Starting phenix.real_space_refine on Mon Apr 6 00:10:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lk6_63169/04_2026/9lk6_63169.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lk6_63169/04_2026/9lk6_63169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lk6_63169/04_2026/9lk6_63169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lk6_63169/04_2026/9lk6_63169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lk6_63169/04_2026/9lk6_63169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lk6_63169/04_2026/9lk6_63169.map" } resolution = 3.27 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= 0.021 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 92 5.16 5 C 9038 2.51 5 N 2462 2.21 5 O 2642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14234 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5711 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 22, 'TRANS': 697} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "C" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 5711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5711 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 22, 'TRANS': 697} Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "F" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Time building chain proxies: 3.23, per 1000 atoms: 0.23 Number of scatterers: 14234 At special positions: 0 Unit cell: (144.8, 112.8, 125.6, 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 92 16.00 O 2642 8.00 N 2462 7.00 C 9038 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: 1.19 Conformation dependent library (CDL) restraints added in 480.3 milliseconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3452 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 6 sheets defined 55.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 removed outlier: 3.630A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 33 removed outlier: 4.078A pdb=" N PHE A 33 " --> pdb=" O HIS A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 33' Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.720A pdb=" N GLN A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 201 through 208 removed outlier: 3.697A pdb=" N LEU A 205 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 206 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.590A pdb=" N GLU A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.814A pdb=" N ARG A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.571A pdb=" N VAL A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.729A pdb=" N THR A 311 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.687A pdb=" N HIS A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 351 " --> pdb=" O HIS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.680A pdb=" N ASN A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.698A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.929A pdb=" N ASP A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 433 removed outlier: 3.782A pdb=" N ASN A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.681A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.861A pdb=" N ALA A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 479 removed outlier: 3.903A pdb=" N ARG A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 471 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 511 through 525 removed outlier: 3.572A pdb=" N LYS A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.874A pdb=" N CYS A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 Processing helix chain 'A' and resid 554 through 571 removed outlier: 3.555A pdb=" N GLN A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 571 " --> pdb=" O ASN A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.738A pdb=" N GLU A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.993A pdb=" N HIS A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 612 removed outlier: 3.586A pdb=" N SER A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 612 " --> pdb=" O HIS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 637 removed outlier: 4.246A pdb=" N SER A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 660 removed outlier: 3.941A pdb=" N CYS A 660 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 removed outlier: 4.054A pdb=" N GLN A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 removed outlier: 4.138A pdb=" N SER A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 Processing helix chain 'A' and resid 708 through 729 Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.618A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE B 34 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.521A pdb=" N GLY B 61 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.859A pdb=" N THR C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 3.812A pdb=" N SER C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 84 removed outlier: 3.820A pdb=" N LYS C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 removed outlier: 3.554A pdb=" N MET C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 removed outlier: 3.709A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 removed outlier: 3.567A pdb=" N PHE D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 33' Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 51 through 66 Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 120 through 130 Processing helix chain 'D' and resid 131 through 138 removed outlier: 3.717A pdb=" N GLN D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 201 through 208 removed