Starting phenix.real_space_refine on Wed Mar 4 15:16:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jth_22473/03_2026/7jth_22473.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jth_22473/03_2026/7jth_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_22473/03_2026/7jth_22473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jth_22473/03_2026/7jth_22473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jth_22473/03_2026/7jth_22473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jth_22473/03_2026/7jth_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-dev-5986/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: 4.12, per 1000 atoms: 0.28 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: 1.13 Conformation dependent library (CDL) restraints added in 853.7 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: 0.48 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: 1.85 Time building geometry restraints manager: 1.53 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: 0.02 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.450 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- 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 : 0.509 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: 0.7874 (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: 0.8351 (t0) cc_final: 0.7931 (t0) REVERT: B 507 ILE cc_start: 0.8071 (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: 0.8380 (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: 0.5227 (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: 0.6699 (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: 0.7654 (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: 0.8815 (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: 0.8732 (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: 0.7950 (t0) REVERT: F 554 TYR cc_start: 0.8399 (t80) cc_final: 0.8172 (t80) REVERT: F 560 GLN cc_start: 0.8355 (tt0) cc_final: 0.7962 (tt0) REVERT: F 564 GLN cc_start: 0.7381 (mm-40) cc_final: 0.6985 (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: 0.7723 (tp) REVERT: G 565 LEU cc_start: 0.8032 (tp) cc_final: 0.7648 (tp) REVERT: G 603 ILE cc_start: 0.8269 (mm) cc_final: 0.8068 (mm) REVERT: G 651 LEU cc_start: 0.8520 (mt) cc_final: 0.8252 (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: 0.0905 time to fit residues: 86.3940 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 : 0.416 ------------------------------------------------------------------------------- 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 : 0.501 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: 0.7906 (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: 0.7990 (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: 0.7628 (OUTLIER) cc_final: 0.7269 (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: 0.8721 (m-80) cc_final: 0.8500 (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: 0.8798 (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: 0.8567 (tttp) cc_final: 0.7998 (ttmt) REVERT: D 538 MET cc_start: 0.8317 (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: 0.7417 (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: 0.8150 (t70) REVERT: E 555 TYR cc_start: 0.8935 (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: 0.8052 (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: 0.7989 (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 448 TRP cc_start: 0.7655 (m-10) cc_final: 0.7455 (m-10) REVERT: H 493 PHE cc_start: 0.8492 (m-80) cc_final: 0.8088 (m-10) REVERT: H 508 LYS cc_start: 0.8564 (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: 0.8502 (tp) outliers start: 39 outliers final: 23 residues processed: 635 average time/residue: 0.0926 time to fit residues: 92.6632 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 : 0.498 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.095930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077603 restraints weight = 86716.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082003 restraints weight = 37197.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.085013 restraints weight = 20592.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087059 restraints weight = 13112.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088429 restraints weight = 9203.282| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 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 = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14926 Z= 0.136 Angle : 0.590 7.715 20594 Z= 0.306 Chirality : 0.039 0.158 2546 Planarity : 0.004 0.057 2716 Dihedral : 4.144 18.661 2398 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.81 % Rotamer: Outliers : 5.12 % Allowed : 32.85 % Favored : 62.