Starting phenix.real_space_refine on Tue Nov 18 13:38:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jth_22473/11_2025/7jth_22473.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jth_22473/11_2025/7jth_22473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jth_22473/11_2025/7jth_22473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jth_22473/11_2025/7jth_22473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jth_22473/11_2025/7jth_22473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jth_22473/11_2025/7jth_22473.map" } resolution = 4.0 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= 0.020 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 44 5.16 5 C 9286 2.51 5 N 2620 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14628 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1823 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 18, 'ASP:plan': 16, 'ARG:plan': 17, 'GLN:plan1': 11, 'ASN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 311 Chain: "B" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 1839 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 599 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 18, 'ARG:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 255 Conformer: "B" Number of residues, atoms: 289, 1839 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 483 Unresolved non-hydrogen angles: 599 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 18, 'ARG:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 255 bond proxies already assigned to first conformer: 1873 Chain: "C" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1830 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 668 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 17, 'ASP:plan': 16, 'GLN:plan1': 11, 'ASN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 313 Chain: "D" Number of atoms: 1820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 1818 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 18, 'ARG:plan': 14, 'GLN:plan1': 11, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 272 Conformer: "B" Number of residues, atoms: 289, 1818 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 18, 'ARG:plan': 14, 'GLN:plan1': 11, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 272 bond proxies already assigned to first conformer: 1852 Restraints were copied for chains: E, F, G, H Time building chain proxies: 4.64, per 1000 atoms: 0.32 Number of scatterers: 14628 At special positions: 0 Unit cell: (138.182, 138.182, 130.188, 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 44 16.00 O 2678 8.00 N 2620 7.00 C 9286 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: 1.30 Conformation dependent library (CDL) restraints added in 886.8 milliseconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 77.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.543A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.904A pdb=" N ASP A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.895A pdb=" N LYS A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.777A pdb=" N ILE A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.681A pdb=" N ILE A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 removed outlier: 3.710A pdb=" N ASN A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 546 removed outlier: 3.872A pdb=" N GLN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 562 through 574 removed outlier: 4.049A pdb=" N PHE A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 610 removed outlier: 4.512A pdb=" N SER A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N CYS A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 643 through 658 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 681 through 700 removed outlier: 3.838A pdb=" N ASP A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 718 removed outlier: 3.880A pdb=" N ARG A 718 " --> pdb=" O GLU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'B' and resid 415 through 423 removed outlier: 3.752A pdb=" N LEU B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 removed outlier: 3.935A pdb=" N SER B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.659A pdb=" N ILE B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 478 removed outlier: 4.374A pdb=" N LYS B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 495 through 514 removed outlier: 3.817A pdb=" N TYR B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 545 removed outlier: 3.595A pdb=" N VAL B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 4.034A pdb=" N ARG B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 removed outlier: 4.103A pdb=" N PHE B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 568 " --> pdb=" O GLN B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 611 Processing helix chain 'B' and resid 631 through 636 Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 662 through 676 removed outlier: 3.748A pdb=" N GLN B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 703 removed outlier: 3.817A pdb=" N ARG B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 690 " --> pdb=" O MET B 686 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.698A pdb=" N LEU B 714 " --> pdb=" O MET B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'C' and resid 415 through 422 removed outlier: 3.949A pdb=" N ALA C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 450 removed outlier: 3.930A pdb=" N ASP C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 478 removed outlier: 3.741A pdb=" N LYS C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 3.681A pdb=" N ILE C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 517 removed outlier: 3.510A pdb=" N ILE C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 516 " --> pdb=" O GLN C 512 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 546 removed outlier: 3.811A pdb=" N GLN C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 562 Processing helix chain 'C' and resid 562 through 575 removed outlier: 4.254A pdb=" N PHE C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 585 removed outlier: 3.720A pdb=" N LYS C 585 " --> pdb=" O PRO C 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 582 through 585' Processing helix chain 'C' and resid 586 through 610 removed outlier: 3.691A pdb=" N ASP C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 643 through 658 Processing helix chain 'C' and resid 663 through 675 Processing helix chain 'C' and resid 681 through 700 removed outlier: 3.840A pdb=" N ASP C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 718 removed outlier: 3.927A pdb=" N ARG C 718 " --> pdb=" O GLU C 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 715 through 718' Processing helix chain 'D' and resid 415 through 423 removed outlier: 3.720A pdb=" N LEU D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 431 removed outlier: 3.920A pdb=" N SER D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 450 removed outlier: 3.690A pdb=" N ILE D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TRP D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 478 removed outlier: 4.278A pdb=" N LYS D 458 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 495 through 514 removed outlier: 3.872A pdb=" N TYR D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 545 removed outlier: 3.631A pdb=" N VAL D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 4.027A pdb=" N ARG D 556 " --> pdb=" O GLU D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 removed outlier: 4.070A pdb=" N PHE D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE D 568 " --> pdb=" O GLN D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 4.171A pdb=" N SER D 588 " --> pdb=" O THR D 584 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS D 589 " --> pdb=" O LYS D 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 584 through 589' Processing helix chain 'D' and resid 590 through 611 Processing helix chain 'D' and resid 631 through 636 Processing helix chain 'D' and resid 643 through 649 Processing helix chain 'D' and resid 662 through 676 removed outlier: 3.750A pdb=" N GLN D 666 " --> pdb=" O LEU D 662 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 669 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 703 removed outlier: 3.712A pdb=" N ARG D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL D 690 " --> pdb=" O MET D 686 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.803A pdb=" N LEU D 714 " --> pdb=" O MET D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 717 No H-bonds generated for 'chain 'D' and resid 715 through 717' Processing helix chain 'E' and resid 415 through 422 removed outlier: 3.923A pdb=" N ALA E 420 " --> pdb=" O PHE E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 429 Processing helix chain 'E' and resid 437 through 450 removed outlier: 3.904A pdb=" N ASP E 447 " --> pdb=" O ASP E 443 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 478 removed outlier: 3.895A pdb=" N LYS E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL E 465 " --> pdb=" O ASP E 461 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN E 477 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 494 removed outlier: 3.777A pdb=" N ILE E 492 " --> pdb=" O SER E 488 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 493 " --> pdb=" O THR E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 515 removed outlier: 3.681A pdb=" N ILE E 507 " --> pdb=" O THR E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 527 removed outlier: 3.710A pdb=" N ASN E 527 " --> pdb=" O GLN E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 546 removed outlier: 3.872A pdb=" N GLN E 536 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E 544 " --> pdb=" O LEU E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 562 Processing helix chain 'E' and resid 562 through 574 removed outlier: 4.049A pdb=" N PHE E 566 " --> pdb=" O THR E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 610 removed outlier: 4.512A pdb=" N SER E 588 " --> pdb=" O THR E 584 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N CYS E 589 " --> pdb=" O LYS E 585 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP E 605 " --> pdb=" O PHE E 601 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP E 606 " --> pdb=" O GLN E 602 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN E 608 " --> pdb=" O ARG E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 638 Processing helix chain 'E' and resid 643 through 658 Processing helix chain 'E' and resid 663 through 675 Processing helix chain 'E' and resid 681 through 700 removed outlier: 3.838A pdb=" N ASP E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 690 " --> pdb=" O MET E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 714 Processing helix chain 'E' and resid 715 through 718 removed outlier: 3.880A pdb=" N ARG E 718 " --> pdb=" O GLU E 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 715 through 718' Processing helix chain 'F' and resid 415 through 423 removed outlier: 3.752A pdb=" N LEU F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU F 423 " --> pdb=" O LYS F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 431 removed outlier: 3.935A pdb=" N SER F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 450 removed outlier: 3.659A pdb=" N ILE F 442 " --> pdb=" O ARG F 438 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP F 443 " --> pdb=" O ASP F 439 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP F 447 " --> pdb=" O ASP F 443 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP F 448 " --> pdb=" O ALA F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 478 removed outlier: 4.374A pdb=" N LYS F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE F 476 " --> pdb=" O LEU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 495 through 514 removed outlier: 3.817A pdb=" N TYR F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 545 removed outlier: 3.595A pdb=" N VAL F 525 " --> pdb=" O SER F 521 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 532 " --> pdb=" O SER F 528 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP F 539 " --> pdb=" O GLY F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 562 removed outlier: 4.034A pdb=" N ARG F 556 " --> pdb=" O GLU F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 572 removed outlier: 4.103A pdb=" N PHE F 566 " --> pdb=" O THR F 562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 589 Processing helix chain 'F' and resid 590 through 611 Processing helix chain 'F' and resid 631 through 636 Processing helix chain 'F' and resid 643 through 649 Processing helix chain 'F' and resid 662 through 676 removed outlier: 3.748A pdb=" N GLN F 666 " --> pdb=" O LEU F 662 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU F 669 " --> pdb=" O LYS F 665 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 673 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU F 674 " --> pdb=" O ASP F 670 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU F 675 " --> pdb=" O ILE F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 703 removed outlier: 3.817A pdb=" N ARG F 682 " --> pdb=" O LEU F 678 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 690 " --> pdb=" O MET F 686 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA F 694 " --> pdb=" O VAL F 690 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 697 " --> pdb=" O ARG F 693 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG F 698 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 699 " --> pdb=" O GLU F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 714 removed outlier: 3.698A pdb=" N LEU F 714 " --> pdb=" O MET F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 717 No H-bonds generated for 'chain 'F' and resid 715 through 717' Processing helix chain 'G' and resid 415 through 422 removed outlier: 3.949A pdb=" N ALA G 420 " --> pdb=" O PHE G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 429 Processing helix chain 'G' and resid 437 through 450 removed outlier: 3.930A pdb=" N ASP G 447 " --> pdb=" O ASP G 443 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP G 448 " --> pdb=" O ALA G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 478 removed outlier: 3.741A pdb=" N LYS G 460 " --> pdb=" O VAL G 456 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL G 465 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE G 476 " --> pdb=" O LEU G 472 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN G 477 " --> pdb=" O LEU G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 494 removed outlier: 3.681A pdb=" N ILE G 492 " --> pdb=" O SER G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 517 removed outlier: 3.510A pdb=" N ILE G 507 " --> pdb=" O THR G 503 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE G 516 " --> pdb=" O GLN G 512 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER G 517 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 546 removed outlier: 3.811A pdb=" N GLN G 536 " --> pdb=" O LEU G 532 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR G 544 " --> pdb=" O LEU G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 562 Processing helix chain 'G' and resid 562 through 575 removed outlier: 4.254A pdb=" N PHE G 566 " --> pdb=" O THR G 562 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN G 575 " --> pdb=" O SER G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 585 removed outlier: 3.720A pdb=" N LYS G 585 " --> pdb=" O PRO G 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 582 through 585' Processing helix chain 'G' and resid 586 through 610 removed outlier: 3.691A pdb=" N ASP G 605 " --> pdb=" O PHE G 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 638 Processing helix chain 'G' and resid 643 through 658 Processing helix chain 'G' and resid 663 through 675 Processing helix chain 'G' and resid 681 through 700 removed outlier: 3.840A pdb=" N ASP G 687 " --> pdb=" O SER G 683 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 714 Processing helix chain 'G' and resid 715 through 718 removed outlier: 3.927A pdb=" N ARG G 718 " --> pdb=" O GLU G 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 715 through 718' Processing helix chain 'H' and resid 415 through 423 removed outlier: 3.720A pdb=" N LEU H 422 " --> pdb=" O GLU H 418 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU H 423 " --> pdb=" O LYS H 419 " (cutoff:3.500A) Processing helix chain 'H' and resid 423 through 431 removed outlier: 3.920A pdb=" N SER H 431 " --> pdb=" O ASP H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 450 removed outlier: 3.690A pdb=" N ILE H 442 " --> pdb=" O ARG H 438 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP H 443 " --> pdb=" O ASP H 439 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP H 447 " --> pdb=" O ASP H 443 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TRP H 448 " --> pdb=" O ALA H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 478 removed outlier: 4.278A pdb=" N LYS H 458 " --> pdb=" O VAL H 454 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE H 476 " --> pdb=" O LEU H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 495 through 514 removed outlier: 3.872A pdb=" N TYR H 504 " --> pdb=" O ASN H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 545 removed outlier: 3.631A pdb=" N VAL H 525 " --> pdb=" O SER H 521 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU H 532 " --> pdb=" O SER H 528 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN H 536 " --> pdb=" O LEU H 532 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP H 539 " --> pdb=" O GLY H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 550 through 562 removed outlier: 4.027A pdb=" N ARG H 556 " --> pdb=" O GLU H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 572 removed outlier: 4.070A pdb=" N PHE H 566 " --> pdb=" O THR H 562 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE H 568 " --> pdb=" O GLN H 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 584 through 589 removed outlier: 4.171A pdb=" N SER H 588 " --> pdb=" O THR H 584 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS H 589 " --> pdb=" O LYS H 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 584 through 589' Processing helix chain 'H' and resid 590 through 611 Processing helix chain 'H' and resid 631 through 636 Processing helix chain 'H' and resid 643 through 649 Processing helix chain 'H' and resid 662 through 676 removed outlier: 3.750A pdb=" N GLN H 666 " --> pdb=" O LEU H 662 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU H 669 " --> pdb=" O LYS H 665 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU H 673 " --> pdb=" O LEU H 669 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU H 675 " --> pdb=" O ILE H 671 " (cutoff:3.500A) Processing helix chain 'H' and resid 676 through 703 removed outlier: 3.712A pdb=" N ARG H 682 " --> pdb=" O LEU H 678 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL H 690 " --> pdb=" O MET H 686 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 694 " --> pdb=" O VAL H 690 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY H 697 " --> pdb=" O ARG H 693 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG H 698 " --> pdb=" O ALA H 694 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE H 699 " --> pdb=" O GLU H 695 " (cutoff:3.500A) Processing helix chain 'H' and resid 709 through 714 removed outlier: 3.803A pdb=" N LEU H 714 " --> pdb=" O MET H 710 " (cutoff:3.500A) Processing helix chain 'H' and resid 715 through 717 No H-bonds generated for 'chain 'H' and resid 715 through 717' 1082 hydrogen bonds defined for protein. 