outlier: 3.509A pdb=" N ALA D 206 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 208 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 235 removed outlier: 3.517A pdb=" N GLU D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.854A pdb=" N ARG D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 291 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 337 through 352 removed outlier: 3.580A pdb=" N PHE D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 348 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER D 350 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.786A pdb=" N ASN D 372 " --> pdb=" O THR D 368 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 391 removed outlier: 3.664A pdb=" N ASN D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 408 removed outlier: 3.960A pdb=" N ASP D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.689A pdb=" N GLU D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 434 through 440 removed outlier: 3.506A pdb=" N GLN D 439 " --> pdb=" O ASP D 435 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 459 removed outlier: 3.735A pdb=" N ALA D 448 " --> pdb=" O ASN D 444 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 478 removed outlier: 4.066A pdb=" N ARG D 466 " --> pdb=" O GLN D 462 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET D 467 " --> pdb=" O ASN D 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 468 " --> pdb=" O MET D 464 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS D 478 " --> pdb=" O ILE D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 508 removed outlier: 3.737A pdb=" N LEU D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 500 " --> pdb=" O GLN D 496 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 501 " --> pdb=" O LEU D 497 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS D 502 " --> pdb=" O LEU D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 524 removed outlier: 3.651A pdb=" N LYS D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 538 removed outlier: 3.886A pdb=" N CYS D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 551 removed outlier: 4.205A pdb=" N LEU D 543 " --> pdb=" O GLN D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.193A pdb=" N LYS D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 561 " --> pdb=" O ILE D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 579 Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.925A pdb=" N HIS D 592 " --> pdb=" O SER D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 611 Processing helix chain 'D' and resid 622 through 637 Processing helix chain 'D' and resid 655 through 660 removed outlier: 4.219A pdb=" N CYS D 660 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 681 removed outlier: 3.827A pdb=" N GLN D 667 " --> pdb=" O THR D 663 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 681 " --> pdb=" O VAL D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 692 removed outlier: 3.782A pdb=" N MET D 688 " --> pdb=" O ARG D 684 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU D 689 " --> pdb=" O TYR D 685 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE D 690 " --> pdb=" O CYS D 686 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 703 removed outlier: 4.101A pdb=" N HIS D 697 " --> pdb=" O GLY D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 729 Processing helix chain 'E' and resid 23 through 36 removed outlier: 4.010A pdb=" N ARG E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 34 " --> pdb=" O ILE E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.596A pdb=" N GLY E 61 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 37 Processing helix chain 'F' and resid 39 through 47 Processing helix chain 'F' and resid 68 through 84 removed outlier: 4.079A pdb=" N LYS F 72 " --> pdb=" O HIS F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 removed outlier: 4.228A pdb=" N MET F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 192 removed outlier: 6.940A pdb=" N LEU A 191 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU A 214 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 242 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.663A pdb=" N ALA B 73 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS C 32 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N ASP B 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AA5, first strand: chain 'D' and resid 190 through 192 removed outlier: 7.086A pdb=" N LEU D 191 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU D 242 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 44 through 45 removed outlier: 3.516A pdb=" N GLY E 76 " --> pdb=" O TYR E 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 73 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LYS F 32 " --> pdb=" O PHE E 15 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N ASP E 17 " --> pdb=" O LYS F 32 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4685 1.34 - 1.46: 1820 1.46 - 1.58: 7855 1.58 - 1.70: 0 1.70 - 1.81: 142 Bond restraints: 14502 Sorted by residual: bond pdb=" N ASP A 39 " pdb=" CA ASP A 39 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.40e+00 bond pdb=" N LEU A 42 " pdb=" CA LEU A 42 " ideal model delta sigma weight residual 1.452 1.487 -0.034 1.25e-02 6.40e+03 7.59e+00 bond pdb=" N CYS A 157 " pdb=" CA CYS A 157 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.48e+00 bond pdb=" N TYR A 154 " pdb=" CA TYR A 154 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.85e+00 bond pdb=" N GLU