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2296 helix: -0.32 (0.12), residues: 1844 sheet: None (None), residues: 0 loop : -2.43 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 464 TYR 0.020 0.002 TYR D 426 PHE 0.029 0.002 PHE G 541 TRP 0.027 0.001 TRP G 630 HIS 0.007 0.001 HIS F 467 Details of bonding type rmsd covalent geometry : bond 0.00280 (14926) covalent geometry : angle 0.58969 (20594) hydrogen bonds : bond 0.03248 ( 1082) hydrogen bonds : angle 4.12309 ( 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 660 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 614 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8853 (t80) cc_final: 0.8303 (t80) REVERT: A 506 ILE cc_start: 0.8515 (mt) cc_final: 0.8157 (tp) REVERT: A 538 MET cc_start: 0.7904 (mmm) cc_final: 0.7440 (mmp) REVERT: A 541 PHE cc_start: 0.8430 (t80) cc_final: 0.8194 (t80) REVERT: A 547 HIS cc_start: 0.8509 (t70) cc_final: 0.8309 (t-90) REVERT: A 630 TRP cc_start: 0.8013 (m100) cc_final: 0.7364 (m100) REVERT: A 656 LYS cc_start: 0.8686 (tttt) cc_final: 0.8402 (ttmm) REVERT: A 664 GLN cc_start: 0.8698 (mt0) cc_final: 0.8491 (mt0) REVERT: A 680 TYR cc_start: 0.8452 (t80) cc_final: 0.8177 (t80) REVERT: B 421 VAL cc_start: 0.8626 (p) cc_final: 0.8228 (p) REVERT: B 500 ASN cc_start: 0.8637 (t0) cc_final: 0.8369 (t0) REVERT: B 508 LYS cc_start: 0.8421 (tttp) cc_final: 0.8138 (ttpp) REVERT: B 560 GLN cc_start: 0.8239 (tt0) cc_final: 0.7873 (tt0) REVERT: B 564 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7506 (mm-40) REVERT: B 587 GLN cc_start: 0.8829 (pp30) cc_final: 0.8118 (pp30) REVERT: B 602 GLN cc_start: 0.8423 (tp40) cc_final: 0.8219 (tp40) REVERT: B 645 MET cc_start: 0.7964 (mmm) cc_final: 0.7379 (mmm) REVERT: C 534 GLN cc_start: 0.7597 (tt0) cc_final: 0.7343 (tt0) REVERT: C 557 MET cc_start: 0.7192 (tmm) cc_final: 0.6991 (tmm) REVERT: C 651 LEU cc_start: 0.8619 (mt) cc_final: 0.8399 (mm) REVERT: C 684 VAL cc_start: 0.8750 (t) cc_final: 0.8544 (p) REVERT: D 416 PHE cc_start: 0.7912 (t80) cc_final: 0.7475 (t80) REVERT: D 426 TYR cc_start: 0.7816 (t80) cc_final: 0.7511 (t80) REVERT: D 493 PHE cc_start: 0.8556 (m-80) cc_final: 0.8209 (m-10) REVERT: D 504 TYR cc_start: 0.7701 (t80) cc_final: 0.7026 (t80) REVERT: D 508 LYS cc_start: 0.8642 (tttp) cc_final: 0.8078 (ttmt) REVERT: D 536 GLN cc_start: 0.8195 (tt0) cc_final: 0.7920 (tt0) REVERT: D 538 MET cc_start: 0.8289 (mmm) cc_final: 0.8074 (tpp) REVERT: D 630 TRP cc_start: 0.7802 (m100) cc_final: 0.7392 (m100) REVERT: D 693 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7432 (mtt90) REVERT: E 441 PHE cc_start: 0.8870 (t80) cc_final: 0.8347 (t80) REVERT: E 510 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8545 (tt) REVERT: E 541 PHE cc_start: 0.8391 (t80) cc_final: 0.8167 (t80) REVERT: E 555 TYR cc_start: 0.8913 (m-10) cc_final: 0.8217 (m-80) REVERT: E 630 TRP cc_start: 0.7870 (m100) cc_final: 0.7240 (m100) REVERT: E 667 PHE cc_start: 0.9226 (t80) cc_final: 0.8947 (t80) REVERT: F 464 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7444 (ttm-80) REVERT: F 493 PHE cc_start: 0.8631 (m-80) cc_final: 0.8357 (m-10) REVERT: F 508 LYS cc_start: 0.8400 (tttp) cc_final: 0.7854 (ttmt) REVERT: F 530 MET cc_start: 0.8071 (mtt) cc_final: 0.7444 (mmm) REVERT: F 564 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7483 (mm-40) REVERT: F 587 GLN cc_start: 0.8820 (pp30) cc_final: 0.8111 (pp30) REVERT: F 591 HIS cc_start: 0.7936 (m-70) cc_final: 0.7310 (m170) REVERT: F 645 MET cc_start: 0.8045 (mmm) cc_final: 0.7803 (mmm) REVERT: G 459 ILE cc_start: 0.8275 (tp) cc_final: 0.8066 (tp) REVERT: G 534 GLN cc_start: 0.7549 (tt0) cc_final: 0.7249 (tt0) REVERT: G 539 ASP cc_start: 0.8019 (t70) cc_final: 0.7695 (t0) REVERT: G 541 PHE cc_start: 0.8532 (t80) cc_final: 0.8074 (t80) REVERT: G 684 VAL cc_start: 0.8728 (t) cc_final: 0.8495 (p) REVERT: H 426 TYR cc_start: 0.7858 (t80) cc_final: 0.7601 (t80) REVERT: H 448 TRP cc_start: 0.7753 (m-10) cc_final: 0.7456 (m-10) REVERT: H 493 PHE cc_start: 0.8504 (m-80) cc_final: 0.8157 (m-10) REVERT: H 508 LYS cc_start: 0.8570 (tttp) cc_final: 0.8066 (ttmt) REVERT: H 536 GLN cc_start: 0.8123 (tt0) cc_final: 0.7881 (tt0) REVERT: H 602 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8345 (tp-100) REVERT: H 630 TRP cc_start: 0.7932 (m100) cc_final: 0.7607 (m100) REVERT: H 671 ILE cc_start: 0.8773 (mm) cc_final: 0.8547 (tp) outliers start: 46 outliers final: 32 residues processed: 618 average time/residue: 0.0898 time to fit residues: 87.5922 Evaluate side-chains 639 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 606 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain H residue 540 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 166 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 227 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 11 optimal weight: 0.0770 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 HIS E 500 ASN ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 HIS H 414 HIS H 500 ASN H 689 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079180 restraints weight = 64356.