3216 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: 2.07 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4998 1.34 - 1.46: 3472 1.46 - 1.58: 6384 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 14926 Sorted by residual: bond pdb=" CB PRO C 481 " pdb=" CG PRO C 481 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.22e+00 bond pdb=" CB PRO G 481 " pdb=" CG PRO G 481 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.22e+00 bond pdb=" C SER C 705 " pdb=" N PRO C 706 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" C SER G 705 " pdb=" N PRO G 706 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" C SER A 705 " pdb=" N PRO A 706 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.07e+00 ... (remaining 14921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 20094 1.75 - 3.50: 422 3.50 - 5.24: 64 5.24 - 6.99: 10 6.99 - 8.74: 4 Bond angle restraints: 20594 Sorted by residual: angle pdb=" N GLU C 580 " pdb=" CA GLU C 580 " pdb=" C GLU C 580 " ideal model delta sigma weight residual 110.80 102.06 8.74 2.13e+00 2.20e-01 1.68e+01 angle pdb=" N GLU G 580 " pdb=" CA GLU G 580 " pdb=" C GLU G 580 " ideal model delta sigma weight residual 110.80 102.06 8.74 2.13e+00 2.20e-01 1.68e+01 angle pdb=" N ASN C 579 " pdb=" CA ASN C 579 " pdb=" C ASN C 579 " ideal model delta sigma weight residual 113.29 107.89 5.40 2.00e+00 2.50e-01 7.30e+00 angle pdb=" N ASN G 579 " pdb=" CA ASN G 579 " pdb=" C ASN G 579 " ideal model delta sigma weight residual 113.29 107.89 5.40 2.00e+00 2.50e-01 7.30e+00 angle pdb=" N VAL G 525 " pdb=" CA VAL G 525 " pdb=" C VAL G 525 " ideal model delta sigma weight residual 113.39 109.68 3.71 1.47e+00 4.63e-01 6.35e+00 ... (remaining 20589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 8126 16.94 - 33.88: 352 33.88 - 50.82: 90 50.82 - 67.77: 8 67.77 - 84.71: 4 Dihedral angle restraints: 8580 sinusoidal: 1768 harmonic: 6812 Sorted by residual: dihedral pdb=" CA THR C 661 " pdb=" C THR C 661 " pdb=" N LEU C 662 " pdb=" CA LEU C 662 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA THR G 661 " pdb=" C THR G 661 " pdb=" N LEU G 662 " pdb=" CA LEU G 662 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA THR E 661 " pdb=" C THR E 661 " pdb=" N LEU E 662 " pdb=" CA LEU E 662 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1700 0.038 - 0.076: 726 0.076 - 0.113: 102 0.113 - 0.151: 16 0.151 - 0.189: 2 Chirality restraints: 2546 Sorted by residual: chirality pdb=" CA PHE G 516 " pdb=" N PHE G 516 " pdb=" C PHE G 516 " pdb=" CB PHE G 516 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA PHE C 516 " pdb=" N PHE C 516 " pdb=" C PHE C 516 " pdb=" CB PHE C 516 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA VAL C 548 " pdb=" N VAL C 548 " pdb=" C VAL C 548 " pdb=" CB VAL C 548 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2543 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 516 " 0.020 2.00e-02 2.50e+03 1.76e-02 5.44e+00 pdb=" CG PHE C 516 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 516 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 516 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 516 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 516 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 516 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 516 " -0.020 2.00e-02 2.50e+03 1.76e-02 5.44e+00 pdb=" CG PHE G 516 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE G 516 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 516 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 516 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 516 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE G 516 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 480 " -0.033 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO C 481 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 481 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 481 " -0.027 5.00e-02 4.00e+02 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3814 2.78 - 3.31: 15082 3.31 - 3.84: 23410 3.84 - 4.37: 25721 4.37 - 4.90: 41741 Nonbonded interactions: 109768 Sorted by model distance: nonbonded pdb=" O MET G 660 " pdb=" OG1 THR G 661 " model vdw 2.250 3.040 nonbonded pdb=" O MET C 660 " pdb=" OG1 THR C 661 " model vdw 2.250 3.040 nonbonded pdb=" O MET A 660 " pdb=" OG1 THR A 661 " model vdw 2.263 3.040 nonbonded pdb=" O MET E 660 " pdb=" OG1 THR E 661 " model vdw 2.263 3.040 nonbonded pdb=" O HIS D 467 " pdb=" OG SER D 470 " model vdw 2.273 3.040 ... (remaining 109763 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.480 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 0.074 14926 Z= 0.125 Angle : 0.626 8.741 20594 Z= 0.357 Chirality : 0.039 0.189 2546 Planarity : 0.005 0.049 2716 Dihedral : 11.388 84.707 4148 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.03 % Favored : 89.35 % Rotamer: Outliers : 0.45 % Allowed : 6.01 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.14), residues: 2296 helix: -2.55 (0.10), residues: 1736 sheet: None (None), residues: 0 loop : -3.54 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 693 TYR 0.013 0.001 TYR D 426 PHE 0.040 0.002 PHE G 516 TRP 0.010 0.001 TRP G 630 HIS 0.015 0.001 HIS H 689 Details of bonding type rmsd covalent geometry : bond 0.00259 (14926) covalent geometry : angle 0.62591 (20594) hydrogen bonds : bond 0.17189 ( 1082) hydrogen bonds : angle 7.28146 ( 3216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 602 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8316 (t80) cc_final: 0.7717 (t80) REVERT: A 451 VAL cc_start: 0.8474 (m) cc_final: 0.8148 (p) REVERT: A 472 LEU cc_start: 0.7656 (mt) cc_final: 0.7431 (mt) REVERT: A 499 VAL cc_start: 0.8653 (t) cc_final: 0.8441 (p) REVERT: A 565 LEU cc_start: 0.7873 (tt) cc_final: 0.7601 (tt) REVERT: A 567 SER cc_start: 0.8345 (p) cc_final: 0.8091 (p) REVERT: A 603 ILE cc_start: 0.7534 (mm) cc_final: 0.7280 (mm) REVERT: A 630 TRP cc_start: 0.7438 (m100) cc_final: 0.7182 (m100) REVERT: A 661 THR cc_start: 0.7236 (m) cc_final: 0.6862 (m) REVERT: B 500 ASN cc_start: 0.8352 (t0) cc_final: 0.7932 (t0) REVERT: B 507 ILE cc_start: 0.8070 (mt) cc_final: 0.7845 (mm) REVERT: B 560 GLN cc_start: 0.8446 (tt0) cc_final: 0.8005 (tt0) REVERT: B 564 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7006 (mm-40) REVERT: B 565 LEU cc_start: 0.7909 (tt) cc_final: 0.7634 (tp) REVERT: B 566 PHE cc_start: 0.8379 (m-80) cc_final: 0.8155 (m-80) REVERT: B 587 GLN cc_start: 0.8460 (pp30) cc_final: 0.7843 (pp30) REVERT: B 591 HIS cc_start: 0.5630 (m-70) cc_final: 0.5228 (m170) REVERT: B 630 TRP cc_start: 0.8177 (m100) cc_final: 0.7825 (m100) REVERT: B 645 MET cc_start: 0.7591 (mmm) cc_final: 0.7302 (mmm) REVERT: C 425 PRO cc_start: 0.9162 (Cg_exo) cc_final: 0.8929 (Cg_endo) REVERT: C 459 ILE cc_start: 0.8256 (tp) cc_final: 0.8044 (tp) REVERT: C 471 LEU cc_start: 0.8908 (mt) cc_final: 0.8636 (mt) REVERT: C 534 GLN cc_start: 0.6960 (tt0) cc_final: 0.6698 (tt0) REVERT: C 558 ILE cc_start: 0.8227 (tp) cc_final: 0.7856 (tp) REVERT: C 651 LEU cc_start: 0.8506 (mt) cc_final: 0.8249 (mm) REVERT: D 416 PHE cc_start: 0.7610 (t80) cc_final: 0.7182 (t80) REVERT: D 429 ILE cc_start: 0.8298 (mt) cc_final: 0.8042 (mm) REVERT: D 493 PHE cc_start: 0.8242 (m-80) cc_final: 0.7952 (m-10) REVERT: D 508 LYS cc_start: 0.8338 (tttp) cc_final: 0.7827 (ttmt) REVERT: D 565 LEU cc_start: 0.7874 (tt) cc_final: 0.7655 (tp) REVERT: D 630 TRP cc_start: 0.7099 (m100) cc_final: 0.6727 (m100) REVERT: E 422 LEU cc_start: 0.8290 (tp) cc_final: 0.8021 (tp) REVERT: E 425 PRO cc_start: 0.8814 (Cg_exo) cc_final: 0.8582 (Cg_endo) REVERT: E 441 PHE cc_start: 0.8378 (t80) cc_final: 0.7809 (t80) REVERT: E 472 LEU cc_start: 0.7639 (mt) cc_final: 0.7438 (mt) REVERT: E 495 SER cc_start: 0.8989 (p) cc_final: 0.8733 (p) REVERT: E 497 GLN cc_start: 0.7284 (tt0) cc_final: 0.7076 (tt0) REVERT: E 499 VAL cc_start: 0.8697 (t) cc_final: 0.8467 (p) REVERT: E 555 TYR cc_start: 0.8714 (m-10) cc_final: 0.8495 (m-80) REVERT: E 565 LEU cc_start: 0.7755 (tt) cc_final: 0.7469 (tt) REVERT: E 567 SER cc_start: 0.8181 (p) cc_final: 0.7942 (p) REVERT: E 630 TRP cc_start: 0.7302 (m100) cc_final: 0.6998 (m100) REVERT: F 500 ASN cc_start: 0.8334 (t0) cc_final: 0.7949 (t0) REVERT: F 554 TYR cc_start: 0.8399 (t80) cc_final: 0.8172 (t80) REVERT: F 560 GLN cc_start: 0.8354 (tt0) cc_final: 0.7962 (tt0) REVERT: F 564 GLN cc_start: 0.7381 (mm-40) cc_final: 0.6984 (mm-40) REVERT: F 565 LEU cc_start: 0.7835 (tt) cc_final: 0.7591 (tp) REVERT: F 566 PHE cc_start: 0.8374 (m-80) cc_final: 0.8173 (m-80) REVERT: F 587 GLN cc_start: 0.8405 (pp30) cc_final: 0.7814 (pp30) REVERT: F 591 HIS cc_start: 0.5679 (m-70) cc_final: 0.5206 (m170) REVERT: F 645 MET cc_start: 0.7641 (mmm) cc_final: 0.7387 (mmm) REVERT: G 471 LEU cc_start: 0.8816 (mt) cc_final: 0.8558 (mt) REVERT: G 534 GLN cc_start: 0.6928 (tt0) cc_final: 0.6675 (tt0) REVERT: G 558 ILE cc_start: 0.8238 (tp) cc_final: 0.7722 (tp) REVERT: G 565 LEU cc_start: 0.8031 (tp) cc_final: 0.7648 (tp) REVERT: G 603 ILE cc_start: 0.8269 (mm) cc_final: 0.8067 (mm) REVERT: G 651 LEU cc_start: 0.8520 (mt) cc_final: 0.8251 (mm) REVERT: H 429 ILE cc_start: 0.8327 (mt) cc_final: 0.8124 (mm) REVERT: H 493 PHE cc_start: 0.8266 (m-80) cc_final: 0.7940 (m-10) REVERT: H 508 LYS cc_start: 0.8386 (tttp) cc_final: 0.7831 (ttmt) REVERT: H 630 TRP cc_start: 0.7369 (m100) cc_final: 0.7067 (m100) outliers start: 4 outliers final: 2 residues processed: 604 average time/residue: 0.0932 time to fit residues: 88.8796 Evaluate side-chains 594 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 592 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 687 ASP Chi-restraints excluded: chain G residue 687 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN A 664 GLN B 467 HIS B 527 ASN B 545 ASN B 547 HIS B 636 HIS C 467 HIS C 664 GLN D 467 HIS D 500 ASN D 575 ASN D 591 HIS D 636 HIS D 644 HIS D 689 HIS E 536 GLN E 664 GLN F 467 HIS F 527 ASN F 545 ASN F 547 HIS F 636 HIS G 664 GLN H 467 HIS H 500 ASN H 575 ASN H 591 HIS H 636 HIS H 644 HIS H 689 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.078882 restraints weight = 56400.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082525 restraints weight = 27850.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.085009 restraints weight = 16548.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.086687 restraints weight = 11074.