_final: 0.8453 (m110) REVERT: A 403 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: A 421 MET cc_start: 0.8382 (mmt) cc_final: 0.8059 (mmt) REVERT: A 446 MET cc_start: 0.9160 (tpt) cc_final: 0.8703 (tpp) REVERT: A 459 SER cc_start: 0.8587 (m) cc_final: 0.8266 (t) REVERT: A 488 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 521 MET cc_start: 0.8915 (mmm) cc_final: 0.8196 (mmm) REVERT: A 531 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 570 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8797 (tm-30) REVERT: A 613 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.7103 (m-10) REVERT: A 712 TYR cc_start: 0.8559 (m-80) cc_final: 0.8216 (m-80) REVERT: B 14 ASN cc_start: 0.7628 (m110) cc_final: 0.7385 (m110) REVERT: B 36 ARG cc_start: 0.8508 (tpp-160) cc_final: 0.8031 (tpp-160) REVERT: B 78 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 182 GLU cc_start: 0.8214 (tt0) cc_final: 0.7941 (tt0) REVERT: B 378 MET cc_start: 0.8580 (mmt) cc_final: 0.8174 (mmm) REVERT: B 446 MET cc_start: 0.9135 (tpt) cc_final: 0.8679 (tpp) REVERT: B 459 SER cc_start: 0.8619 (m) cc_final: 0.8267 (t) REVERT: B 488 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7552 (mt-10) REVERT: B 512 LYS cc_start: 0.9106 (tttp) cc_final: 0.8280 (tttm) REVERT: B 531 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: B 613 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: B 702 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6291 (mm) REVERT: B 712 TYR cc_start: 0.8603 (m-80) cc_final: 0.8217 (m-80) outliers start: 42 outliers final: 25 residues processed: 293 average time/residue: 0.0898 time to fit residues: 39.0714 Evaluate side-chains 282 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 670 HIS Chi-restraints excluded: chain B residue 702 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 17 optimal weight: 0.0000 chunk 31 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 397 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111680 restraints weight = 18669.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114829 restraints weight = 10063.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116836 restraints weight = 6846.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118014 restraints weight = 5371.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118819 restraints weight = 4671.863| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.129 Angle : 0.650 8.334 15348 Z= 0.331 Chirality : 0.044 0.162 1744 Planarity : 0.005 0.043 1914 Dihedral : 6.356 58.788 1478 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 4.74 % Allowed : 16.55 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.23), residues: 1354 helix: 0.09 (0.18), residues: 888 sheet: -2.93 (1.06), residues: 30 loop : -3.28 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 698 TYR 0.015 0.002 TYR A 468 PHE 0.024 0.001 PHE A 428 TRP 0.016 0.001 TRP B 525 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00301 (11272) covalent geometry : angle 0.65030 (15348) hydrogen bonds : bond 0.03132 ( 557) hydrogen bonds : angle 3.77208 ( 1653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8412 (tpp-160) cc_final: 0.7326 (mmm160) REVERT: A 47 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7014 (pp) REVERT: A 78 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 190 GLN cc_start: 0.8334 (tp40) cc_final: 0.8005 (tp40) REVERT: A 257 ASN cc_start: 0.8660 (m-40) cc_final: 0.8454 (m110) REVERT: A 299 ASP cc_start: 0.6956 (m-30) cc_final: 0.6741 (t0) REVERT: A 307 LYS cc_start: 0.8458 (mttt) cc_final: 0.8147 (ttmt) REVERT: A 403 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: A 421 MET cc_start: 0.8400 (mmt) cc_final: 0.8194 (mmt) REVERT: A 446 MET cc_start: 0.9175 (tpt) cc_final: 0.8750 (tpp) REVERT: A 459 SER cc_start: 0.8662 (m) cc_final: 0.8311 (t) REVERT: A 488 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 505 ILE cc_start: 0.8532 (tt) cc_final: 0.8314 (tt) REVERT: A 521 MET cc_start: 0.9059 (mmm) cc_final: 0.8795 (mmm) REVERT: A 531 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: A 570 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8837 (tm-30) REVERT: A 613 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.7043 (m-10) REVERT: A 712 TYR cc_start: 0.8586 (m-80) cc_final: 0.8129 (m-80) REVERT: B 14 ASN cc_start: 0.7771 (m110) cc_final: 0.7499 (m110) REVERT: B 36 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8175 (tpp80) REVERT: B 47 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6968 (pp) REVERT: B 78 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 182 GLU cc_start: 0.8194 (tt0) cc_final: 0.7931 (tt0) REVERT: B 446 MET cc_start: 0.9163 (tpt) cc_final: 0.8723 (tpp) REVERT: B 459 SER cc_start: 0.8667 (m) cc_final: 0.8293 (t) REVERT: B 488 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 512 LYS cc_start: 0.9073 (tttp) cc_final: 0.8279 (tttm) REVERT: B 531 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: B 613 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.6944 (m-10) REVERT: B 702 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6234 (mm) REVERT: B 712 TYR cc_start: 0.8600 (m-80) cc_final: 0.8193 (m-80) outliers start: 55 outliers final: 32 residues processed: 296 average time/residue: 0.0893 time to fit residues: 39.4984 Evaluate side-chains 288 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 670 HIS Chi-restraints excluded: chain B residue 702 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 124 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 29 optimal weight: 0.0060 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112748 restraints weight = 18611.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116004 restraints weight = 9850.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118037 restraints weight = 6592.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119317 restraints weight = 5148.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120076 restraints weight = 4431.261| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11272 Z= 0.125 Angle : 0.645 7.767 15348 Z= 0.327 Chirality : 0.043 0.158 1744 Planarity : 0.005 0.043 1914 Dihedral : 6.032 57.786 1476 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.45 % Allowed : 19.05 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.23), residues: 1354 helix: 0.33 (0.18), residues: 892 sheet: -2.91 (1.05), residues: 30 loop : -3.23 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 698 TYR 0.014 0.001 TYR A 468 PHE 0.025 0.001 PHE A 428 TRP 0.012 0.001 TRP A 624 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00293 (11272) covalent geometry : angle 0.64490 (15348) hydrogen bonds : bond 0.02993 ( 557) hydrogen bonds : angle 3.72332 ( 1653) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7795 (m110) cc_final: 0.7536 (m110) REVERT: A 36 ARG cc_start: 0.8424 (tpp-160) cc_final: 0.7301 (mmm160) REVERT: A 47 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7055 (pp) REVERT: A 78 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7388 (tm-30) REVERT: A 182 GLU cc_start: 0.8171 (tt0) cc_final: 0.7924 (tt0) REVERT: A 190 GLN cc_start: 0.8348 (tp40) cc_final: 0.7983 (tp40) REVERT: A 299 ASP cc_start: 0.6954 (m-30) cc_final: 0.6736 (t0) REVERT: A 307 LYS cc_start: 0.8417 (mttt) cc_final: 0.8182 (ttmt) REVERT: A 403 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: A 436 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 446 MET cc_start: 0.9158 (tpt) cc_final: 0.8742 (tpp) REVERT: A 459 SER cc_start: 0.8673 (m) cc_final: 0.8317 (t) REVERT: A 488 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 531 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: A 570 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8838 (tm-30) REVERT: A 613 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: A 712 TYR cc_start: 0.8602 (m-80) cc_final: 0.8131 (m-80) REVERT: B 14 ASN cc_start: 0.7908 (m110) cc_final: 0.7537 (m110) REVERT: B 36 ARG cc_start: 0.8587 (tpp-160) cc_final: 0.7805 (mmm160) REVERT: B 47 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6948 (pp) REVERT: B 78 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 421 MET cc_start: 0.8077 (tpp) cc_final: 0.7748 (mmt) REVERT: B 446 MET cc_start: 0.9182 (tpt) cc_final: 0.8765 (tpp) REVERT: B 459 SER cc_start: 0.8666 (m) cc_final: 0.8294 (t) REVERT: B 488 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 521 MET cc_start: 0.9056 (mmp) cc_final: 0.8805 (mmm) REVERT: B 531 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: B 613 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.6951 (m-10) REVERT: B 643 MET cc_start: 0.8023 (tpp) cc_final: 0.7784 (mtt) REVERT: B 712 TYR cc_start: 0.8599 (m-80) cc_final: 0.8188 (m-80) outliers start: 40 outliers final: 28 residues processed: 280 average time/residue: 0.0873 time to fit residues: 37.1703 Evaluate side-chains 284 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 670 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 0.0470 chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116345 restraints weight = 18617.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119601 restraints weight = 9960.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121664 restraints weight = 6707.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122902 restraints weight = 5255.