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.083099 restraints weight = 30567.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.085775 restraints weight = 17780.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.087613 restraints weight = 11673.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.088830 restraints weight = 8385.107| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 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 = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14926 Z= 0.121 Angle : 0.576 9.305 20594 Z= 0.295 Chirality : 0.038 0.130 2546 Planarity : 0.004 0.043 2716 Dihedral : 3.973 19.075 2398 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.81 % Rotamer: Outliers : 5.68 % Allowed : 35.86 % Favored : 58.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2296 helix: 0.11 (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 0.017 0.001 TYR D 426 PHE 0.019 0.002 PHE B 493 TRP 0.013 0.001 TRP G 630 HIS 0.009 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00254 (14926) covalent geometry : angle 0.57642 (20594) hydrogen bonds : bond 0.02942 ( 1082) hydrogen bonds : angle 3.87109 ( 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 650 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 599 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8860 (t80) cc_final: 0.8243 (t80) REVERT: A 471 LEU cc_start: 0.8857 (tp) cc_final: 0.8588 (tt) REVERT: A 503 THR cc_start: 0.8775 (m) cc_final: 0.8128 (t) REVERT: A 506 ILE cc_start: 0.8497 (mt) cc_final: 0.8105 (tp) REVERT: A 538 MET cc_start: 0.8057 (mmm) cc_final: 0.7628 (mmp) REVERT: A 557 MET cc_start: 0.7966 (tmm) cc_final: 0.7755 (tmm) REVERT: A 558 ILE cc_start: 0.8421 (tp) cc_final: 0.8212 (tp) REVERT: A 630 TRP cc_start: 0.7917 (m100) cc_final: 0.7564 (m100) REVERT: A 656 LYS cc_start: 0.8673 (tttt) cc_final: 0.8393 (ttmm) REVERT: A 664 GLN cc_start: 0.8721 (mt0) cc_final: 0.8449 (mt0) REVERT: A 680 TYR cc_start: 0.8499 (t80) cc_final: 0.8282 (t80) REVERT: B 421 VAL cc_start: 0.8667 (p) cc_final: 0.8408 (p) REVERT: B 500 ASN cc_start: 0.8649 (t0) cc_final: 0.8398 (t0) REVERT: B 508 LYS cc_start: 0.8343 (tttp) cc_final: 0.8018 (ttpp) REVERT: B 560 GLN cc_start: 0.8191 (tt0) cc_final: 0.7814 (tt0) REVERT: B 564 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7511 (mm-40) REVERT: B 587 GLN cc_start: 0.8852 (pp30) cc_final: 0.8120 (pp30) REVERT: B 602 GLN cc_start: 0.8429 (tp40) cc_final: 0.8175 (tp40) REVERT: B 645 MET cc_start: 0.7904 (mmm) cc_final: 0.7373 (mmm) REVERT: C 534 GLN cc_start: 0.7607 (tt0) cc_final: 0.7344 (tt0) REVERT: C 651 LEU cc_start: 0.8601 (mt) cc_final: 0.8382 (mm) REVERT: C 667 PHE cc_start: 0.8901 (t80) cc_final: 0.8672 (t80) REVERT: D 416 PHE cc_start: 0.7923 (t80) cc_final: 0.7473 (t80) REVERT: D 426 TYR cc_start: 0.7812 (t80) cc_final: 0.7520 (t80) REVERT: D 489 THR cc_start: 0.8670 (p) cc_final: 0.8370 (m) REVERT: D 493 PHE cc_start: 0.8547 (m-80) cc_final: 0.8260 (m-10) REVERT: D 504 TYR cc_start: 0.7718 (t80) cc_final: 0.7104 (t80) REVERT: D 508 LYS cc_start: 0.8608 (tttp) cc_final: 0.8054 (ttmt) REVERT: D 536 GLN cc_start: 0.8182 (tt0) cc_final: 0.7905 (tt0) REVERT: D 538 MET cc_start: 0.8289 (mmm) cc_final: 0.8048 (tpp) REVERT: D 630 TRP cc_start: 0.7787 (m100) cc_final: 0.7388 (m100) REVERT: D 680 TYR cc_start: 0.8558 (t80) cc_final: 0.8149 (t80) REVERT: D 689 HIS cc_start: 0.7901 (m-70) cc_final: 0.7496 (m90) REVERT: D 693 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7411 (mtt90) REVERT: E 441 PHE cc_start: 0.8868 (t80) cc_final: 0.8304 (t80) REVERT: E 503 THR cc_start: 0.8698 (m) cc_final: 0.8235 (t) REVERT: E 510 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8570 (tt) REVERT: E 534 GLN cc_start: 0.7430 (tm-30) cc_final: 0.7198 (tm-30) REVERT: E 541 PHE cc_start: 0.8439 (t80) cc_final: 0.8168 (t80) REVERT: E 630 TRP cc_start: 0.7805 (m100) cc_final: 0.7396 (m100) REVERT: E 667 PHE cc_start: 0.9206 (t80) cc_final: 0.8905 (t80) REVERT: F 464 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7451 (ttm-80) REVERT: F 493 PHE cc_start: 0.8638 (m-80) cc_final: 0.8354 (m-10) REVERT: F 508 LYS cc_start: 0.8358 (tttp) cc_final: 0.7845 (ttmt) REVERT: F 530 MET cc_start: 0.8014 (mtt) cc_final: 0.7430 (mmm) REVERT: F 564 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7460 (mm-40) REVERT: F 587 GLN cc_start: 0.8879 (pp30) cc_final: 0.8159 (pp30) REVERT: F 591 HIS cc_start: 0.7941 (m-70) cc_final: 0.7308 (m170) REVERT: F 645 MET cc_start: 0.8012 (mmm) cc_final: 0.7764 (mmm) REVERT: G 459 ILE cc_start: 0.8189 (tp) cc_final: 0.7965 (tp) REVERT: G 473 LEU cc_start: 0.8539 (mt) cc_final: 0.8279 (mm) REVERT: G 534 GLN cc_start: 0.7557 (tt0) cc_final: 0.7234 (tt0) REVERT: G 667 PHE cc_start: 0.8900 (t80) cc_final: 0.8666 (t80) REVERT: H 426 TYR cc_start: 0.7816 (t80) cc_final: 0.7587 (t80) REVERT: H 493 PHE cc_start: 0.8507 (m-80) cc_final: 