A 155 " pdb=" CA GLU A 155 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.34e-02 5.57e+03 6.27e+00 ... (remaining 14497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 19135 1.57 - 3.13: 382 3.13 - 4.70: 75 4.70 - 6.26: 30 6.26 - 7.83: 10 Bond angle restraints: 19632 Sorted by residual: angle pdb=" CA GLN A 38 " pdb=" C GLN A 38 " pdb=" O GLN A 38 " ideal model delta sigma weight residual 121.55 116.91 4.64 1.06e+00 8.90e-01 1.92e+01 angle pdb=" CA GLU D 549 " pdb=" CB GLU D 549 " pdb=" CG GLU D 549 " ideal model delta sigma weight residual 114.10 121.16 -7.06 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA ARG A 37 " pdb=" C ARG A 37 " pdb=" O ARG A 37 " ideal model delta sigma weight residual 121.36 117.68 3.68 1.06e+00 8.90e-01 1.20e+01 angle pdb=" O ASP A 152 " pdb=" C ASP A 152 " pdb=" N PRO A 153 " ideal model delta sigma weight residual 121.32 117.44 3.88 1.15e+00 7.56e-01 1.14e+01 angle pdb=" CA THR A 41 " pdb=" C THR A 41 " pdb=" O THR A 41 " ideal model delta sigma weight residual 121.47 117.76 3.71 1.15e+00 7.56e-01 1.04e+01 ... (remaining 19627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 7400 17.20 - 34.39: 1045 34.39 - 51.59: 294 51.59 - 68.78: 60 68.78 - 85.98: 23 Dihedral angle restraints: 8822 sinusoidal: 3548 harmonic: 5274 Sorted by residual: dihedral pdb=" CA ASP E 48 " pdb=" CB ASP E 48 " pdb=" CG ASP E 48 " pdb=" OD1 ASP E 48 " ideal model delta sinusoidal sigma weight residual -30.00 -90.37 60.37 1 2.00e+01 2.50e-03 1.21e+01 dihedral pdb=" CA GLU A 490 " pdb=" C GLU A 490 " pdb=" N LEU A 491 " pdb=" CA LEU A 491 " ideal model delta harmonic sigma weight residual 180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB GLU F 64 " pdb=" CG GLU F 64 " pdb=" CD GLU F 64 " pdb=" OE1 GLU F 64 " ideal model delta sinusoidal sigma weight residual 0.00 85.98 -85.98 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 8819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1664 0.041 - 0.081: 498 0.081 - 0.122: 116 0.122 - 0.162: 11 0.162 - 0.203: 5 Chirality restraints: 2294 Sorted by residual: chirality pdb=" CG LEU A 562 " pdb=" CB LEU A 562 " pdb=" CD1 LEU A 562 " pdb=" CD2 LEU A 562 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ARG A 37 " pdb=" N ARG A 37 " pdb=" C ARG A 37 " pdb=" CB ARG A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA ARG D 37 " pdb=" N ARG D 37 " pdb=" C ARG D 37 " pdb=" CB ARG D 37 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 2291 not shown) Planarity restraints: 2506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.187 9.50e-02 1.11e+02 8.40e-02 4.35e+00 pdb=" NE ARG A 156 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 96 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO C 97 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 97 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 97 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 111 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ASP F 111 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP F 111 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS F 112 " 0.011 2.00e-02 2.50e+03 ... (remaining 2503 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4895 2.86 - 3.37: 13671 3.37 - 3.88: 21908 3.88 - 4.39: 24580 4.39 - 4.90: 43043 Nonbonded interactions: 108097 Sorted by model distance: nonbonded pdb=" O ASP A 582 " pdb=" CD2 HIS A 586 " model vdw 2.349 3.260 nonbonded pdb=" O ARG A 495 " pdb=" CG LEU A 498 " model vdw 2.405 3.470 nonbonded pdb=" CE MET A 579 " pdb=" CD2 LEU A 609 " model vdw 2.468 3.880 nonbonded pdb=" NZ LYS D 208 " pdb=" O GLU D 235 " model vdw 2.491 3.120 nonbonded pdb=" N GLU F 34 " pdb=" OE1 GLU F 34 " model vdw 2.505 3.120 ... (remaining 108092 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14502 Z= 0.145 Angle : 0.595 7.828 19632 Z= 0.323 Chirality : 0.040 0.203 2294 Planarity : 0.004 0.084 2506 Dihedral : 17.781 85.978 5370 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 2.90 % Allowed : 24.81 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1784 helix: 0.12 (0.17), residues: 914 sheet: -1.18 (0.46), residues: 150 loop : -1.82 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 37 TYR 0.024 0.001 TYR F 76 PHE 0.010 0.001 PHE A 158 TRP 0.015 0.001 TRP A 617 HIS 0.007 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00278 (14502) covalent geometry : angle 0.59526 (19632) hydrogen bonds : bond 0.18563 ( 611) hydrogen bonds : angle 5.61365 ( 1755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.553 Fit side-chains REVERT: A 390 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7257 (mp) REVERT: A 411 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7932 (mp) REVERT: A 454 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: C 85 ASN cc_start: 0.8450 (t0) cc_final: 0.8210 (t0) REVERT: D 158 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7222 (t80) REVERT: D 239 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7647 (mp) REVERT: D 259 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7232 (mp) REVERT: D 399 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7330 (mtt) REVERT: D 426 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7391 (tttm) REVERT: D 644 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.5374 (mm-30) outliers start: 46 outliers final: 28 residues processed: 224 average time/residue: 0.1065 time to fit residues: 36.5636 Evaluate side-chains 203 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 426 LYS Chi-restraints excluded: chain D residue 453 