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.087956 restraints weight = 8084.504| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14926 Z= 0.205 Angle : 0.672 8.444 20594 Z= 0.359 Chirality : 0.042 0.150 2546 Planarity : 0.005 0.045 2716 Dihedral : 4.886 45.371 2402 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 4.34 % Allowed : 26.61 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.17), residues: 2296 helix: -0.92 (0.12), residues: 1808 sheet: None (None), residues: 0 loop : -2.83 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 464 TYR 0.019 0.002 TYR A 680 PHE 0.022 0.002 PHE A 541 TRP 0.014 0.001 TRP B 542 HIS 0.011 0.002 HIS H 467 Details of bonding type rmsd covalent geometry : bond 0.00389 (14926) covalent geometry : angle 0.67243 (20594) hydrogen bonds : bond 0.03762 ( 1082) hydrogen bonds : angle 4.73357 ( 3216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 632 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8873 (t80) cc_final: 0.8265 (t80) REVERT: A 506 ILE cc_start: 0.8483 (mt) cc_final: 0.8142 (tp) REVERT: A 538 MET cc_start: 0.7907 (mmm) cc_final: 0.7651 (mmp) REVERT: A 541 PHE cc_start: 0.8462 (t80) cc_final: 0.8199 (t80) REVERT: A 561 LYS cc_start: 0.8611 (ttpt) cc_final: 0.8352 (ttmm) REVERT: A 567 SER cc_start: 0.8318 (p) cc_final: 0.7989 (p) REVERT: A 630 TRP cc_start: 0.8079 (m100) cc_final: 0.7329 (m100) REVERT: A 656 LYS cc_start: 0.8690 (tttt) cc_final: 0.8465 (tttp) REVERT: A 661 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7270 (p) REVERT: A 664 GLN cc_start: 0.8740 (mt0) cc_final: 0.8322 (mt0) REVERT: B 421 VAL cc_start: 0.8649 (p) cc_final: 0.8310 (p) REVERT: B 500 ASN cc_start: 0.8668 (t0) cc_final: 0.8368 (t0) REVERT: B 508 LYS cc_start: 0.8480 (tttp) cc_final: 0.8132 (ttpp) REVERT: B 560 GLN cc_start: 0.8379 (tt0) cc_final: 0.8039 (tt0) REVERT: B 564 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7549 (mm-40) REVERT: B 566 PHE cc_start: 0.8720 (m-80) cc_final: 0.8499 (m-80) REVERT: B 587 GLN cc_start: 0.8801 (pp30) cc_final: 0.7980 (pp30) REVERT: B 591 HIS cc_start: 0.7699 (m-70) cc_final: 0.7054 (m170) REVERT: B 602 GLN cc_start: 0.8425 (tp40) cc_final: 0.8180 (tp40) REVERT: B 645 MET cc_start: 0.7940 (mmm) cc_final: 0.7359 (mmm) REVERT: C 534 GLN cc_start: 0.7597 (tt0) cc_final: 0.7314 (tt0) REVERT: C 539 ASP cc_start: 0.7912 (t70) cc_final: 0.7665 (t0) REVERT: C 651 LEU cc_start: 0.8672 (mt) cc_final: 0.8433 (mm) REVERT: C 684 VAL cc_start: 0.8797 (t) cc_final: 0.8589 (p) REVERT: D 416 PHE cc_start: 0.7913 (t80) cc_final: 0.7491 (t80) REVERT: D 426 TYR cc_start: 0.7777 (t80) cc_final: 0.7517 (t80) REVERT: D 493 PHE cc_start: 0.8530 (m-80) cc_final: 0.8178 (m-10) REVERT: D 504 TYR cc_start: 0.7842 (t80) cc_final: 0.7167 (t80) REVERT: D 508 LYS cc_start: 0.8568 (tttp) cc_final: 0.7998 (ttmt) REVERT: D 538 MET cc_start: 0.8318 (mmm) cc_final: 0.7973 (mmm) REVERT: D 630 TRP cc_start: 0.7796 (m100) cc_final: 0.7400 (m100) REVERT: D 693 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7418 (mtt90) REVERT: E 441 PHE cc_start: 0.8895 (t80) cc_final: 0.8381 (t80) REVERT: E 506 ILE cc_start: 0.8360 (mt) cc_final: 0.8078 (tp) REVERT: E 541 PHE cc_start: 0.8371 (t80) cc_final: 0.8116 (t80) REVERT: E 547 HIS cc_start: 0.8549 (t70) cc_final: 0.8149 (t70) REVERT: E 555 TYR cc_start: 0.8936 (m-10) cc_final: 0.8117 (m-80) REVERT: E 630 TRP cc_start: 0.7965 (m100) cc_final: 0.7169 (m100) REVERT: F 497 GLN cc_start: 0.8126 (mt0) cc_final: 0.7818 (mm-40) REVERT: F 500 ASN cc_start: 0.8538 (t0) cc_final: 0.8286 (t0) REVERT: F 508 LYS cc_start: 0.8429 (tttp) cc_final: 0.7841 (ttmt) REVERT: F 556 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7458 (ttm110) REVERT: F 564 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7532 (mm-40) REVERT: F 587 GLN cc_start: 0.8771 (pp30) cc_final: 0.7964 (pp30) REVERT: F 591 HIS cc_start: 0.7872 (m-70) cc_final: 0.7198 (m170) REVERT: F 645 MET cc_start: 0.8051 (mmm) cc_final: 0.7804 (mmm) REVERT: G 529 ILE cc_start: 0.8717 (tp) cc_final: 0.8461 (tp) REVERT: G 534 GLN cc_start: 0.7574 (tt0) cc_final: 0.7283 (tt0) REVERT: G 539 ASP cc_start: 0.7988 (t70) cc_final: 0.7725 (t0) REVERT: G 565 LEU cc_start: 0.8502 (tp) cc_final: 0.8161 (tp) REVERT: G 651 LEU cc_start: 0.8692 (mt) cc_final: 0.8435 (mm) REVERT: G 668 VAL cc_start: 0.8841 (t) cc_final: 0.8585 (m) REVERT: H 416 PHE cc_start: 0.8016 (t80) cc_final: 0.7520 (t80) REVERT: H 426 TYR cc_start: 0.7831 (t80) cc_final: 0.7630 (t80) REVERT: H 493 PHE cc_start: 0.8492 (m-80) cc_final: 0.8088 (m-10) REVERT: H 508 LYS cc_start: 0.8563 (tttp) cc_final: 0.7955 (ttmt) REVERT: H 602 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8340 (tp-100) REVERT: H 630 TRP cc_start: 0.7942 (m100) cc_final: 0.7585 (m100) REVERT: H 671 ILE cc_start: 0.8773 (mm) cc_final: 0.8501 (tp) outliers start: 39 outliers final: 23 residues processed: 635 average time/residue: 0.0903 time to fit residues: 90.1905 Evaluate side-chains 651 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 627 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain E residue 624 ASP Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 3 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 27 optimal weight: 0.0010 chunk 70 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 164 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN D 644 HIS E 500 ASN E 664 GLN F 467 HIS G 467 HIS G 664 GLN H 689 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.077463 restraints weight = 86754.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081847 restraints weight = 37181.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084865 restraints weight = 20570.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086875 restraints weight = 13102.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.088276 restraints weight = 9219.125| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14926 Z= 0.139 Angle : 0.590 7.794 20594 Z= 0.307 Chirality : 0.039 0.148 2546 Planarity : 0.004 0.051 2716 Dihedral : 4.151 18.695 2398 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.10 % Favored : 94.72 % Rotamer: Outliers : 5.12 % Allowed : 32.96 % Favored : 61.92 % 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: -1.20 (0.18), residues: 2296 helix: -0.33 (0.12), residues: 1832 sheet: None (None), residues: 0 loop : -2.23 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 464 TYR 0.020 0.001 TYR D 426 PHE 0.027 0.002 PHE G 541 TRP 0.020 0.001 TRP G 630 HIS 0.007 0.001 HIS F 467 Details of bonding type rmsd covalent geometry : bond 0.00281 (14926) covalent geometry : angle 0.58992 (20594) hydrogen bonds : bond 0.03275 ( 1082) hydrogen bonds : angle 4.14778 ( 3216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 613 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8849 (t80) cc_final: 0.8297 (t80) REVERT: A 506 ILE cc_start: 0.8454 (mt) cc_final: 0.8111 (tp) REVERT: A 538 MET cc_start: 0.7907 (mmm) cc_final: 0.7527 (mmp) REVERT: A 541 PHE cc_start: 0.8430 (t80) cc_final: 0.8202 (t80) REVERT: A 630 TRP cc_start: 0.8013 (m100) cc_final: 0.7386 (m100) REVERT: A 656 LYS cc_start: 0.8684 (tttt) cc_final: 0.8404 (ttmm) REVERT: A 664 GLN cc_start: 0.8691 (mt0) cc_final: 0.8478 (mt0) REVERT: B 421 VAL cc_start: 0.8631 (p) cc_final: 0.8249 (p) REVERT: B 500 ASN cc_start: 0.8639 (t0) cc_final: 0.8376 (t0) REVERT: B 508 LYS cc_start: 0.8423 (tttp) cc_final: 0.8137 (ttpp) REVERT: B 560 GLN cc_start: 0.8246 (tt0) cc_final: 0.7881 (tt0) REVERT: B 564 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7509 (mm-40) REVERT: B 587 GLN cc_start: 0.8826 (pp30) cc_final: 0.8112 (pp30) REVERT: B 602 GLN cc_start: 0.8422 (tp40) cc_final: 0.8218 (tp40) REVERT: B 645 MET cc_start: 0.7960 (mmm) cc_final: 0.7378 (mmm) REVERT: C 534 GLN cc_start: 0.7597 (tt0) cc_final: 0.7342 (tt0) REVERT: C 651 LEU cc_start: 0.8628 (mt) cc_final: 0.8406 (mm) REVERT: C 684 VAL cc_start: 0.8750 (t) cc_final: 0.8545 (p) REVERT: D 416 PHE cc_start: 0.7910 (t80) cc_final: 0.7470 (t80) REVERT: D 426 TYR cc_start: 0.7798 (t80) cc_final: 0.7479 (t80) REVERT: D 493 PHE cc_start: 0.8559 (m-80) cc_final: 0.8206 (m-10) REVERT: D 504 TYR cc_start: 0.7709 (t80) cc_final: 0.7028 (t80) REVERT: D 508 LYS cc_start: 0.8641 (tttp) cc_final: 0.8076 (ttmt) REVERT: D 536 GLN cc_start: 0.8191 (tt0) cc_final: 0.7913 (tt0) REVERT: D 538 MET cc_start: 0.8315 (mmm) cc_final: 0.8107 (tpp) REVERT: D 630 TRP cc_start: 0.7797 (m100) cc_final: 0.7386 (m100) REVERT: D 693 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7430 (mtt90) REVERT: E 441 PHE cc_start: 0.8871 (t80) cc_final: 0.8347 (t80) REVERT: E 510 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8530 (tt) REVERT: E 541 PHE cc_start: 0.8390 (t80) cc_final: 0.8153 (t80) REVERT: E 555 TYR cc_start: 0.8914 (m-10) cc_final: 0.8202 (m-80) REVERT: E 630 TRP cc_start: 0.7868 (m100) cc_final: 0.7247 (m100) REVERT: E 667 PHE cc_start: 0.9222 (t80) cc_final: 0.8941 (t80) REVERT: F 464 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7439 (ttm-80) REVERT: F 493 PHE cc_start: 0.8629 (m-80) cc_final: 0.8355 (m-10) REVERT: F 508 LYS cc_start: 0.8404 (tttp) cc_final: 0.7855 (ttmt) REVERT: F 530 MET cc_start: 0.8065 (mtt) cc_final: 0.7433 (mmm) REVERT: F 564 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7486 (mm-40) REVERT: F 587 GLN cc_start: 0.8818 (pp30) cc_final: 0.8106 (pp30) REVERT: F 591 HIS cc_start: 0.7931 (m-70) cc_final: 0.7306 (m170) REVERT: F 645 MET cc_start: 0.8046 (mmm) cc_final: 0.7802 (mmm) REVERT: G 459 ILE cc_start: 0.8276 (tp) cc_final: 0.8058 (tp) REVERT: G 534 GLN cc_start: 0.7543 (tt0) cc_final: 0.7241 (tt0) REVERT: G 539 ASP cc_start: 0.7996 (t70) cc_final: 0.7709 (t0) REVERT: G 541 PHE cc_start: 0.8542 (t80) cc_final: 0.8165 (t80) REVERT: G 684 VAL cc_start: 0.8728 (t) cc_final: 0.8496 (p) REVERT: H 426 TYR cc_start: 0.7832 (t80) cc_final: 0.7556 (t80) REVERT: H 493 PHE cc_start: 0.8504 (m-80) cc_final: 0.8120 (m-10) REVERT: H 508 LYS cc_start: 0.8568 (tttp) cc_final: 0.8063 (ttmt) REVERT: H 602 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8356 (tp-100) REVERT: H 630 TRP cc_start: 0.7935 (m100) cc_final: 0.7552 (m100) REVERT: H 671 ILE cc_start: 0.8770 (mm) cc_final: 0.8520 (tp) outliers start: 46 outliers final: 32 residues processed: 617 average time/residue: 0.0925 time to fit residues: 89.9916 Evaluate side-chains 637 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 604 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 ILE Chi-restraints excluded: chain E residue 624 ASP Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 166 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 chunk 23 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN B 467 HIS E 500 ASN E 534 GLN F 467 HIS H 414 HIS H 689 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.079308 restraints weight = 64239.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083251 restraints weight = 30392.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.085944 restraints weight = 17623.