0.8214 (m-10) REVERT: H 508 LYS cc_start: 0.8608 (tttp) cc_final: 0.8105 (ttmt) REVERT: H 536 GLN cc_start: 0.8096 (tt0) cc_final: 0.7823 (tt0) REVERT: H 602 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8331 (tp-100) REVERT: H 630 TRP cc_start: 0.7962 (m100) cc_final: 0.7608 (m100) REVERT: H 671 ILE cc_start: 0.8747 (mm) cc_final: 0.8527 (tp) outliers start: 51 outliers final: 41 residues processed: 609 average time/residue: 0.0907 time to fit residues: 87.2787 Evaluate side-chains 640 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 598 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 E residue 671 ILE 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 705 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 20 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 89 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 226 optimal weight: 0.0000 overall best weight: 0.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN A 547 HIS B 414 HIS B 545 ASN C 664 GLN D 414 HIS D 644 HIS E 534 GLN E 664 GLN F 467 HIS H 414 HIS H 497 GLN H 500 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.080423 restraints weight = 51259.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083972 restraints weight = 26054.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.086334 restraints weight = 15732.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.088055 restraints weight = 10648.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.089202 restraints weight = 7799.389| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 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 = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14926 Z= 0.127 Angle : 0.568 9.339 20594 Z= 0.291 Chirality : 0.038 0.147 2546 Planarity : 0.004 0.044 2716 Dihedral : 3.825 17.187 2398 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.76 % Favored : 95.07 % Rotamer: Outliers : 6.79 % Allowed : 37.86 % Favored : 55.35 % 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: 0.05 (0.18), residues: 2296 helix: 0.54 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.69 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 464 TYR 0.017 0.001 TYR A 426 PHE 0.026 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 0.00264 (14926) covalent geometry : angle 0.56802 (20594) hydrogen bonds : bond 0.02849 ( 1082) hydrogen bonds : angle 3.73824 ( 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 660 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 599 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8832 (t80) cc_final: 0.8206 (t80) REVERT: A 471 LEU cc_start: 0.8832 (tp) cc_final: 0.8577 (tt) REVERT: A 503 THR cc_start: 0.8700 (m) cc_final: 0.8123 (t) REVERT: A 506 ILE cc_start: 0.8483 (mt) cc_final: 0.8121 (tp) REVERT: A 538 MET cc_start: 0.8046 (mmm) cc_final: 0.7753 (mmp) REVERT: A 557 MET cc_start: 0.7948 (tmm) cc_final: 0.7738 (tmm) REVERT: A 558 ILE cc_start: 0.8440 (tp) cc_final: 0.8223 (tp) REVERT: A 630 TRP cc_start: 0.7944 (m100) cc_final: 0.7562 (m100) REVERT: A 656 LYS cc_start: 0.8711 (tttt) cc_final: 0.8392 (ttmm) REVERT: A 664 GLN cc_start: 0.8676 (mt0) cc_final: 0.8328 (mt0) REVERT: A 680 TYR cc_start: 0.8553 (t80) cc_final: 0.8331 (t80) REVERT: B 421 VAL cc_start: 0.8702 (p) cc_final: 0.8362 (p) REVERT: B 500 ASN cc_start: 0.8633 (t0) cc_final: 0.8374 (t0) REVERT: B 508 LYS cc_start: 0.8345 (tttp) cc_final: 0.7958 (ttmt) REVERT: B 560 GLN cc_start: 0.8193 (tt0) cc_final: 0.7951 (tt0) REVERT: B 564 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7489 (mm-40) REVERT: B 587 GLN cc_start: 0.8870 (pp30) cc_final: 0.8190 (pp30) REVERT: B 645 MET cc_start: 0.7857 (mmm) cc_final: 0.7353 (mmm) REVERT: C 534 GLN cc_start: 0.7644 (tt0) cc_final: 0.7430 (tt0) REVERT: C 651 LEU cc_start: 0.8595 (mt) cc_final: 0.8380 (mm) REVERT: C 667 PHE cc_start: 0.8901 (t80) cc_final: 0.8649 (t80) REVERT: D 416 PHE cc_start: 0.7924 (t80) cc_final: 0.7486 (t80) REVERT: D 426 TYR cc_start: 0.7811 (t80) cc_final: 0.7521 (t80) REVERT: D 489 THR cc_start: 0.8654 (p) cc_final: 0.8389 (m) REVERT: D 493 PHE cc_start: 0.8574 (m-80) cc_final: 0.8295 (m-10) REVERT: D 504 TYR cc_start: 0.7721 (t80) cc_final: 0.7126 (t80) REVERT: D 508 LYS cc_start: 0.8575 (tttp) cc_final: 0.8038 (ttmt) REVERT: D 536 GLN cc_start: 0.8191 (tt0) cc_final: 0.7880 (tt0) REVERT: D 538 MET cc_start: 0.8256 (mmm) cc_final: 0.7997 (tpp) REVERT: D 630 TRP cc_start: 0.7788 (m100) cc_final: 0.7349 (m100) REVERT: D 680 TYR cc_start: 0.8579 (t80) cc_final: 0.8213 (t80) REVERT: D 689 HIS cc_start: 0.7944 (m-70) cc_final: 0.7554 (m90) REVERT: E 441 PHE cc_start: 0.8871 (t80) cc_final: 0.8302 (t80) REVERT: E 471 LEU cc_start: 0.8851 (tp) cc_final: 0.8572 (tt) REVERT: E 503 THR cc_start: 0.8700 (m) cc_final: 0.8350 (t) REVERT: E 534 GLN cc_start: 0.7554 (tm130) cc_final: 0.7204 (tm-30) REVERT: E 541 PHE cc_start: 0.8438 (t80) cc_final: 0.8172 (t80) REVERT: E 630 TRP cc_start: 0.7843 (m100) cc_final: 0.7356 (m100) REVERT: E 667 PHE cc_start: 0.9198 (t80) cc_final: 0.8907 (t80) REVERT: F 415 ILE cc_start: 0.8361 (mm) cc_final: 0.7831 (tp) REVERT: F 464 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7422 (ttm-80) REVERT: F 493 PHE cc_start: 0.8633 (m-80) cc_final: 0.8349 (m-10) REVERT: F 508 LYS cc_start: 0.8365 (tttp) cc_final: 0.7883 (ttmt) REVERT: F 530 MET cc_start: 0.8059 (mtt) cc_final: 0.7450 (mmm) REVERT: F 564 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7467 (mm-40) REVERT: F 587 GLN cc_start: 0.8899 (pp30) cc_final: 0.8203 (pp30) REVERT: F 591 HIS cc_start: 0.7965 (m-70) cc_final: 0.7342 (m170) REVERT: F 645 MET cc_start: 0.8032 (mmm) cc_final: 0.7598 (mmm) REVERT: G 473 LEU cc_start: 0.8537 (mt) cc_final: 0.8242 (mm) REVERT: G 534 GLN cc_start: 0.7589 (tt0) cc_final: 0.7267 (tt0) REVERT: G 542 TRP cc_start: 0.8080 (m-10) cc_final: 0.7793 (m-10) REVERT: G 664 GLN cc_start: 0.8462 (mt0) cc_final: 0.8231 (pt0) REVERT: H 426 TYR cc_start: 0.7828 (t80) cc_final: 0.7588 (t80) REVERT: H 489 THR cc_start: 0.8706 (p) cc_final: 0.8422 (m) REVERT: H 493 PHE cc_start: 0.8553 (m-80) cc_final: 0.8301 (m-10) REVERT: H 508 LYS cc_start: 0.8579 (tttp) cc_final: 0.8084 (ttmt) REVERT: H 599 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: H 630 TRP cc_start: 0.7914 (m100) cc_final: 0.7562 (m100) REVERT: H 671 ILE cc_start: 0.8742 (mm) cc_final: 0.8542 (tp) outliers start: 61 outliers final: 51 residues processed: 610 average time/residue: 0.0896 time to fit residues: 85.9885 Evaluate side-chains 647 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 596 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 636 HIS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 414 HIS 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 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 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 661 THR 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 442 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 503 THR 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 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 531 ILE Chi-restraints excluded: chain H residue 540 LEU 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: 0.9990 chunk 184 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 182 optimal weight: 0.0670 chunk 143 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS E 664 GLN F 467 HIS ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 500 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.077729 restraints weight = 65123.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.081609 restraints weight = 30931.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084269 restraints weight = 17977.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.086090 restraints weight = 11790.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087318 restraints weight = 8477.413| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 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 = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14926 Z= 0.168 Angle : 0.588 9.403 20594 Z= 0.307 Chirality : 0.039 0.160 2546 Planarity : 0.004 0.045 2716 Dihedral : 3.878 16.998 2398 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 7.02 % Allowed : 37.64 % Favored : 55.35 % 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: 0.39 (0.19), residues: 2296 helix: 0.77 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 464 TYR 0.017 0.001 TYR E 426 PHE 0.027 0.002 PHE A 541 TRP 0.036 0.001 TRP G 630 HIS 0.014 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00333 (14926) covalent geometry : angle 0.58798 (20594) hydrogen bonds : bond 0.03007 ( 1082) hydrogen bonds : angle 3.84529 ( 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 665 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 602 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8840 (t80) cc_final: 0.8221 (t80) REVERT: A 471 LEU cc_start: 0.8846 (tp) cc_final: 0.8566 (tt) REVERT: A 503 THR cc_start: 0.8647 (m) cc_final: 0.8101 (t) REVERT: A 506 ILE cc_start: 0.8501 (mt) cc_final: 0.8121 (tp) REVERT: A 538 MET cc_start: 0.8066 (mmm) cc_final: 0.7806 (mmp) REVERT: A 541 PHE cc_start: 0.8435 (t80) cc_final: 0.8197 (t80) REVERT: A 557 MET cc_start: 0.7976 (tmm) cc_final: 0.7766 (tmm) REVERT: A 558 ILE cc_start: 0.8482 (tp) cc_final: 0.8261 (tp) REVERT: A 656 LYS cc_start: 0.8727 (tttt) cc_final: 0.8415 (ttmm) REVERT: A 664 GLN cc_start: 0.8738 (mt0) cc_final: 0.8410 (mt0) REVERT: A 680 TYR cc_start: 0.8596 (t80) cc_final: 0.8385 (t80) REVERT: B 421 VAL cc_start: 0.8690 (p) cc_final: 0.8249 (p) REVERT: B 500 ASN cc_start: 0.8629 (t0) cc_final: 0.8377 (t0) REVERT: B 508 LYS cc_start: 0.8372 (tttp) cc_final: 0.7990 (ttmt) REVERT: B 560 GLN cc_start: 0.8186 (tt0) cc_final: 0.7970 (tt0) REVERT: B 564 