MET Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain I residue 5 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0040 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.5852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN C 35 HIS D 575 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.183757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.137552 restraints weight = 18904.175| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.96 r_work: 0.3572 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14502 Z= 0.107 Angle : 0.525 11.632 19632 Z= 0.271 Chirality : 0.039 0.156 2294 Planarity : 0.003 0.039 2506 Dihedral : 7.135 76.403 1980 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.04 % Allowed : 24.12 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.75 (0.20), residues: 1784 helix: 0.59 (0.18), residues: 892 sheet: -1.14 (0.49), residues: 128 loop : -1.70 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.016 0.001 TYR F 76 PHE 0.010 0.001 PHE E 25 TRP 0.011 0.001 TRP D 455 HIS 0.008 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00234 (14502) covalent geometry : angle 0.52542 (19632) hydrogen bonds : bond 0.04101 ( 611) hydrogen bonds : angle 4.09372 ( 1755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 0.501 Fit side-chains REVERT: A 189 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: A 390 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6673 (mp) REVERT: A 567 ASN cc_start: 0.7990 (m110) cc_final: 0.7774 (m110) REVERT: D 158 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7142 (t80) REVERT: D 259 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6806 (mp) REVERT: D 399 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7763 (mtm) REVERT: D 440 ASP cc_start: 0.7111 (t0) cc_final: 0.6738 (t0) REVERT: D 545 MET cc_start: 0.8497 (mpp) cc_final: 0.8136 (mpp) REVERT: F 111 ASP cc_start: 0.8246 (t0) cc_final: 0.7973 (t0) outliers start: 80 outliers final: 39 residues processed: 236 average time/residue: 0.0964 time to fit residues: 35.7774 Evaluate side-chains 205 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain I residue 5 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 68 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS A 567 ASN ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN D 559 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.183023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.137067 restraints weight = 18689.900| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.97 r_work: 0.3560 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14502 Z= 0.104 Angle : 0.505 11.793 19632 Z= 0.260 Chirality : 0.039 0.155 2294 Planarity : 0.003 0.042 2506 Dihedral : 5.183 59.803 1929 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.97 % Allowed : 25.00 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1784 helix: 0.80 (0.18), residues: 890 sheet: -0.94 (0.50), residues: 128 loop : -1.67 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 33 TYR 0.016 0.001 TYR C 76 PHE 0.008 0.001 PHE A 287 TRP 0.011 0.001 TRP A 455 HIS 0.007 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00237 (14502) covalent geometry : angle 0.50519 (19632) hydrogen bonds : bond 0.03758 ( 611) hydrogen bonds : angle 3.86232 ( 1755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8956 (mm) REVERT: A 188 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8182 (tp) REVERT: A 189 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 231 ASP cc_start: 0.7712 (t0) cc_final: 0.7498 (m-30) REVERT: A 390 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6750 (mp) REVERT: A 567 ASN cc_start: 0.7979 (m-40) cc_final: 0.7633 (m110) REVERT: D 158 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7194 (t80) REVERT: D 329 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: D 399 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7845 (mtm) REVERT: D 439 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6900 (mp10) REVERT: D 644 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.4891 (tp30) REVERT: D 646 VAL cc_start: 0.8236 (m) cc_final: 0.7996 (t) outliers start: 63 outliers final: 43 residues processed: 215 average time/residue: 0.1049 time to fit residues: 34.6718 Evaluate side-chains 212 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain I residue 5 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 129 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS A 710 HIS ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.181655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.135245 restraints weight = 19024.402| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.02 r_work: 0.3536 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14502 Z= 0.125 Angle : 0.519 9.528 19632 Z= 0.267 Chirality : 0.040 0.170 2294 Planarity : 0.003 0.039 2506 Dihedral : 5.134 59.819 1925 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.42 % Allowed : 24.12 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1784 helix: 0.77 (0.18), residues: 890 sheet: -0.95 (0.49), residues: 132 loop : -1.70 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 33 TYR 0.018 0.001 TYR C 76 PHE 0.011 0.001 PHE A 287 TRP 0.014 0.001 TRP A 455 HIS 0.007 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00303 (14502) covalent geometry : angle 0.51920 (19632) hydrogen bonds : bond 0.03757 ( 611) hydrogen bonds : angle 3.77160 ( 1755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 172 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 34 CYS