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.087776 restraints weight = 11556.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.089025 restraints weight = 8291.933| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14926 Z= 0.122 Angle : 0.576 9.108 20594 Z= 0.296 Chirality : 0.038 0.130 2546 Planarity : 0.004 0.041 2716 Dihedral : 3.977 18.967 2398 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 5.35 % Allowed : 36.08 % Favored : 58.57 % 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: -0.58 (0.18), residues: 2296 helix: 0.10 (0.12), residues: 1832 sheet: None (None), residues: 0 loop : -1.97 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 464 TYR 0.019 0.001 TYR A 426 PHE 0.020 0.002 PHE B 493 TRP 0.015 0.001 TRP H 448 HIS 0.010 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00254 (14926) covalent geometry : angle 0.57611 (20594) hydrogen bonds : bond 0.02933 ( 1082) hydrogen bonds : angle 3.87100 ( 3216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 598 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8837 (t80) cc_final: 0.8213 (t80) REVERT: A 471 LEU cc_start: 0.8859 (tp) cc_final: 0.8580 (tt) REVERT: A 503 THR cc_start: 0.8779 (m) cc_final: 0.8140 (t) REVERT: A 506 ILE cc_start: 0.8499 (mt) cc_final: 0.8111 (tp) REVERT: A 534 GLN cc_start: 0.7688 (tm130) cc_final: 0.7452 (tp40) REVERT: A 538 MET cc_start: 0.8045 (mmm) cc_final: 0.7623 (mmp) REVERT: A 558 ILE cc_start: 0.8411 (tp) cc_final: 0.8200 (tp) REVERT: A 630 TRP cc_start: 0.7927 (m100) cc_final: 0.7551 (m100) REVERT: A 656 LYS cc_start: 0.8678 (tttt) cc_final: 0.8394 (ttmm) REVERT: A 664 GLN cc_start: 0.8727 (mt0) cc_final: 0.8442 (mt0) REVERT: B 421 VAL cc_start: 0.8680 (p) cc_final: 0.8410 (p) REVERT: B 500 ASN cc_start: 0.8643 (t0) cc_final: 0.8399 (t0) REVERT: B 508 LYS cc_start: 0.8329 (tttp) cc_final: 0.7932 (ttpp) REVERT: B 560 GLN cc_start: 0.8184 (tt0) cc_final: 0.7816 (tt0) REVERT: B 564 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7514 (mm-40) REVERT: B 587 GLN cc_start: 0.8853 (pp30) cc_final: 0.8119 (pp30) REVERT: B 602 GLN cc_start: 0.8436 (tp40) cc_final: 0.8178 (tp40) REVERT: B 645 MET cc_start: 0.7906 (mmm) cc_final: 0.7377 (mmm) REVERT: C 534 GLN cc_start: 0.7620 (tt0) cc_final: 0.7356 (tt0) REVERT: C 651 LEU cc_start: 0.8595 (mt) cc_final: 0.8381 (mm) REVERT: C 667 PHE cc_start: 0.8908 (t80) cc_final: 0.8674 (t80) REVERT: D 416 PHE cc_start: 0.7920 (t80) cc_final: 0.7472 (t80) REVERT: D 426 TYR cc_start: 0.7826 (t80) cc_final: 0.7529 (t80) REVERT: D 489 THR cc_start: 0.8670 (p) cc_final: 0.8369 (m) REVERT: D 493 PHE cc_start: 0.8543 (m-80) cc_final: 0.8258 (m-10) REVERT: D 504 TYR cc_start: 0.7730 (t80) cc_final: 0.7105 (t80) REVERT: D 508 LYS cc_start: 0.8605 (tttp) cc_final: 0.8055 (ttmt) REVERT: D 536 GLN cc_start: 0.8212 (tt0) cc_final: 0.7936 (tt0) REVERT: D 538 MET cc_start: 0.8288 (mmm) cc_final: 0.8054 (tpp) REVERT: D 630 TRP cc_start: 0.7791 (m100) cc_final: 0.7384 (m100) REVERT: D 680 TYR cc_start: 0.8566 (t80) cc_final: 0.8159 (t80) REVERT: D 689 HIS cc_start: 0.7912 (m-70) cc_final: 0.7513 (m90) REVERT: D 693 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7421 (mtt90) REVERT: E 441 PHE cc_start: 0.8872 (t80) cc_final: 0.8350 (t80) REVERT: E 503 THR cc_start: 0.8700 (m) cc_final: 0.8228 (t) REVERT: E 510 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8589 (tt) REVERT: E 534 GLN cc_start: 0.7474 (tm130) cc_final: 0.7236 (tm-30) REVERT: E 541 PHE cc_start: 0.8437 (t80) cc_final: 0.8171 (t80) REVERT: E 555 TYR cc_start: 0.8902 (m-10) cc_final: 0.8195 (m-80) REVERT: E 630 TRP cc_start: 0.7821 (m100) cc_final: 0.7395 (m100) REVERT: E 667 PHE cc_start: 0.9209 (t80) cc_final: 0.8917 (t80) REVERT: F 464 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7457 (ttm-80) REVERT: F 493 PHE cc_start: 0.8639 (m-80) cc_final: 0.8357 (m-10) REVERT: F 508 LYS cc_start: 0.8359 (tttp) cc_final: 0.7846 (ttmt) REVERT: F 530 MET cc_start: 0.8043 (mtt) cc_final: 0.7461 (mmm) REVERT: F 564 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7459 (mm-40) REVERT: F 587 GLN cc_start: 0.8882 (pp30) cc_final: 0.8157 (pp30) REVERT: F 591 HIS cc_start: 0.7946 (m-70) cc_final: 0.7308 (m170) REVERT: F 645 MET cc_start: 0.8027 (mmm) cc_final: 0.7776 (mmm) REVERT: G 459 ILE cc_start: 0.8200 (tp) cc_final: 0.7968 (tp) REVERT: G 534 GLN cc_start: 0.7568 (tt0) cc_final: 0.7248 (tt0) REVERT: G 667 PHE cc_start: 0.8906 (t80) cc_final: 0.8657 (t80) REVERT: H 426 TYR cc_start: 0.7839 (t80) cc_final: 0.7606 (t80) REVERT: H 493 PHE cc_start: 0.8509 (m-80) cc_final: 0.8212 (m-10) REVERT: H 508 LYS cc_start: 0.8601 (tttp) cc_final: 0.8096 (ttmt) REVERT: H 602 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8341 (tp-100) REVERT: H 630 TRP cc_start: 0.7966 (m100) cc_final: 0.7604 (m100) REVERT: H 671 ILE cc_start: 0.8749 (mm) cc_final: 0.8535 (tp) outliers start: 48 outliers final: 39 residues processed: 608 average time/residue: 0.0945 time to fit residues: 89.8923 Evaluate side-chains 637 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 597 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 510 ILE Chi-restraints excluded: chain E residue 631 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 20 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 222 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 210 optimal weight: 0.0770 chunk 207 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 179 optimal weight: 0.0980 chunk 226 optimal weight: 0.0670 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 HIS B 414 HIS B 545 ASN C 664 GLN D 414 HIS D 644 HIS E 664 GLN F 467 HIS H 414 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081183 restraints weight = 51343.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.084751 restraints weight = 26088.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.087170 restraints weight = 15714.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.088802 restraints weight = 10585.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.089956 restraints weight = 7778.597| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14926 Z= 0.110 Angle : 0.556 9.317 20594 Z= 0.283 Chirality : 0.037 0.146 2546 Planarity : 0.004 0.047 2716 Dihedral : 3.760 16.728 2398 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.41 % Favored : 95.42 % Rotamer: Outliers : 6.68 % Allowed : 37.53 % Favored : 55.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.11 (0.18), residues: 2296 helix: 0.59 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.71 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 464 TYR 0.016 0.001 TYR H 504 PHE 0.027 0.002 PHE A 667 TRP 0.031 0.001 TRP G 630 HIS 0.012 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00239 (14926) covalent geometry : angle 0.55618 (20594) hydrogen bonds : bond 0.02738 ( 1082) hydrogen bonds : angle 3.65170 ( 3216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 595 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8822 (t80) cc_final: 0.8229 (t80) REVERT: A 471 LEU cc_start: 0.8819 (tp) cc_final: 0.8563 (tt) REVERT: A 500 ASN cc_start: 0.8333 (t0) cc_final: 0.8131 (t0) REVERT: A 503 THR cc_start: 0.8613 (m) cc_final: 0.8045 (t) REVERT: A 506 ILE cc_start: 0.8468 (mt) cc_final: 0.8091 (tp) REVERT: A 534 GLN cc_start: 0.7717 (tm130) cc_final: 0.7195 (tm-30) REVERT: A 538 MET cc_start: 0.8046 (mmm) cc_final: 0.7696 (mmp) REVERT: A 541 PHE cc_start: 0.8414 (t80) cc_final: 0.8127 (t80) REVERT: A 656 LYS cc_start: 0.8701 (tttt) cc_final: 0.8386 (ttmm) REVERT: A 664 GLN cc_start: 0.8642 (mt0) cc_final: 0.8295 (mt0) REVERT: B 421 VAL cc_start: 0.8676 (p) cc_final: 0.8312 (p) REVERT: B 500 ASN cc_start: 0.8616 (t0) cc_final: 0.8379 (t0) REVERT: B 508 LYS cc_start: 0.8307 (tttp) cc_final: 0.7925 (ttmt) REVERT: B 560 GLN cc_start: 0.8225 (tt0) cc_final: 0.7868 (tt0) REVERT: B 564 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7478 (mm-40) REVERT: B 587 GLN cc_start: 0.8877 (pp30) cc_final: 0.8026 (pp30) REVERT: B 645 MET cc_start: 0.7897 (mmm) cc_final: 0.7365 (mmm) REVERT: B 680 TYR cc_start: 0.8680 (t80) cc_final: 0.8448 (t80) REVERT: C 534 GLN cc_start: 0.7617 (tt0) cc_final: 0.7405 (tt0) REVERT: C 651 LEU cc_start: 0.8580 (mt) cc_final: 0.8367 (mm) REVERT: C 667 PHE cc_start: 0.8907 (t80) cc_final: 0.8641 (t80) REVERT: D 426 TYR cc_start: 0.7804 (t80) cc_final: 0.7468 (t80) REVERT: D 489 THR cc_start: 0.8616 (p) cc_final: 0.8350 (m) REVERT: D 493 PHE cc_start: 0.8547 (m-80) cc_final: 0.8252 (m-10) REVERT: D 504 TYR cc_start: 0.7721 (t80) cc_final: 0.7132 (t80) REVERT: D 508 LYS cc_start: 0.8588 (tttp) cc_final: 0.8040 (ttmt) REVERT: D 536 GLN cc_start: 0.8176 (tt0) cc_final: 0.7882 (tt0) REVERT: D 538 MET cc_start: 0.8252 (mmm) cc_final: 0.7978 (tpp) REVERT: D 630 TRP cc_start: 0.7780 (m100) cc_final: 0.7341 (m100) REVERT: D 680 TYR cc_start: 0.8567 (t80) cc_final: 0.8202 (t80) REVERT: D 689 HIS cc_start: 0.7937 (m-70) cc_final: 0.7545 (m90) REVERT: E 441 PHE cc_start: 0.8859 (t80) cc_final: 0.8296 (t80) REVERT: E 471 LEU cc_start: 0.8843 (tp) cc_final: 0.8561 (tt) REVERT: E 503 THR cc_start: 0.8670 (m) cc_final: 0.8331 (t) REVERT: E 541 PHE cc_start: 0.8431 (t80) cc_final: 0.8157 (t80) REVERT: E 630 TRP cc_start: 0.7821 (m100) cc_final: 0.7368 (m100) REVERT: E 667 PHE cc_start: 0.9193 (t80) cc_final: 0.8906 (t80) REVERT: F 415 ILE cc_start: 0.8359 (mm) cc_final: 0.7830 (tp) REVERT: F 464 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7447 (ttm-80) REVERT: F 493 PHE cc_start: 0.8613 (m-80) cc_final: 0.8339 (m-10) REVERT: F 508 LYS cc_start: 0.8341 (tttp) cc_final: 0.7853 (ttmt) REVERT: F 530 MET cc_start: 0.8047 (mtt) cc_final: 0.7412 (mmm) REVERT: F 564 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7418 (mm-40) REVERT: F 587 GLN cc_start: 0.8877 (pp30) cc_final: 0.8125 (pp30) REVERT: F 591 HIS cc_start: 0.7970 (m-70) cc_final: 0.7277 (m170) REVERT: F 645 MET cc_start: 0.8061 (mmm) cc_final: 0.7757 (mmm) REVERT: G 473 LEU cc_start: 0.8520 (mt) cc_final: 0.8266 (mm) REVERT: G 534 GLN cc_start: 0.7544 (tt0) cc_final: 0.7224 (tt0) REVERT: G 542 TRP cc_start: 0.8062 (m-10) cc_final: 0.7801 (m-10) REVERT: G 664 GLN cc_start: 0.8337 (mt0) cc_final: 0.8065 (pt0) REVERT: G 668 VAL cc_start: 0.8834 (t) cc_final: 0.8631 (m) REVERT: H 426 TYR cc_start: 0.7820 (t80) cc_final: 0.7572 (t80) REVERT: H 489 THR cc_start: 0.8694 (p) cc_final: 0.8389 (m) REVERT: H 493 PHE cc_start: 0.8518 (m-80) cc_final: 0.8286 (m-10) REVERT: H 508 LYS cc_start: 0.8588 (tttp) cc_final: 0.8094 (ttmt) REVERT: H 599 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: H 602 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8340 (tp-100) REVERT: H 630 TRP cc_start: 0.7895 (m100) cc_final: 0.7494 (m100) REVERT: H 671 ILE cc_start: 0.8737 (mm) cc_final: 0.8533 (tp) outliers start: 60 outliers final: 52 residues processed: 607 average time/residue: 0.0948 time to fit residues: 90.3030 Evaluate side-chains 645 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 593 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 664 GLN Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 631 SER Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 661 THR Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 500 ASN Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 132 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 182 optimal weight: 0.1980 chunk 143 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN A 664 GLN B 414 HIS E 500 ASN E 534 GLN E 664 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078420 restraints weight = 65153.