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7551 (mm-40) REVERT: B 587 GLN cc_start: 0.8896 (pp30) cc_final: 0.7948 (pp30) REVERT: B 591 HIS cc_start: 0.7879 (m-70) cc_final: 0.7027 (m170) REVERT: B 645 MET cc_start: 0.7819 (mmm) cc_final: 0.7329 (mmm) REVERT: C 473 LEU cc_start: 0.8544 (mt) cc_final: 0.8224 (mm) REVERT: D 426 TYR cc_start: 0.7906 (t80) cc_final: 0.7433 (t80) REVERT: D 465 VAL cc_start: 0.8329 (m) cc_final: 0.7944 (p) REVERT: D 489 THR cc_start: 0.8667 (p) cc_final: 0.8397 (m) REVERT: D 493 PHE cc_start: 0.8595 (m-80) cc_final: 0.8369 (m-10) REVERT: D 504 TYR cc_start: 0.7713 (t80) cc_final: 0.7102 (t80) REVERT: D 508 LYS cc_start: 0.8536 (tttp) cc_final: 0.8019 (ttmt) REVERT: D 536 GLN cc_start: 0.8319 (tt0) cc_final: 0.7992 (tt0) REVERT: D 538 MET cc_start: 0.8249 (mmm) cc_final: 0.8006 (tpp) REVERT: D 630 TRP cc_start: 0.7820 (m100) cc_final: 0.7354 (m100) REVERT: D 680 TYR cc_start: 0.8597 (t80) cc_final: 0.8265 (t80) REVERT: D 689 HIS cc_start: 0.8055 (m-70) cc_final: 0.7810 (m-70) REVERT: D 693 ARG cc_start: 0.7574 (mtt90) cc_final: 0.7212 (mtt90) REVERT: E 441 PHE cc_start: 0.8880 (t80) cc_final: 0.8347 (t80) REVERT: E 471 LEU cc_start: 0.8887 (tp) cc_final: 0.8606 (tt) REVERT: E 503 THR cc_start: 0.8756 (m) cc_final: 0.8391 (t) REVERT: E 541 PHE cc_start: 0.8454 (t80) cc_final: 0.8178 (t80) REVERT: E 630 TRP cc_start: 0.7863 (m100) cc_final: 0.7366 (m100) REVERT: E 667 PHE cc_start: 0.9236 (t80) cc_final: 0.8911 (t80) REVERT: F 464 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7370 (ttm110) REVERT: F 493 PHE cc_start: 0.8628 (m-80) cc_final: 0.8364 (m-10) REVERT: F 508 LYS cc_start: 0.8372 (tttp) cc_final: 0.7814 (ttmt) REVERT: F 538 MET cc_start: 0.7718 (mmm) cc_final: 0.7383 (mmm) REVERT: F 564 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7498 (mm-40) REVERT: F 587 GLN cc_start: 0.8914 (pp30) cc_final: 0.8159 (pp30) REVERT: F 591 HIS cc_start: 0.8041 (m-70) cc_final: 0.7335 (m170) REVERT: F 645 MET cc_start: 0.7959 (mmm) cc_final: 0.7622 (mmm) REVERT: G 473 LEU cc_start: 0.8536 (mt) cc_final: 0.8261 (mm) REVERT: G 534 GLN cc_start: 0.7590 (tt0) cc_final: 0.7293 (tt0) REVERT: G 542 TRP cc_start: 0.8095 (m-10) cc_final: 0.7809 (m-10) REVERT: G 630 TRP cc_start: 0.7653 (m-10) cc_final: 0.7225 (m-10) REVERT: H 426 TYR cc_start: 0.7894 (t80) cc_final: 0.7679 (t80) REVERT: H 489 THR cc_start: 0.8703 (p) cc_final: 0.8425 (m) REVERT: H 508 LYS cc_start: 0.8586 (tttp) cc_final: 0.8120 (ttmt) REVERT: H 599 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7907 (ttm-80) REVERT: H 630 TRP cc_start: 0.7937 (m100) cc_final: 0.7618 (m100) outliers start: 63 outliers final: 53 residues processed: 614 average time/residue: 0.0939 time to fit residues: 90.8261 Evaluate side-chains 654 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 601 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 643 SER 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: 0.6980 chunk 128 optimal weight: 0.5980 chunk 65 optimal weight: 0.0050 chunk 86 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 105 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 534 GLN E 664 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 500 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.095633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078908 restraints weight = 64461.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082865 restraints weight = 30609.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085498 restraints weight = 17738.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.087348 restraints weight = 11683.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.088645 restraints weight = 8395.629| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14926 Z= 0.121 Angle : 0.579 10.043 20594 Z= 0.292 Chirality : 0.038 0.137 2546 Planarity : 0.004 0.039 2716 Dihedral : 3.731 17.812 2398 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.46 % Rotamer: Outliers : 6.35 % Allowed : 38.86 % Favored : 54.79 % 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: 0.84 (0.19), residues: 2296 helix: 1.07 (0.13), residues: 1836 sheet: None (None), residues: 0 loop : -1.36 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 464 TYR 0.017 0.001 TYR D 426 PHE 0.026 0.002 PHE H 493 TRP 0.019 0.001 TRP G 630 HIS 0.011 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00259 (14926) covalent geometry : angle 0.57894 (20594) hydrogen bonds : bond 0.02761 ( 1082) hydrogen bonds : angle 3.64867 ( 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 661 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 604 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8816 (t80) cc_final: 0.8225 (t80) REVERT: A 471 LEU cc_start: 0.8820 (tp) cc_final: 0.8554 (tt) REVERT: A 503 THR cc_start: 0.8601 (m) cc_final: 0.8254 (t) REVERT: A 538 MET cc_start: 0.8018 (mmm) cc_final: 0.7810 (mmp) REVERT: A 557 MET