cc_start: 0.7985 (p) cc_final: 0.7765 (p) REVERT: A 67 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8974 (mm) REVERT: A 158 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.6626 (t80) REVERT: A 189 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 390 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6826 (mp) REVERT: A 411 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 454 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6750 (mp10) REVERT: A 567 ASN cc_start: 0.7931 (m-40) cc_final: 0.7655 (m110) REVERT: A 617 TRP cc_start: 0.6955 (t-100) cc_final: 0.6405 (t-100) REVERT: C 70 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7709 (tt) REVERT: C 85 ASN cc_start: 0.8973 (t0) cc_final: 0.8551 (t0) REVERT: D 158 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7219 (t80) REVERT: D 329 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: D 353 HIS cc_start: 0.7589 (t-90) cc_final: 0.7356 (t-170) REVERT: D 399 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7849 (mtm) REVERT: D 439 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: D 644 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.5365 (mm-30) REVERT: E 65 GLN cc_start: 0.7906 (mp10) cc_final: 0.7634 (mp10) REVERT: F 111 ASP cc_start: 0.8219 (t0) cc_final: 0.8016 (t0) outliers start: 86 outliers final: 52 residues processed: 240 average time/residue: 0.0966 time to fit residues: 36.2853 Evaluate side-chains 227 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain I residue 5 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 79 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 174 optimal weight: 0.0770 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS A 710 HIS A 729 HIS ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.176574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129732 restraints weight = 19285.819| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.40 r_work: 0.3473 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14502 Z= 0.241 Angle : 0.655 10.494 19632 Z= 0.338 Chirality : 0.045 0.192 2294 Planarity : 0.004 0.043 2506 Dihedral : 5.694 59.578 1925 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 6.99 % Allowed : 24.43 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.20), residues: 1784 helix: 0.12 (0.17), residues: 902 sheet: -0.84 (0.53), residues: 120 loop : -2.00 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 33 TYR 0.023 0.002 TYR F 79 PHE 0.018 0.002 PHE A 287 TRP 0.017 0.002 TRP A 455 HIS 0.009 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00595 (14502) covalent geometry : angle 0.65495 (19632) hydrogen bonds : bond 0.05000 ( 611) hydrogen bonds : angle 4.16536 ( 1755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 171 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 10 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5431 (mtt) REVERT: A 67 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9053 (mm) REVERT: A 158 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7140 (t80) REVERT: A 167 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8056 (tp) REVERT: A 390 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7149 (mp) REVERT: A 450 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7492 (ttmm) REVERT: A 454 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6877 (mp10) REVERT: A 567 ASN cc_start: 0.7956 (m-40) cc_final: 0.7573 (m110) REVERT: C 70 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7970 (tt) REVERT: C 85 ASN cc_start: 0.9033 (t0) cc_final: 0.8636 (t0) REVERT: D 158 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7333 (t80) REVERT: D 216 MET cc_start: 0.7622 (ptm) cc_final: 0.7406 (ptt) REVERT: D 239 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7749 (mp) REVERT: D 329 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: D 399 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7937 (mtm) REVERT: D 434 SER cc_start: 0.8603 (m) cc_final: 0.8108 (p) REVERT: D 439 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: D 644 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5389 (mm-30) REVERT: E 65 GLN cc_start: 0.8043 (mp10) cc_final: 0.7750 (mp10) REVERT: F 27 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7742 (m90) REVERT: F 46 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6270 (mt) outliers start: 111 outliers final: 65 residues processed: 260 average time/residue: 0.0978 time to fit residues: 39.3970 Evaluate side-chains 247 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 166 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain I residue 5 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 119 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 30 optimal weight: 0.0170 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN A 710 HIS ** B 49 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 = 0.4328 r_free = 0.4328 target = 0.182159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136209 restraints weight = 19134.351| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.23 r_work: 0.3540 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14502 Z= 0.102 Angle : 0.543 12.968 19632 Z= 0.275 Chirality : 0.039 0.162 2294 Planarity : 0.003 0.047 2506 Dihedral : 5.310 59.289 1925 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.53 % Allowed : 27.58 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1784 helix: 0.66 (0.18), residues: 902 sheet: -0.73 (0.50), residues: 126 loop : -1.76 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 546 TYR 