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123621 restraints weight = 4553.553| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11272 Z= 0.117 Angle : 0.635 8.366 15348 Z= 0.321 Chirality : 0.043 0.156 1744 Planarity : 0.005 0.043 1914 Dihedral : 5.831 53.208 1476 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 3.79 % Allowed : 19.57 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1354 helix: 0.55 (0.18), residues: 902 sheet: -2.88 (1.05), residues: 30 loop : -3.18 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 698 TYR 0.013 0.001 TYR A 468 PHE 0.026 0.001 PHE A 428 TRP 0.011 0.001 TRP B 525 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00271 (11272) covalent geometry : angle 0.63515 (15348) hydrogen bonds : bond 0.02919 ( 557) hydrogen bonds : angle 3.72098 ( 1653) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7799 (m110) cc_final: 0.7519 (m110) REVERT: A 36 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.7573 (mmm160) REVERT: A 47 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7072 (pp) REVERT: A 78 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 182 GLU cc_start: 0.8158 (tt0) cc_final: 0.7903 (tt0) REVERT: A 190 GLN cc_start: 0.8295 (tp40) cc_final: 0.7925 (tp40) REVERT: A 307 LYS cc_start: 0.8412 (mttt) cc_final: 0.8167 (ttmt) REVERT: A 370 SER cc_start: 0.8826 (p) cc_final: 0.8537 (t) REVERT: A 403 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: A 436 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8508 (mm) REVERT: A 446 MET cc_start: 0.9075 (tpt) cc_final: 0.8645 (tpp) REVERT: A 459 SER cc_start: 0.8644 (m) cc_final: 0.8218 (t) REVERT: A 488 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 531 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: A 570 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8863 (tm-30) REVERT: A 613 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7008 (m-10) REVERT: A 643 MET cc_start: 0.8299 (tpp) cc_final: 0.8053 (mtt) REVERT: A 712 TYR cc_start: 0.8611 (m-80) cc_final: 0.8206 (m-80) REVERT: B 14 ASN cc_start: 0.8002 (m110) cc_final: 0.7609 (m110) REVERT: B 36 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.7804 (mmm160) REVERT: B 47 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6952 (pp) REVERT: B 421 MET cc_start: 0.8054 (tpp) cc_final: 0.7793 (mmt) REVERT: B 446 MET cc_start: 0.9213 (tpt) cc_final: 0.8811 (tpp) REVERT: B 459 SER cc_start: 0.8625 (m) cc_final: 0.8240 (t) REVERT: B 488 GLU cc_start: 0.8128 (mt-10) cc_final: 0.6675 (mt-10) REVERT: B 512 LYS cc_start: 0.8970 (tttp) cc_final: 0.8125 (ttmm) REVERT: B 531 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: B 613 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7298 (m-10) REVERT: B 702 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6125 (mm) REVERT: B 712 TYR cc_start: 0.8618 (m-80) cc_final: 0.8188 (m-80) outliers start: 44 outliers final: 29 residues processed: 300 average time/residue: 0.0836 time to fit residues: 38.3608 Evaluate side-chains 298 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 670 HIS Chi-restraints excluded: chain B residue 702 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 70 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117739 restraints weight = 18538.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120988 restraints weight = 9927.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123065 restraints weight = 6698.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124259 restraints weight = 5245.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125040 restraints weight = 4558.101| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11272 Z= 0.116 Angle : 0.642 8.646 15348 Z= 0.323 Chirality : 0.043 0.164 1744 Planarity : 0.005 0.044 1914 Dihedral : 5.660 48.771 1476 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 4.22 % Allowed : 20.95 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1354 helix: 0.69 (0.18), residues: 900 sheet: -2.82 (1.06), residues: 30 loop : -3.11 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 698 TYR 0.013 0.001 TYR A 468 PHE 0.026 0.001 PHE A 428 TRP 0.010 0.001 TRP A 624 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00266 (11272) covalent geometry : angle 0.64164 (15348) hydrogen bonds : bond 0.02862 ( 557) hydrogen bonds : angle 3.73426 ( 1653) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7889 (m110) cc_final: 0.7599 (m110) REVERT: A 36 ARG cc_start: 0.8333 (tpp-160) cc_final: 0.7547 (mmm160) REVERT: A 47 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7119 (pp) REVERT: A 126 THR cc_start: 0.7828 (p) cc_final: 0.7611 (t) REVERT: A 378 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7844 (mmm) REVERT: A 403 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: A 436 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8485 (mm) REVERT: A 446 MET cc_start: 0.9087 (tpt) cc_final: 0.8616 (tpp) REVERT: A 459 SER cc_start: 0.8561 (m) cc_final: 0.8187 (t) REVERT: A 488 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7277 (mt-10) REVERT: A 512 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8608 (mmtp) REVERT: A 521 MET cc_start: 0.8951 (mmm) cc_final: 0.8667 (mmm) REVERT: A 531 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: A 570 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8834 (tm-30) REVERT: A 613 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7072 (m-10) REVERT: A 712 TYR cc_start: 0.8614 (m-80) cc_final: 0.8201 (m-80) REVERT: B 36 ARG cc_start: 0.8574 (tpp-160) cc_final: 0.7784 (mmm160) REVERT: B 47 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6907 (pp) REVERT: B 250 LYS cc_start: 0.8797 (tttt) cc_final: 0.8542 (ttpp) REVERT: B 378 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7790 (mmm) REVERT: B 420 PHE cc_start: 0.7381 (t80) cc_final: 0.6886 (m-10) REVERT: B 421 MET cc_start: 0.8060 (tpp) cc_final: 0.7767 (mmt) REVERT: B 446 MET cc_start: 0.9210 (tpt) cc_final: 0.8773 (tpp) REVERT: B 459 SER cc_start: 0.8675 (m) cc_final: 0.8305 (t) REVERT: B 488 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7770 (mt-10) REVERT: B 512 LYS cc_start: 0.8973 (tttp) cc_final: 0.8405 (tttm) REVERT: B 521 MET cc_start: 0.8744 (mmp) cc_final: 0.8328 (mmm) REVERT: B 531 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: B 576 TYR cc_start: 0.8374 (m-80) cc_final: 0.8072 (m-80) REVERT: B 613 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7327 (m-10) REVERT: B 702 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6092 (mm) REVERT: B 712 TYR cc_start: 0.8680 (m-80) cc_final: 0.8270 (m-80) outliers start: 49 outliers final: 32 residues processed: 298 average time/residue: 0.0884 time to fit residues: 39.7818 Evaluate side-chains 292 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 702 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN B 151 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115106 restraints weight = 18621.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118336 restraints weight = 9982.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120370 restraints weight = 6736.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121629 restraints weight = 5309.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122293 restraints weight = 4593.427| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11272 Z= 0.145 Angle : 0.670 8.734 15348 Z= 0.340 Chirality : 0.044 0.159 1744 Planarity : 0.005 0.046 1914 Dihedral : 5.642 48.068 1476 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 4.05 % Allowed : 21.72 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.24), residues: 1354 helix: 0.80 (0.18), residues: 888 sheet: -2.74 (1.08), residues: 30 loop : -3.04 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 698 TYR 0.015 0.002 TYR A 468 PHE 0.035 0.001 PHE B 428 TRP 0.013 0.001 TRP B 624 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00348 (11272) covalent geometry : angle 0.66956 (15348) hydrogen bonds : bond 0.03020 ( 557) hydrogen bonds : angle 3.79989 ( 1653) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8322 (tpp-160) cc_final: 0.7673 (tpp80) REVERT: A 47 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7167 (pp) REVERT: A 126 THR cc_start: 0.8097 (p) cc_final: 0.7850 (t) REVERT: A 161 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8266 (t) REVERT: A 307 LYS cc_start: 0.8369 (mttt) cc_final: 0.8159 (mttt) REVERT: A 370 SER cc_start: 0.8944 (p) cc_final: 0.8718 (t) REVERT: A 403 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: A 436 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8526 (mm) REVERT: A 446 MET cc_start: 0.9137 (tpt) cc_final: 0.8674 (tpp) REVERT: A 459 SER cc_start: 0.8662 (m) cc_final: 0.8365 (t) REVERT: A 488 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7357 (mt-10) REVERT: A 512 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8526 (mmtp) REVERT: A 521 MET cc_start: 0.9028 (mmm) cc_final: 0.8614 (mmm) REVERT: A 531 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: A 570 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8843 (tm-30) REVERT: A 613 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.7025 (m-10) REVERT: A 712 TYR cc_start: 0.8647 (m-80) cc_final: 0.8055 (m-80) REVERT: B 36 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.7803 (mmm160) REVERT: B 47 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6930 (pp) REVERT: B 420 PHE cc_start: 0.7409 (t80) cc_final: 0.6914 (m-10) REVERT: B 421 MET cc_start: 0.8146 (tpp) cc_final: 0.7848 (mmt) REVERT: B 446 MET cc_start: 0.9264 (tpt) cc_final: 0.8836 (tpp) REVERT: B 448 MET cc_start: 0.8709 (ttp) cc_final: 0.8269 (ttp) REVERT: B 459 SER cc_start: 0.8738 (m) cc_final: 0.8351 (t) REVERT: B 488 GLU cc_start: 0.8254 (mt-10) cc_final: 0.6659 (mt-10) REVERT: B 512 LYS cc_start: 0.8999 (tttp) cc_final: 0.8187 (ttmm) REVERT: B 521 MET cc_start: 0.9066 (mmp) cc_final: 0.8375 (mmm) REVERT: B 531 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: B 613 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.7308 (m-10) REVERT: B 712 TYR cc_start: 0.8645 (m-80) cc_final: 0.8118 (m-80) outliers start: 47 outliers final: 31 residues processed: 280 average time/residue: 0.0834 time to fit residues: 35.5561 Evaluate side-chains 280 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 63 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117370 restraints weight = 18525.