cc_start: 0.7942 (tmm) cc_final: 0.7724 (tmm) REVERT: A 558 ILE cc_start: 0.8444 (tp) cc_final: 0.8227 (tp) REVERT: A 630 TRP cc_start: 0.7823 (m100) cc_final: 0.7202 (m100) REVERT: A 656 LYS cc_start: 0.8700 (tttt) cc_final: 0.8372 (ttmm) REVERT: A 664 GLN cc_start: 0.8674 (mt0) cc_final: 0.8421 (mt0) REVERT: B 421 VAL cc_start: 0.8665 (p) cc_final: 0.8396 (p) REVERT: B 500 ASN cc_start: 0.8566 (t0) cc_final: 0.8354 (t0) REVERT: B 508 LYS cc_start: 0.8336 (tttp) cc_final: 0.7952 (ttmt) REVERT: B 560 GLN cc_start: 0.8196 (tt0) cc_final: 0.7972 (tt0) REVERT: B 564 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7515 (mm-40) REVERT: B 587 GLN cc_start: 0.8901 (pp30) cc_final: 0.7919 (pp30) REVERT: B 591 HIS cc_start: 0.7870 (m-70) cc_final: 0.6973 (m170) REVERT: B 645 MET cc_start: 0.7782 (mmm) cc_final: 0.7342 (mmm) REVERT: C 473 LEU cc_start: 0.8522 (mt) cc_final: 0.8189 (mm) REVERT: C 566 PHE cc_start: 0.8402 (m-10) cc_final: 0.8012 (m-80) REVERT: D 426 TYR cc_start: 0.7857 (t80) cc_final: 0.7398 (t80) REVERT: D 465 VAL cc_start: 0.8273 (m) cc_final: 0.7905 (p) REVERT: D 489 THR cc_start: 0.8613 (p) cc_final: 0.8350 (m) REVERT: D 493 PHE cc_start: 0.8598 (m-80) cc_final: 0.8381 (m-10) REVERT: D 504 TYR cc_start: 0.7692 (t80) cc_final: 0.7107 (t80) REVERT: D 508 LYS cc_start: 0.8596 (tttp) cc_final: 0.8080 (ttmt) REVERT: D 536 GLN cc_start: 0.8281 (tt0) cc_final: 0.7925 (tt0) REVERT: D 538 MET cc_start: 0.8240 (mmm) cc_final: 0.7973 (tpp) REVERT: D 630 TRP cc_start: 0.7789 (m100) cc_final: 0.7284 (m100) REVERT: D 680 TYR cc_start: 0.8597 (t80) cc_final: 0.8272 (t80) REVERT: D 689 HIS cc_start: 0.7914 (m-70) cc_final: 0.7605 (m-70) REVERT: D 693 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7192 (mtt90) REVERT: E 441 PHE cc_start: 0.8852 (t80) cc_final: 0.8324 (t80) REVERT: E 471 LEU cc_start: 0.8836 (tp) cc_final: 0.8550 (tt) REVERT: E 503 THR cc_start: 0.8662 (m) cc_final: 0.8226 (t) REVERT: E 534 GLN cc_start: 0.7708 (tm130) cc_final: 0.7112 (tm-30) REVERT: E 541 PHE cc_start: 0.8428 (t80) cc_final: 0.8155 (t80) REVERT: E 630 TRP cc_start: 0.7816 (m100) cc_final: 0.7366 (m100) REVERT: E 667 PHE cc_start: 0.9225 (t80) cc_final: 0.8906 (t80) REVERT: F 415 ILE cc_start: 0.8340 (mm) cc_final: 0.7845 (tp) REVERT: F 464 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7525 (ttm110) REVERT: F 493 PHE cc_start: 0.8586 (m-80) cc_final: 0.8319 (m-10) REVERT: F 508 LYS cc_start: 0.8268 (tttp) cc_final: 0.7725 (ttmt) REVERT: F 564 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7467 (mm-40) REVERT: F 587 GLN cc_start: 0.8889 (pp30) cc_final: 0.8146 (pp30) REVERT: F 591 HIS cc_start: 0.7998 (m-70) cc_final: 0.7253 (m170) REVERT: F 645 MET cc_start: 0.7882 (mmm) cc_final: 0.7584 (mmm) REVERT: G 473 LEU cc_start: 0.8480 (mt) cc_final: 0.8204 (mm) REVERT: G 534 GLN cc_start: 0.7537 (tt0) cc_final: 0.7256 (tt0) REVERT: G 541 PHE cc_start: 0.8483 (t80) cc_final: 0.8054 (t80) REVERT: G 542 TRP cc_start: 0.8060 (m-10) cc_final: 0.7705 (m-10) REVERT: G 630 TRP cc_start: 0.7414 (m-10) cc_final: 0.6934 (m-10) REVERT: G 680 TYR cc_start: 0.8087 (t80) cc_final: 0.7882 (t80) REVERT: H 426 TYR cc_start: 0.7842 (t80) cc_final: 0.7579 (t80) REVERT: H 489 THR cc_start: 0.8699 (p) cc_final: 0.8413 (m) REVERT: H 493 PHE cc_start: 0.8449 (m-80) cc_final: 0.8220 (m-10) REVERT: H 508 LYS cc_start: 0.8583 (tttp) cc_final: 0.8108 (ttmt) REVERT: H 599 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: H 630 TRP cc_start: 0.7897 (m100) cc_final: 0.7540 (m100) outliers start: 57 outliers final: 53 residues processed: 615 average time/residue: 0.0933 time to fit residues: 89.8248 Evaluate side-chains 657 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 604 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 550 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 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 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 661 THR Chi-restraints excluded: chain G residue 705 SER Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 500 ASN 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 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: 0.9990 chunk 182 optimal weight: 0.0670 chunk 113 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- 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 F 414 HIS ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 500 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.091696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.073413 restraints weight = 82157.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077705 restraints weight = 36010.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.080666 restraints weight = 20174.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082654 restraints weight = 12924.