0.019 0.001 TYR C 76 PHE 0.009 0.001 PHE D 516 TRP 0.009 0.001 TRP D 455 HIS 0.007 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00228 (14502) covalent geometry : angle 0.54282 (19632) hydrogen bonds : bond 0.03254 ( 611) hydrogen bonds : angle 3.74220 ( 1755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.557 Fit side-chains REVERT: A 67 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8955 (mm) REVERT: A 134 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7573 (mt) REVERT: A 158 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.6994 (t80) REVERT: A 167 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7949 (tp) REVERT: A 174 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: A 189 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 321 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: A 390 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6723 (mp) REVERT: A 411 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 567 ASN cc_start: 0.7929 (m-40) cc_final: 0.7549 (m110) REVERT: A 617 TRP cc_start: 0.7100 (t-100) cc_final: 0.6505 (t-100) REVERT: C 70 LEU cc_start: 0.8072 (tt) cc_final: 0.7845 (tt) REVERT: D 43 CYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6327 (t) REVERT: D 158 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7199 (t80) REVERT: D 329 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: D 399 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7865 (mtm) REVERT: D 439 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: D 440 ASP cc_start: 0.7268 (t0) cc_final: 0.6896 (t0) REVERT: D 642 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.5017 (pm20) REVERT: D 644 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.5068 (mm-30) REVERT: E 65 GLN cc_start: 0.7996 (mp10) cc_final: 0.7752 (mp10) REVERT: F 27 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7748 (m90) outliers start: 56 outliers final: 28 residues processed: 214 average time/residue: 0.0995 time to fit residues: 32.9060 Evaluate side-chains 207 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain I residue 5 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 78 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** B 49 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 = 0.4317 r_free = 0.4317 target = 0.180765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.135174 restraints weight = 18698.910| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.04 r_work: 0.3523 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14502 Z= 0.116 Angle : 0.561 14.617 19632 Z= 0.280 Chirality : 0.040 0.181 2294 Planarity : 0.003 0.040 2506 Dihedral : 5.109 59.638 1923 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.90 % Allowed : 27.64 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1784 helix: 0.72 (0.18), residues: 904 sheet: -0.70 (0.50), residues: 126 loop : -1.82 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 63 TYR 0.023 0.001 TYR C 76 PHE 0.011 0.001 PHE A 544 TRP 0.011 0.001 TRP A 455 HIS 0.008 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00277 (14502) covalent geometry : angle 0.56062 (19632) hydrogen bonds : bond 0.03485 ( 611) hydrogen bonds : angle 3.73708 ( 1755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 173 time to evaluate : 0.521 Fit side-chains REVERT: A 67 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8980 (mm) REVERT: A 158 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.6992 (t80) REVERT: A 167 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8004 (tp) REVERT: A 174 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6325 (m-80) REVERT: A 189 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: A 390 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6831 (mp) REVERT: A 411 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 454 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.6691 (mp10) REVERT: A 567 ASN cc_start: 0.7928 (m-40) cc_final: 0.7539 (m110) REVERT: A 617 TRP cc_start: 0.7161 (t-100) cc_final: 0.6526 (t-100) REVERT: C 70 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7881 (tt) REVERT: D 43 CYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6318 (t) REVERT: D 158 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7164 (t80) REVERT: D 239 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7668 (mp) REVERT: D 329 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: D 399 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7911 (mtm) REVERT: D 439 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: D 440 ASP cc_start: 0.7266 (t0) cc_final: 0.6901 (t0) REVERT: D 545 MET cc_start: 0.8006 (mmm) cc_final: 0.7407 (ttm) REVERT: D 642 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.5050 (pm20) REVERT: D 644 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.5101 (mm-30) REVERT: D 648 TYR cc_start: 0.8036 (m-80) cc_final: 0.7786 (m-80) REVERT: E 46 LYS cc_start: 0.1775 (OUTLIER) cc_final: 0.1082 (ttmt) REVERT: E 65 GLN cc_start: 0.8033 (mp10) cc_final: 0.7810 (mp10) REVERT: F 27 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.7765 (m90) outliers start: 62 outliers final: 38 residues processed: 220 average time/residue: 0.1002 time to fit residues: 34.0439 Evaluate side-chains 222 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain I residue 5 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 54 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 11 optimal weight: 0.0030 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** B 49 