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.082358 restraints weight = 31077.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.085023 restraints weight = 18050.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086856 restraints weight = 11842.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.088136 restraints weight = 8510.196| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14926 Z= 0.151 Angle : 0.577 9.405 20594 Z= 0.297 Chirality : 0.039 0.136 2546 Planarity : 0.004 0.049 2716 Dihedral : 3.770 16.641 2398 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.06 % Favored : 94.76 % Rotamer: Outliers : 7.24 % Allowed : 37.64 % Favored : 55.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.19), residues: 2296 helix: 0.84 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.56 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 464 TYR 0.017 0.001 TYR H 504 PHE 0.024 0.002 PHE A 667 TRP 0.027 0.001 TRP G 630 HIS 0.016 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00305 (14926) covalent geometry : angle 0.57748 (20594) hydrogen bonds : bond 0.02874 ( 1082) hydrogen bonds : angle 3.71943 ( 3216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 603 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8833 (t80) cc_final: 0.8240 (t80) REVERT: A 471 LEU cc_start: 0.8852 (tp) cc_final: 0.8575 (tt) REVERT: A 503 THR cc_start: 0.8634 (m) cc_final: 0.8276 (t) REVERT: A 538 MET cc_start: 0.8049 (mmm) cc_final: 0.7839 (mmp) REVERT: A 630 TRP cc_start: 0.7803 (m100) cc_final: 0.7333 (m100) REVERT: A 656 LYS cc_start: 0.8716 (tttt) cc_final: 0.8394 (ttmm) REVERT: A 664 GLN cc_start: 0.8673 (mt0) cc_final: 0.8334 (mt0) REVERT: B 421 VAL cc_start: 0.8664 (p) cc_final: 0.8249 (p) REVERT: B 500 ASN cc_start: 0.8637 (t0) cc_final: 0.8386 (t0) REVERT: B 508 LYS cc_start: 0.8335 (tttp) cc_final: 0.7954 (ttmt) REVERT: B 560 GLN cc_start: 0.8220 (tt0) cc_final: 0.8000 (tt0) REVERT: B 564 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7524 (mm-40) REVERT: B 587 GLN cc_start: 0.8899 (pp30) cc_final: 0.7951 (pp30) REVERT: B 591 HIS cc_start: 0.7848 (m-70) cc_final: 0.7008 (m170) REVERT: B 645 MET cc_start: 0.7832 (mmm) cc_final: 0.7344 (mmm) REVERT: B 680 TYR cc_start: 0.8721 (t80) cc_final: 0.8484 (t80) REVERT: C 651 LEU cc_start: 0.8602 (mt) cc_final: 0.8397 (mm) REVERT: D 426 TYR cc_start: 0.7845 (t80) cc_final: 0.7393 (t80) REVERT: D 465 VAL cc_start: 0.8329 (m) cc_final: 0.7962 (p) REVERT: D 489 THR cc_start: 0.8652 (p) cc_final: 0.8377 (m) REVERT: D 493 PHE cc_start: 0.8585 (m-80) cc_final: 0.8344 (m-10) REVERT: D 504 TYR cc_start: 0.7700 (t80) cc_final: 0.7110 (t80) REVERT: D 508 LYS cc_start: 0.8581 (tttp) cc_final: 0.8060 (ttmt) REVERT: D 536 GLN cc_start: 0.8212 (tt0) cc_final: 0.7867 (tt0) REVERT: D 538 MET cc_start: 0.8260 (mmm) cc_final: 0.7998 (tpp) REVERT: D 630 TRP cc_start: 0.7799 (m100) cc_final: 0.7349 (m100) REVERT: D 680 TYR cc_start: 0.8594 (t80) cc_final: 0.8265 (t80) REVERT: D 689 HIS cc_start: 0.7963 (m-70) cc_final: 0.7691 (m-70) REVERT: D 693 ARG cc_start: 0.7528 (mtt90) cc_final: 0.7171 (mtt90) REVERT: E 441 PHE cc_start: 0.8875 (t80) cc_final: 0.8341 (t80) REVERT: E 471 LEU cc_start: 0.8880 (tp) cc_final: 0.8603 (tt) REVERT: E 503 THR cc_start: 0.8697 (m) cc_final: 0.8334 (t) REVERT: E 541 PHE cc_start: 0.8449 (t80) cc_final: 0.8164 (t80) REVERT: E 630 TRP cc_start: 0.7850 (m100) cc_final: 0.7380 (m100) REVERT: E 667 PHE cc_start: 0.9220 (t80) cc_final: 0.8917 (t80) REVERT: F 415 ILE cc_start: 0.8352 (mm) cc_final: 0.7844 (tp) REVERT: F 464 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7291 (ttm110) REVERT: F 493 PHE cc_start: 0.8614 (m-80) cc_final: 0.8342 (m-10) REVERT: F 508 LYS cc_start: 0.8361 (tttp) cc_final: 0.7809 (ttmt) REVERT: F 564 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7466 (mm-40) REVERT: F 587 GLN cc_start: 0.8925 (pp30) cc_final: 0.8162 (pp30) REVERT: F 591 HIS cc_start: 0.7987 (m-70) cc_final: 0.7287 (m170) REVERT: F 645 MET cc_start: 0.7962 (mmm) cc_final: 0.7616 (mmm) REVERT: G 473 LEU cc_start: 0.8564 (mt) cc_final: 0.8294 (mm) REVERT: G 534 GLN cc_start: 0.7578 (tt0) cc_final: 0.7280 (tt0) REVERT: G 542 TRP cc_start: 0.8077 (m-10) cc_final: 0.7819 (m-10) REVERT: G 664 GLN cc_start: 0.8401 (mt0) cc_final: 0.8188 (pt0) REVERT: H 426 TYR cc_start: 0.7851 (t80) cc_final: 0.7588 (t80) REVERT: H 508 LYS cc_start: 0.8577 (tttp) cc_final: 0.8125 (ttmt) REVERT: H 599 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7900 (ttm-80) REVERT: H 602 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8356 (tp-100) REVERT: H 630 TRP cc_start: 0.7921 (m100) cc_final: 0.7565 (m100) outliers start: 65 outliers final: 55 residues processed: 614 average time/residue: 0.0931 time to fit residues: 89.5758 Evaluate side-chains 656 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 601 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 624 ASP Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 661 THR Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 126 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 178 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 0.0970 chunk 172 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 534 GLN E 664 GLN ** F 664 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 = 0.3379 r_free = 0.3379 target = 0.095475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078802 restraints weight = 64671.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082728 restraints weight = 30894.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085366 restraints weight = 17964.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087211 restraints weight = 11841.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.088502 restraints weight = 8495.432| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14926 Z= 0.128 Angle : 0.579 10.894 20594 Z= 0.292 Chirality : 0.038 0.139 2546 Planarity : 0.004 0.043 2716 Dihedral : 3.695 17.044 2398 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.11 % Rotamer: Outliers : 6.57 % Allowed : 38.20 % Favored : 55.23 % 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: 0.86 (0.19), residues: 2296 helix: 1.10 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.37 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 464 TYR 0.016 0.001 TYR E 426 PHE 0.030 0.002 PHE A 541 TRP 0.018 0.001 TRP G 630 HIS 0.011 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00276 (14926) covalent geometry : angle 0.57886 (20594) hydrogen bonds : bond 0.02779 ( 1082) hydrogen bonds : angle 3.64179 ( 3216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 604 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8819 (t80) cc_final: 0.8223 (t80) REVERT: A 471 LEU cc_start: 0.8823 (tp) cc_final: 0.8560 (tt) REVERT: A 503 THR cc_start: 0.8628 (m) cc_final: 0.8239 (t) REVERT: A 538 MET cc_start: 0.8068 (mmm) cc_final: 0.7798 (mmp) REVERT: A 630 TRP cc_start: 0.7744 (m100) cc_final: 0.7361 (m100) REVERT: A 656 LYS cc_start: 0.8708 (tttt) cc_final: 0.8381 (ttmm) REVERT: A 664 GLN cc_start: 0.8629 (mt0) cc_final: 0.8306 (mt0) REVERT: B 421 VAL cc_start: 0.8654 (p) cc_final: 0.8194 (p) REVERT: B 500 ASN cc_start: 0.8567 (t0) cc_final: 0.8361 (t0) REVERT: B 508 LYS cc_start: 0.8306 (tttp) cc_final: 0.7910 (ttmt) REVERT: B 560 GLN cc_start: 0.8233 (tt0) cc_final: 0.8018 (tt0) REVERT: B 564 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7522 (mm-40) REVERT: B 587 GLN cc_start: 0.8900 (pp30) cc_final: 0.7928 (pp30) REVERT: B 591 HIS cc_start: 0.7863 (m-70) cc_final: 0.6968 (m170) REVERT: B 645 MET cc_start: 0.7801 (mmm) cc_final: 0.7364 (mmm) REVERT: B 680 TYR cc_start: 0.8694 (t80) cc_final: 0.8477 (t80) REVERT: C 541 PHE cc_start: 0.8456 (t80) cc_final: 0.8092 (t80) REVERT: D 426 TYR cc_start: 0.7844 (t80) cc_final: 0.7383 (t80) REVERT: D 465 VAL cc_start: 0.8323 (m) cc_final: 0.7919 (p) REVERT: D 489 THR cc_start: 0.8595 (p) cc_final: 0.8362 (m) REVERT: D 493 PHE cc_start: 0.8599 (m-80) cc_final: 0.8367 (m-10) REVERT: D 504 TYR cc_start: 0.7719 (t80) cc_final: 0.7140 (t80) REVERT: D 508 LYS cc_start: 0.8573 (tttp) cc_final: 0.8059 (ttmt) REVERT: D 536 GLN cc_start: 0.8256 (tt0) cc_final: 0.7915 (tt0) REVERT: D 538 MET cc_start: 0.8252 (mmm) cc_final: 0.7990 (tpp) REVERT: D 630 TRP cc_start: 0.7786 (m100) cc_final: 0.7292 (m100) REVERT: D 680 TYR cc_start: 0.8596 (t80) cc_final: 0.8274 (t80) REVERT: D 689 HIS cc_start: 0.7916 (m-70) cc_final: 0.7609 (m-70) REVERT: D 693 ARG cc_start: 0.7531 (mtt90) cc_final: 0.7180 (mtt90) REVERT: E 441 PHE cc_start: 0.8859 (t80) cc_final: 0.8317 (t80) REVERT: E 471 LEU cc_start: 0.8849 (tp) cc_final: 0.8561 (tt) REVERT: E 503 THR cc_start: 0.8665 (m) cc_final: 0.8220 (t) REVERT: E 534 GLN cc_start: 0.7850 (tm130) cc_final: 0.7591 (tp40) REVERT: E 541 PHE cc_start: 0.8441 (t80) cc_final: 0.8213 (t80) REVERT: E 557 MET cc_start: 0.7849 (tmm) cc_final: 0.7611 (tmm) REVERT: E 630 TRP cc_start: 0.7818 (m100) cc_final: 0.7488 (m100) REVERT: E 667 PHE