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120692 restraints weight = 9810.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122764 restraints weight = 6576.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124021 restraints weight = 5159.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124818 restraints weight = 4475.852| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11272 Z= 0.136 Angle : 0.686 12.087 15348 Z= 0.345 Chirality : 0.044 0.164 1744 Planarity : 0.005 0.046 1914 Dihedral : 5.575 42.489 1476 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 3.62 % Allowed : 22.33 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.24), residues: 1354 helix: 0.80 (0.18), residues: 890 sheet: -2.67 (1.09), residues: 30 loop : -2.96 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 698 TYR 0.015 0.002 TYR B 576 PHE 0.033 0.001 PHE B 428 TRP 0.014 0.001 TRP B 525 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00322 (11272) covalent geometry : angle 0.68643 (15348) hydrogen bonds : bond 0.03066 ( 557) hydrogen bonds : angle 3.84997 ( 1653) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.7627 (tpp80) REVERT: A 47 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7163 (pp) REVERT: A 126 THR cc_start: 0.8125 (p) cc_final: 0.7885 (t) REVERT: A 161 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 370 SER cc_start: 0.8976 (p) cc_final: 0.8757 (t) REVERT: A 403 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: A 436 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8521 (mm) REVERT: A 446 MET cc_start: 0.9105 (tpt) cc_final: 0.8682 (tpp) REVERT: A 459 SER cc_start: 0.8656 (m) cc_final: 0.8372 (t) REVERT: A 488 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7338 (mt-10) REVERT: A 512 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8600 (mmtp) REVERT: A 521 MET cc_start: 0.9177 (mmm) cc_final: 0.8761 (mmm) REVERT: A 531 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: A 570 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8848 (tm-30) REVERT: A 613 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: A 712 TYR cc_start: 0.8646 (m-80) cc_final: 0.8017 (m-80) REVERT: B 36 ARG cc_start: 0.8598 (tpp-160) cc_final: 0.7796 (mmm160) REVERT: B 47 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6958 (pp) REVERT: B 420 PHE cc_start: 0.7401 (t80) cc_final: 0.6862 (m-10) REVERT: B 421 MET cc_start: 0.8134 (tpp) cc_final: 0.7820 (mmt) REVERT: B 446 MET cc_start: 0.9214 (tpt) cc_final: 0.8785 (tpt) REVERT: B 459 SER cc_start: 0.8723 (m) cc_final: 0.8370 (t) REVERT: B 488 GLU cc_start: 0.8243 (mt-10) cc_final: 0.6648 (mt-10) REVERT: B 512 LYS cc_start: 0.8956 (tttp) cc_final: 0.8167 (ttmm) REVERT: B 521 MET cc_start: 0.9053 (mmp) cc_final: 0.8495 (mmm) REVERT: B 531 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: B 613 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.6986 (m-10) REVERT: B 712 TYR cc_start: 0.8691 (m-80) cc_final: 0.8181 (m-80) outliers start: 42 outliers final: 30 residues processed: 271 average time/residue: 0.0859 time to fit residues: 35.8729 Evaluate side-chains 278 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 8.9990 chunk 98 optimal weight: 0.2980 chunk 120 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 40 optimal weight: 0.0040 chunk 69 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117789 restraints weight = 18479.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121013 restraints weight = 9904.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123064 restraints weight = 6732.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124320 restraints weight = 5310.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125075 restraints weight = 4612.320| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11272 Z= 0.121 Angle : 0.663 8.323 15348 Z= 0.335 Chirality : 0.043 0.167 1744 Planarity : 0.005 0.046 1914 Dihedral : 5.376 42.400 1474 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.36 % Allowed : 22.50 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.24), residues: 1354 helix: 0.86 (0.18), residues: 888 sheet: -2.60 (1.11), residues: 30 loop : -2.96 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 698 TYR 0.014 0.001 TYR B 576 PHE 0.030 0.001 PHE B 428 TRP 0.015 0.001 TRP B 525 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00280 (11272) covalent geometry : angle 0.66323 (15348) hydrogen bonds : bond 0.02997 ( 557) hydrogen bonds : angle 3.81948 ( 1653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1922.02 seconds wall clock time: 33 minutes 59.35 seconds (2039.35 seconds total)