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 = 0.4312 r_free = 0.4312 target = 0.179499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133082 restraints weight = 19144.708| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.34 r_work: 0.3514 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14502 Z= 0.141 Angle : 0.582 13.562 19632 Z= 0.293 Chirality : 0.041 0.307 2294 Planarity : 0.003 0.041 2506 Dihedral : 5.183 59.593 1923 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.85 % Allowed : 27.02 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.20), residues: 1784 helix: 0.64 (0.18), residues: 902 sheet: -0.74 (0.51), residues: 126 loop : -1.82 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 546 TYR 0.023 0.001 TYR C 76 PHE 0.011 0.001 PHE A 287 TRP 0.011 0.001 TRP A 455 HIS 0.009 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00343 (14502) covalent geometry : angle 0.58169 (19632) hydrogen bonds : bond 0.03789 ( 611) hydrogen bonds : angle 3.81002 ( 1755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 178 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 134 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 158 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7066 (t80) REVERT: A 167 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7972 (tt) REVERT: A 174 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: A 189 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: A 390 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7015 (mp) REVERT: A 411 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 454 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.6840 (mp10) REVERT: A 539 GLN cc_start: 0.7581 (tp40) cc_final: 0.7340 (tp40) REVERT: A 567 ASN cc_start: 0.7957 (m-40) cc_final: 0.7523 (m110) REVERT: A 617 TRP cc_start: 0.7200 (t-100) cc_final: 0.6555 (t-100) REVERT: C 70 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7951 (tt) REVERT: C 85 ASN cc_start: 0.8998 (t0) cc_final: 0.8719 (t0) REVERT: C 92 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 43 CYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6509 (t) REVERT: D 158 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7107 (t80) REVERT: D 239 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7694 (mp) REVERT: D 329 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: D 399 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7923 (mtm) REVERT: D 439 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: D 440 ASP cc_start: 0.7316 (t0) cc_final: 0.6981 (t0) REVERT: D 545 MET cc_start: 0.7996 (mmm) cc_final: 0.7510 (ttm) REVERT: D 642 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.4997 (pm20) REVERT: D 644 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.5091 (mm-30) REVERT: D 648 TYR cc_start: 0.8050 (m-80) cc_final: 0.7758 (m-80) REVERT: E 46 LYS cc_start: 0.1935 (OUTLIER) cc_final: 0.1300 (ttmt) REVERT: E 65 GLN cc_start: 0.8041 (mp10) cc_final: 0.7816 (mp10) REVERT: F 27 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.7747 (m90) outliers start: 77 outliers final: 48 residues processed: 238 average time/residue: 0.0969 time to fit residues: 35.5210 Evaluate side-chains 242 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain I residue 5 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 87 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 710 HIS ** B 49 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 = 0.4325 r_free = 0.4325 target = 0.180827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.134842 restraints weight = 18602.816| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.94 r_work: 0.3550 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14502 Z= 0.118 Angle : 0.582 15.715 19632 Z= 0.290 Chirality : 0.040 0.282 2294 Planarity : 0.003 0.042 2506 Dihedral : 5.082 59.491 1923 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.41 % Allowed : 27.90 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1784 helix: 0.73 (0.18), residues: 904 sheet: -0.78 (0.50), residues: 126 loop : -1.81 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 546 TYR 0.028 0.001 TYR C 76 PHE 0.009 0.001 PHE A 544 TRP 0.010 0.001 TRP A 455 HIS 0.009 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00282 (14502) covalent geometry : angle 0.58245 (19632) hydrogen bonds : bond 0.03405 ( 611) hydrogen bonds : angle 3.71523 ( 1755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9036 (mm) REVERT: A 134 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 158 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7024 (t80) REVERT: A 167 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8048 (tt) REVERT: A 174 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: A 189 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 321 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: A 390 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6933 (mp) REVERT: A 411 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 454 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: A 567 ASN cc_start: 0.8034 (m-40) cc_final: 0.7608 (m110) REVERT: A 617 TRP cc_start: 0.7166 (t-100) cc_final: 0.6509 (t-100) REVERT: C 70 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7961 (tt) REVERT: C 92 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7379 (tm-30) REVERT: D 43 CYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6474 (t) REVERT: D 158 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7144 (t80) REVERT: D 239 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7703 (mp) REVERT: D 329 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: D 399 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8074 (mtm) REVERT: D 439 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: D 440 ASP cc_start: 0.7639 (t0) cc_final: 0.7270 (t0) REVERT: D 545 MET cc_start: 0.8090 (mmm) cc_final: 0.7605 (ttm) REVERT: D 642 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5020 (pm20) REVERT: D 644 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.5069 (mm-30) REVERT: D 648 TYR cc_start: 0.8010 (m-80) cc_final: 0.7787 (m-80) REVERT: E 46 LYS cc_start: 0.1833 (OUTLIER) cc_final: 0.1264 (ttmt) REVERT: E 65 GLN cc_start: 0.8055 (mp10) cc_final: 0.7847 (mp10) REVERT: F 27 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.7770 (m90) outliers start: 70 outliers final: 44 residues processed: 231 average time/residue: 0.1019 time to fit residues: 36.3929 Evaluate side-chains 238 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 77 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 163 optimal weight: 0.0050 chunk 109 optimal weight: 0.0370 overall best weight: 0.6052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS B 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.182149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.135798 restraints weight = 19106.621| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.24 r_work: 0.3551 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14502 Z= 0.109 Angle : 0.581 15.725 19632 Z= 0.288 Chirality : 0.040 0.272 2294 Planarity : 0.003 0.054 2506 Dihedral : 4.751 59.720 1921 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.22 % Allowed : 27.90 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1784 helix: 0.83 (0.18), residues: 904 sheet: -0.76 (0.50), residues: 126 loop : -1.79 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 546 TYR 0.026 0.001 TYR C 76 PHE 0.008 0.001 PHE A 544 TRP 0.011 0.001 TRP A 617 HIS 0.009 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00253 (14502) covalent geometry : angle 0.58141 (19632) hydrogen bonds : bond 0.03250 ( 611) hydrogen bonds : angle 3.67018 ( 1755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9003 (mm) REVERT: A 134 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7585 (mt) REVERT: A 158 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.6949 (t80) REVERT: A 167 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7934 (tt) REVERT: A 174 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6189 (m-80) REVERT: A 188 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 189 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: A 321 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: A 390 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6909 (mp) REVERT: A 411 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7901 (mp) REVERT: A 454 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.6872 (mp10) REVERT: A 567 ASN cc_start: 0.7984 (m-40) cc_final: 0.7573 (m110) REVERT: A 617 TRP cc_start: 0.7182 (t-100) cc_final: 0.6526 (t-100) REVERT: C 70 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (tt) REVERT: C 92 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7139 (tm-30) REVERT: D 43 CYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6416 (t) REVERT: D 81 MET cc_start: 0.7411 (tpp) cc_final: 0.7039 (mmt) REVERT: D 158 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7142 (t80) REVERT: D 239 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7687 (mp) REVERT: D 329 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: D 399 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7879 (mtm) REVERT: D 439 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: D 440 ASP cc_start: 0.7326 (t0) cc_final: 0.6978 (t0) REVERT: D 545 MET cc_start: 0.8005 (mmm) cc_final: 0.7638 (ttm) REVERT: D 642 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5052 (pm20) REVERT: D 644 GLU cc_start: 0.5545 (OUTLIER) cc_final: 0.5136 (mm-30) REVERT: D 648 TYR cc_start: 0.8012 (m-80) cc_final: 0.7729 (m-80) REVERT: E 46 LYS cc_start: 0.1804 (OUTLIER) cc_final: 0.1323 (ttmt) REVERT: F 27 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7714 (m90) outliers start: 67 outliers final: 41 residues processed: 223 average time/residue: 0.0974 time to fit residues: 33.9417 Evaluate side-chains 233 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 586 HIS Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 HIS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.179256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133667 restraints weight = 18871.675| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.05 r_work: 0.3520 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14502 Z= 0.153 Angle : 0.618 15.727 19632 Z= 0.310 Chirality : 0.042 0.290 2294 Planarity : 0.003 0.051 2506 Dihedral : 4.904 57.657 1921 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.79 % Allowed : 27.46 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1784 helix: 0.64 (0.18), residues: 906 sheet: -0.84 (0.50), residues: 126 loop : -1.83 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 546 TYR 0.025 0.002 TYR C 76 PHE 0.016 0.001 PHE A 544 TRP 0.014 0.001 TRP A 455 HIS 0.009 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00376 (14502) covalent geometry : angle 0.61761 (19632) hydrogen bonds : bond 0.03867 ( 611) hydrogen bonds : angle 3.81157 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.66 seconds wall clock time: 62 minutes 50.76 seconds (3770.76 seconds total)