cc_start: 0.9226 (t80) cc_final: 0.8901 (t80) REVERT: F 415 ILE cc_start: 0.8329 (mm) cc_final: 0.7821 (tp) REVERT: F 464 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7527 (ttm110) REVERT: F 493 PHE cc_start: 0.8592 (m-80) cc_final: 0.8309 (m-10) REVERT: F 508 LYS cc_start: 0.8308 (tttp) cc_final: 0.7762 (ttmt) REVERT: F 564 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7472 (mm-40) REVERT: F 587 GLN cc_start: 0.8887 (pp30) cc_final: 0.8133 (pp30) REVERT: F 591 HIS cc_start: 0.7982 (m-70) cc_final: 0.7215 (m170) REVERT: F 645 MET cc_start: 0.7890 (mmm) cc_final: 0.7585 (mmm) REVERT: G 473 LEU cc_start: 0.8543 (mt) cc_final: 0.8263 (mm) REVERT: G 534 GLN cc_start: 0.7573 (tt0) cc_final: 0.7280 (tt0) REVERT: G 542 TRP cc_start: 0.8053 (m-10) cc_final: 0.7804 (m-10) REVERT: G 664 GLN cc_start: 0.8358 (mt0) cc_final: 0.8125 (pt0) REVERT: H 426 TYR cc_start: 0.7854 (t80) cc_final: 0.7560 (t80) REVERT: H 493 PHE cc_start: 0.8447 (m-80) cc_final: 0.8222 (m-10) REVERT: H 508 LYS cc_start: 0.8566 (tttp) cc_final: 0.8078 (ttmt) REVERT: H 599 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: H 630 TRP cc_start: 0.7913 (m100) cc_final: 0.7527 (m100) outliers start: 59 outliers final: 51 residues processed: 615 average time/residue: 0.0909 time to fit residues: 88.0323 Evaluate side-chains 655 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 604 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 661 THR Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 489 THR Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 94 optimal weight: 0.8980 chunk 182 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 202 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS E 500 ASN E 664 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074672 restraints weight = 82304.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078962 restraints weight = 36334.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081888 restraints weight = 20431.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.083856 restraints weight = 13174.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085292 restraints weight = 9357.650| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14926 Z= 0.159 Angle : 0.602 10.727 20594 Z= 0.306 Chirality : 0.039 0.169 2546 Planarity : 0.004 0.040 2716 Dihedral : 3.756 16.078 2398 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 6.24 % Allowed : 39.09 % Favored : 54.68 % 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: 0.99 (0.19), residues: 2296 helix: 1.19 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.30 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 464 TYR 0.015 0.001 TYR D 426 PHE 0.036 0.002 PHE A 541 TRP 0.028 0.001 TRP B 448 HIS 0.011 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00329 (14926) covalent geometry : angle 0.60203 (20594) hydrogen bonds : bond 0.02903 ( 1082) hydrogen bonds : angle 3.74681 ( 3216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 608 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8820 (t80) cc_final: 0.8225 (t80) REVERT: A 471 LEU cc_start: 0.8833 (tp) cc_final: 0.8559 (tt) REVERT: A 503 THR cc_start: 0.8691 (m) cc_final: 0.8245 (t) REVERT: A 538 MET cc_start: 0.8065 (mmm) cc_final: 0.7856 (mmp) REVERT: A 630 TRP cc_start: 0.7751 (m100) cc_final: 0.7346 (m100) REVERT: A 656 LYS cc_start: 0.8742 (tttt) cc_final: 0.8430 (ttmm) REVERT: A 664 GLN cc_start: 0.8664 (mt0) cc_final: 0.8345 (mt0) REVERT: B 421 VAL cc_start: 0.8681 (p) cc_final: 0.8164 (p) REVERT: B 500 ASN cc_start: 0.8533 (t0) cc_final: 0.8302 (t0) REVERT: B 508 LYS cc_start: 0.8305 (tttp) cc_final: 0.7922 (ttmt) REVERT: B 560 GLN cc_start: 0.8296 (tt0) cc_final: 0.8060 (tt0) REVERT: B 564 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7556 (mm-40) REVERT: B 587 GLN cc_start: 0.8915 (pp30) cc_final: 0.7906 (pp30) REVERT: B 591 HIS cc_start: 0.7895 (m-70) cc_final: 0.7010 (m170) REVERT: B 645 MET cc_start: 0.7695 (mmm) cc_final: 0.7322 (mmm) REVERT: B 680 TYR cc_start: 0.8733 (t80) cc_final: 0.8508 (t80) REVERT: C 508 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8394 (ttpp) REVERT: C 541 PHE cc_start: 0.8447 (t80) cc_final: 0.8075 (t80) REVERT: C 566 PHE cc_start: 0.8441 (m-10) cc_final: 0.8070 (m-80) REVERT: D 426 TYR cc_start: 0.7850 (t80) cc_final: 0.7355 (t80) REVERT: D 465 VAL cc_start: 0.8288 (m) cc_final: 0.7897 (p) REVERT: D 489 THR cc_start: 0.8661 (p) cc_final: 0.8392 (m) REVERT: D 493 PHE cc_start: 0.8617 (m-80) cc_final: 0.8410 (m-10) REVERT: D 504 TYR cc_start: 0.7753 (t80) cc_final: 0.7118 (t80) REVERT: D 508 LYS cc_start: 0.8543 (tttp) cc_final: 0.8016 (ttmt) REVERT: D 536 GLN cc_start: 0.8301 (tt0) cc_final: 0.7948 (tt0) REVERT: D 538 MET cc_start: 0.8261 (mmm) cc_final: 0.8015 (tpp) REVERT: D 630 TRP cc_start: 0.7790 (m100) cc_final: 0.7305 (m100) REVERT: D 680 TYR cc_start: 0.8610 (t80) cc_final: 0.8323 (t80) REVERT: D 689 HIS cc_start: 0.7926 (m-70) cc_final: 0.7637 (m-70) REVERT: D 693 ARG cc_start: 0.7589 (mtt90) cc_final: 0.7260 (mtt90) REVERT: E 441 PHE cc_start: 0.8865 (t80) cc_final: 0.8331 (t80) REVERT: E 471 LEU cc_start: 0.8873 (tp) cc_final: 0.8578 (tt) REVERT: E 503 THR cc_start: 0.8661 (m) cc_final: 0.8243 (t) REVERT: E 534 GLN cc_start: 0.7868 (tm130) cc_final: 0.7253 (tm-30) REVERT: E 541 PHE cc_start: 0.8467 (t80) cc_final: 0.8219 (t80) REVERT: E 557 MET cc_start: 0.7915 (tmm) cc_final: 0.7641 (tmm) REVERT: E 630 TRP cc_start: 0.7836 (m100) cc_final: 0.7448 (m100) REVERT: E 667 PHE cc_start: 0.9235 (t80) cc_final: 0.8873 (t80) REVERT: F 415 ILE cc_start: 0.8308 (mm) cc_final: 0.7800 (tp) REVERT: F 464 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7536 (ttm110) REVERT: F 493 PHE cc_start: 0.8578 (m-80) cc_final: 0.8315 (m-10) REVERT: F 508 LYS cc_start: 0.8285 (tttp) cc_final: 0.7762 (ttmt) REVERT: F 538 MET cc_start: 0.7688 (mmm) cc_final: 0.7352 (mmm) REVERT: F 564 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7523 (mm-40) REVERT: F 587 GLN cc_start: 0.8894 (pp30) cc_final: 0.8133 (pp30) REVERT: F 591 HIS cc_start: 0.8021 (m-70) cc_final: 0.7217 (m170) REVERT: F 645 MET cc_start: 0.7810 (mmm) cc_final: 0.7594 (mmm) REVERT: F 680 TYR cc_start: 0.8807 (t80) cc_final: 0.8206 (t80) REVERT: G 473 LEU cc_start: 0.8571 (mt) cc_final: 0.8286 (mm) REVERT: G 534 GLN cc_start: 0.7590 (tt0) cc_final: 0.7318 (tt0) REVERT: G 542 TRP cc_start: 0.8090 (m-10) cc_final: 0.7868 (m-10) REVERT: H 426 TYR cc_start: 0.7905 (t80) cc_final: 0.7599 (t80) REVERT: H 493 PHE cc_start: 0.8505 (m-80) cc_final: 0.8232 (m-10) REVERT: H 508 LYS cc_start: 0.8568 (tttp) cc_final: 0.8073 (ttmt) REVERT: H 630 TRP cc_start: 0.7913 (m100) cc_final: 0.7532 (m100) outliers start: 56 outliers final: 52 residues processed: 618 average time/residue: 0.0918 time to fit residues: 88.9761 Evaluate side-chains 658 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 606 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 661 THR Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 565 LEU Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 59 optimal weight: 0.3980 chunk 182 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 170 optimal weight: 0.3980 chunk 195 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS E 664 GLN F 414 HIS ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076320 restraints weight = 56044.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.080038 restraints weight = 27738.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082577 restraints weight = 16558.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084318 restraints weight = 11109.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.085578 restraints weight = 8114.589| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14926 Z= 0.147 Angle : 0.607 11.277 20594 Z= 0.307 Chirality : 0.039 0.139 2546 Planarity : 0.004 0.039 2716 Dihedral : 3.756 16.437 2398 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.89 % Favored : 94.94 % Rotamer: Outliers : 6.24 % Allowed : 39.53 % Favored : 54.23 % 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: 1.13 (0.19), residues: 2296 helix: 1.28 (0.13), residues: 1832 sheet: None (None), residues: 0 loop : -1.25 (0.32), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 464 TYR 0.026 0.001 TYR F 426 PHE 0.038 0.002 PHE A 541 TRP 0.030 0.001 TRP F 448 HIS 0.016 0.001 HIS D 644 Details of bonding type rmsd covalent geometry : bond 0.00311 (14926) covalent geometry : angle 0.60726 (20594) hydrogen bonds : bond 0.02895 ( 1082) hydrogen bonds : angle 3.70763 ( 3216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 605 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8830 (t80) cc_final: 0.8231 (t80) REVERT: A 471 LEU cc_start: 0.8820 (tp) cc_final: 0.8544 (tt) REVERT: A 503 THR cc_start: 0.8621 (m) cc_final: 0.8074 (t) REVERT: A 506 ILE cc_start: 0.8478 (mt) cc_final: 0.8136 (tp) REVERT: A 656 LYS cc_start: 0.8738 (tttt) cc_final: 0.8427 (ttmm) REVERT: A 664 GLN cc_start: 0.8661 (mt0) cc_final: 0.8339 (mt0) REVERT: B 421 VAL cc_start: 0.8684 (p) cc_final: 0.8175 (p) REVERT: B 500 ASN cc_start: 0.8565 (t0) cc_final: 0.8350 (t0) REVERT: B 508 LYS cc_start: 0.8276 (tttp) cc_final: 0.7897 (ttmt) REVERT: B 560 GLN cc_start: 0.8310 (tt0) cc_final: 0.8087 (tt0) REVERT: B 564 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7561 (mm-40) REVERT: B 587 GLN cc_start: 0.8913 (pp30) cc_final: 0.7972 (pp30) REVERT: B 591 HIS cc_start: 0.7904 (m-70) cc_final: 0.6956 (m170) REVERT: B 645 MET cc_start: 0.7710 (mmm) cc_final: 0.7296 (mmm) REVERT: C 541 PHE cc_start: 0.8432 (t80) cc_final: 0.8078 (t80) REVERT: C 566 PHE cc_start: 0.8429 (m-10) cc_final: 0.8068 (m-80) REVERT: D 426 TYR cc_start: 0.7874 (t80) cc_final: 0.7386 (t80) REVERT: D 465 VAL cc_start: 0.8278 (m) cc_final: 0.7901 (p) REVERT: D 489 THR cc_start: 0.8675 (p) cc_final: 0.8387 (m) REVERT: D 493 PHE cc_start: 0.8628 (m-80) cc_final: 0.8420 (m-10) REVERT: D 504 TYR cc_start: 0.7665 (t80) cc_final: 0.7066 (t80) REVERT: D 508 LYS cc_start: 0.8523 (tttp) cc_final: 0.8019 (ttmt) REVERT: D 536 GLN cc_start: 0.8331 (tt0) cc_final: 0.7958 (tt0) REVERT: D 538 MET cc_start: 0.8256 (mmm) cc_final: 0.8009 (tpp) REVERT: D 566 PHE cc_start: 0.8400 (m-80) cc_final: 0.7693 (m-80) REVERT: D 630 TRP cc_start: 0.7802 (m100) cc_final: 0.7296 (m100) REVERT: D 680 TYR cc_start: 0.8608 (t80) cc_final: 0.8326 (t80) REVERT: D 689 HIS cc_start: 0.7918 (m-70) cc_final: 0.7620 (m-70) REVERT: D 693 ARG cc_start: 0.7601 (mtt90) cc_final: 0.7275 (mtt90) REVERT: E 441 PHE cc_start: 0.8864 (t80) cc_final: 0.8352 (t80) REVERT: E 471 LEU cc_start: 0.8837 (tp) cc_final: 0.8543 (tt) REVERT: E 503 THR cc_start: 0.8651 (m) cc_final: 0.8223 (t) REVERT: E 534 GLN cc_start: 0.7870 (tm130) cc_final: 0.7262 (tm-30) REVERT: E 541 PHE cc_start: 0.8495 (t80) cc_final: 0.8232 (t80) REVERT: E 557 MET cc_start: 0.7910 (tmm) cc_final: 0.7617 (tmm) REVERT: E 630 TRP cc_start: 0.7818 (m100) cc_final: 0.7429 (m100) REVERT: E 667 PHE cc_start: 0.9179 (t80) cc_final: 0.8808 (t80) REVERT: F 415 ILE cc_start: 0.8231 (mm) cc_final: 0.7743 (tp) REVERT: F 493 PHE cc_start: 0.8525 (m-80) cc_final: 0.8255 (m-10) REVERT: F 508 LYS cc_start: 0.8286 (tttp) cc_final: 0.7767 (ttmt) REVERT: F 538 MET cc_start: 0.7683 (mmm) cc_final: 0.7341 (mmm) REVERT: F 564 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7487 (mm-40) REVERT: F 587 GLN cc_start: 0.8894 (pp30) cc_final: 0.8115 (pp30) REVERT: F 591 HIS cc_start: 0.8002 (m-70) cc_final: 0.7199 (m170) REVERT: F 645 MET cc_start: 0.7827 (mmm) cc_final: 0.7597 (mmm) REVERT: F 680 TYR cc_start: 0.8822 (t80) cc_final: 0.8210 (t80) REVERT: G 473 LEU cc_start: 0.8571 (mt) cc_final: 0.8255 (mm) REVERT: G 534 GLN cc_start: 0.7604 (tt0) cc_final: 0.7331 (tt0) REVERT: G 542 TRP cc_start: 0.8079 (m-10) cc_final: 0.7854 (m-10) REVERT: G 664 GLN cc_start: 0.8601 (mt0) cc_final: 0.8385 (pt0) REVERT: H 426 TYR cc_start: 0.7911 (t80) cc_final: 0.7604 (t80) REVERT: H 493 PHE cc_start: 0.8522 (m-80) cc_final: 0.8266 (m-10) REVERT: H 508 LYS cc_start: 0.8554 (tttp) cc_final: 0.8055 (ttmt) REVERT: H 630 TRP cc_start: 0.7902 (m100) cc_final: 0.7524 (m100) outliers start: 56 outliers final: 55 residues processed: 616 average time/residue: 0.0935 time to fit residues: 90.5742 Evaluate side-chains 660 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 605 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 414 HIS Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 661 THR Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 565 LEU Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 59 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 142 optimal weight: 0.0270 chunk 222 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 226 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS E 500 ASN E 664 GLN F 414 HIS ** F 664 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 = 0.3360 r_free = 0.3360 target = 0.094483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.077155 restraints weight = 73636.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081267 restraints weight = 33502.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.084093 restraints weight = 19046.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.086028 restraints weight = 12312.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087352 restraints weight = 8737.253| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14926 Z= 0.142 Angle : 0.625 12.173 20594 Z= 0.313 Chirality : 0.039 0.201 2546 Planarity : 0.004 0.047 2716 Dihedral : 3.758 15.904 2398 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.84 % Favored : 94.98 % Rotamer: Outliers : 6.12 % Allowed : 40.53 % Favored : 53.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 2296 helix: 1.35 (0.13), residues: 1832 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 464 TYR 0.023 0.001 TYR F 426 PHE 0.042 0.002 PHE C 667 TRP 0.056 0.002 TRP A 630 HIS 0.012 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00305 (14926) covalent geometry : angle 0.62480 (20594) hydrogen bonds : bond 0.02877 ( 1082) hydrogen bonds : angle 3.71108 ( 3216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 608 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8826 (t80) cc_final: 0.8226 (t80) REVERT: A 471 LEU cc_start: 0.8818 (tp) cc_final: 0.8530 (tt) REVERT: A 503 THR cc_start: 0.8593 (m) cc_final: 0.8010 (t) REVERT: A 506 ILE cc_start: 0.8471 (mt) cc_final: 0.8124 (tp) REVERT: A 541 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8119 (t80) REVERT: A 555 TYR cc_start: 0.8767 (m-80) cc_final: 0.8412 (m-80) REVERT: A 630 TRP cc_start: 0.7517 (m100) cc_final: 0.7223 (m100) REVERT: A 664 GLN cc_start: 0.8636 (mt0) cc_final: 0.8323 (mt0) REVERT: B 500 ASN cc_start: 0.8510 (t0) cc_final: 0.8215 (t0) REVERT: B 508 LYS cc_start: 0.8263 (tttp) cc_final: 0.7860 (ttmt) REVERT: B 560 GLN cc_start: 0.8336 (tt0) cc_final: 0.8106 (tt0) REVERT: B 564 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7570 (mm-40) REVERT: B 587 GLN cc_start: 0.8917 (pp30) cc_final: 0.7969 (pp30) REVERT: B 591 HIS cc_start: 0.7901 (m-70) cc_final: 0.6945 (m170) REVERT: B 608 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8133 (mm-40) REVERT: B 645 MET cc_start: 0.7641 (mmm) cc_final: 0.7359 (mmm) REVERT: C 541 PHE cc_start: 0.8432 (t80) cc_final: 0.8060 (t80) REVERT: C 566 PHE cc_start: 0.8424 (m-10) cc_final: 0.8073 (m-80) REVERT: D 426 TYR cc_start: 0.7840 (t80) cc_final: 0.7337 (t80) REVERT: D 465 VAL cc_start: 0.8284 (m) cc_final: 0.7874 (p) REVERT: D 489 THR cc_start: 0.8600 (p) cc_final: 0.8332 (m) REVERT: D 504 TYR cc_start: 0.7643 (t80) cc_final: 0.7053 (t80) REVERT: D 508 LYS cc_start: 0.8532 (tttp) cc_final: 0.8033 (ttmt) REVERT: D 536 GLN cc_start: 0.8331 (tt0) cc_final: 0.7952 (tt0) REVERT: D 538 MET cc_start: 0.8248 (mmm) cc_final: 0.7999 (tpp) REVERT: D 566 PHE cc_start: 0.8360 (m-80) cc_final: 0.7809 (m-80) REVERT: D 599 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7536 (ttm-80) REVERT: D 630 TRP cc_start: 0.7788 (m100) cc_final: 0.7370 (m100) REVERT: D 680 TYR cc_start: 0.8601 (t80) cc_final: 0.8328 (t80) REVERT: D 689 HIS cc_start: 0.7879 (m-70) cc_final: 0.7532 (m-70) REVERT: D 693 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7254 (mtt90) REVERT: E 441 PHE cc_start: 0.8833 (t80) cc_final: 0.8348 (t80) REVERT: E 471 LEU cc_start: 0.8842 (tp) cc_final: 0.8541 (tt) REVERT: E 503 THR cc_start: 0.8644 (m) cc_final: 0.8244 (t) REVERT: E 534 GLN cc_start: 0.7883 (tm130) cc_final: 0.7267 (tm-30) REVERT: E 541 PHE cc_start: 0.8482 (t80) cc_final: 0.8218 (t80) REVERT: E 557 MET cc_start: 0.7897 (tmm) cc_final: 0.7696 (tmm) REVERT: E 630 TRP cc_start: 0.7802 (m100) cc_final: 0.7417 (m100) REVERT: E 667 PHE cc_start: 0.9188 (t80) cc_final: 0.8815 (t80) REVERT: F 415 ILE cc_start: 0.8333 (mm) cc_final: 0.8026 (mm) REVERT: F 493 PHE cc_start: 0.8490 (m-80) cc_final: 0.8234 (m-10) REVERT: F 508 LYS cc_start: 0.8282 (tttp) cc_final: 0.7765 (ttmt) REVERT: F 538 MET cc_start: 0.7667 (mmm) cc_final: 0.7329 (mmm) REVERT: F 564 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7496 (mm-40) REVERT: F 587 GLN cc_start: 0.8898 (pp30) cc_final: 0.8096 (pp30) REVERT: F 591 HIS cc_start: 0.8000 (m-70) cc_final: 0.7195 (m170) REVERT: F 645 MET cc_start: 0.7805 (mmm) cc_final: 0.7571 (mmm) REVERT: F 680 TYR cc_start: 0.8814 (t80) cc_final: 0.8273 (t80) REVERT: G 429 ILE cc_start: 0.8886 (pt) cc_final: 0.8645 (mp) REVERT: G 473 LEU cc_start: 0.8564 (mt) cc_final: 0.8261 (mm) REVERT: G 534 GLN cc_start: 0.7566 (tt0) cc_final: 0.7303 (tt0) REVERT: G 542 TRP cc_start: 0.8094 (m-10) cc_final: 0.7859 (m-10) REVERT: H 426 TYR cc_start: 0.7917 (t80) cc_final: 0.7494 (t80) REVERT: H 465 VAL cc_start: 0.8352 (m) cc_final: 0.8000 (p) REVERT: H 493 PHE cc_start: 0.8532 (m-80) cc_final: 0.8261 (m-10) REVERT: H 508 LYS cc_start: 0.8551 (tttp) cc_final: 0.8049 (ttmt) REVERT: H 630 TRP cc_start: 0.7898 (m100) cc_final: 0.7518 (m100) outliers start: 55 outliers final: 49 residues processed: 617 average time/residue: 0.0957 time to fit residues: 92.9890 Evaluate side-chains 658 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 608 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 643 SER Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 660 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 661 THR Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 689 HIS Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 625 LEU Chi-restraints excluded: chain F residue 639 HIS Chi-restraints excluded: chain G residue 451 VAL Chi-restraints excluded: chain G residue 510 ILE Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 661 THR Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 531 ILE Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 660 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 131 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 204 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 0.0010 chunk 153 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 106 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS E 664 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.094670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078143 restraints weight = 62464.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081994 restraints weight = 29919.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.084633 restraints weight = 17474.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086429 restraints weight = 11523.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087736 restraints weight = 8314.517| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14926 Z= 0.135 Angle : 0.624 11.996 20594 Z= 0.310 Chirality : 0.039 0.186 2546 Planarity : 0.004 0.039 2716 Dihedral : 3.732 16.056 2398 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.84 % Favored : 94.98 % Rotamer: Outliers : 5.57 % Allowed : 41.43 % Favored : 53.01 % 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: 1.42 (0.19), residues: 2296 helix: 1.49 (0.13), residues: 1832 sheet: None (None), residues: 0 loop : -1.18 (0.32), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 464 TYR 0.026 0.002 TYR B 680 PHE 0.037 0.002 PHE D 493 TRP 0.033 0.001 TRP A 630 HIS 0.020 0.001 HIS D 644 Details of bonding type rmsd covalent geometry : bond 0.00296 (14926) covalent geometry : angle 0.62428 (20594) hydrogen bonds : bond 0.02836 ( 1082) hydrogen bonds : angle 3.66907 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2839.16 seconds wall clock time: 49 minutes 29.99 seconds (2969.99 seconds total)