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084106 restraints weight = 9162.716| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14926 Z= 0.192 Angle : 0.618 11.263 20594 Z= 0.320 Chirality : 0.040 0.156 2546 Planarity : 0.004 0.038 2716 Dihedral : 3.870 16.072 2398 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 7.24 % Allowed : 38.31 % Favored : 54.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 2296 helix: 1.10 (0.13), residues: 1836 sheet: None (None), residues: 0 loop : -1.29 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 464 TYR 0.018 0.002 TYR E 426 PHE 0.026 0.002 PHE H 493 TRP 0.030 0.001 TRP B 448 HIS 0.011 0.001 HIS D 636 Details of bonding type rmsd covalent geometry : bond 0.00376 (14926) covalent geometry : angle 0.61750 (20594) hydrogen bonds : bond 0.03075 ( 1082) hydrogen bonds : angle 3.87768 ( 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 674 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 609 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8831 (t80) cc_final: 0.8251 (t80) REVERT: A 471 LEU cc_start: 0.8740 (tp) cc_final: 0.8468 (tt) REVERT: A 503 THR cc_start: 0.8635 (m) cc_final: 0.8231 (t) REVERT: A 538 MET cc_start: 0.8097 (mmm) cc_final: 0.7866 (mmp) REVERT: A 557 MET cc_start: 0.8001 (tmm) cc_final: 0.7773 (tmm) REVERT: A 558 ILE cc_start: 0.8478 (tp) cc_final: 0.8254 (tp) REVERT: A 630 TRP cc_start: 0.7851 (m100) cc_final: 0.7202 (m100) REVERT: A 656 LYS cc_start: 0.8747 (tttt) cc_final: 0.8442 (ttmm) REVERT: A 664 GLN cc_start: 0.8738 (mt0) cc_final: 0.8398 (mt0) REVERT: B 421 VAL cc_start: 0.8692 (p) cc_final: 0.8294 (p) REVERT: B 500 ASN cc_start: 0.8589 (t0) cc_final: 0.8375 (t0) REVERT: B 508 LYS cc_start: 0.8377 (tttp) cc_final: 0.7992 (ttmt) REVERT: B 560 GLN cc_start: 0.8293 (tt0) cc_final: 0.8073 (tt0) REVERT: B 564 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7570 (mm-40) REVERT: B 587 GLN cc_start: 0.8916 (pp30) cc_final: 0.7903 (pp30) REVERT: B 591 HIS cc_start: 0.7922 (m-70) cc_final: 0.7013 (m170) REVERT: B 645 MET cc_start: 0.7685 (mmm) cc_final: 0.7298 (mmm) REVERT: C 473 LEU cc_start: 0.8626 (mt) cc_final: 0.8306 (mm) REVERT: C 541 PHE cc_start: 0.8464 (t80) cc_final: 0.8165 (t80) REVERT: C 566 PHE cc_start: 0.8459 (m-10) cc_final: 0.8089 (m-80) REVERT: D 426 TYR cc_start: 0.7940 (t80) cc_final: 0.7438 (t80) REVERT: D 465 VAL cc_start: 0.8349 (m) cc_final: 0.7967 (p) REVERT: D 489 THR cc_start: 0.8649 (p) cc_final: 0.8389 (m) REVERT: D 504 TYR cc_start: 0.7727 (t80) cc_final: 0.7120 (t80) REVERT: D 508 LYS cc_start: 0.8542 (tttp) cc_final: 0.8034 (ttmt) REVERT: D 536 GLN cc_start: 0.8341 (tt0) cc_final: 0.7979 (tt0) REVERT: D 538 MET cc_start: 0.8231 (mmm) cc_final: 0.7919 (tpp) REVERT: D 630 TRP cc_start: 0.7798 (m100) cc_final: 0.7355 (m100) REVERT: D 680 TYR cc_start: 0.8611 (t80) cc_final: 0.8325 (t80) REVERT: D 689 HIS cc_start: 0.8004 (m-70) cc_final: 0.7725 (m-70) REVERT: D 693 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7308 (mtt90) REVERT: E 441 PHE cc_start: 0.8892 (t80) cc_final: 0.8349 (t80) REVERT: E 471 LEU cc_start: 0.8850 (tp) cc_final: 0.8574 (tt) REVERT: E 503 THR cc_start: 0.8666 (m) cc_final: 0.8226 (t) REVERT: E 541 PHE cc_start: 0.8428 (t80) cc_final: 0.8148 (t80) REVERT: E 630 TRP cc_start: 0.7850 (m100) cc_final: 0.7343 (m100) REVERT: E 667 PHE cc_start: 0.9166 (t80) cc_final: 0.8832 (t80) REVERT: F 464 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7624 (ttm110) REVERT: F 493 PHE cc_start: 0.8597 (m-80) cc_final: 0.8347 (m-10) REVERT: F 508 LYS cc_start: 0.8307 (tttp) cc_final: 0.7781 (ttmt) REVERT: F 538 MET cc_start: 0.7741 (mmm) cc_final: 0.7378 (mmm) REVERT: F 564 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7535 (mm-40) REVERT: F 587 GLN cc_start: 0.8895 (pp30) cc_final: 0.8114 (pp30) REVERT: F 591 HIS cc_start: 0.8037 (m-70) cc_final: 0.7233 (m170) REVERT: F 645 MET cc_start: 0.7827 (mmm) cc_final: 0.7601 (mmm) REVERT: F 680 TYR cc_start: 0.8816 (t80) cc_final: 0.8197 (t80) REVERT: G 473 LEU cc_start: 0.8596 (mt) cc_final: 0.8287 (mm) REVERT: G 534 GLN cc_start: 0.7616 (tt0) cc_final: 0.7339 (tt0) REVERT: G 542 TRP cc_start: 0.8113 (m-10) cc_final: 0.7840 (m-10) REVERT: G 630 TRP cc_start: 0.7408 (m-10) cc_final: 0.7062 (m-10) REVERT: H 426 TYR cc_start: 0.7913 (t80) cc_final: 0.7637 (t80) REVERT: H 493 PHE cc_start: 0.8560 (m-80) cc_final: 0.8318 (m-10) REVERT: H 508 LYS cc_start: 0.8589 (tttp) cc_final: 0.8109 (ttmt) REVERT: H 630 TRP cc_start: 0.7918 (m100) cc_final: 0.7557 (m100) outliers start: 65 outliers final: 58 residues processed: 620 average time/residue: 0.0920 time to fit residues: 90.0439 Evaluate side-chains 666 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 608 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 705 SER 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 705 SER Chi-restraints excluded: chain D residue 451 VAL 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 510 ILE Chi-restraints excluded: chain E residue 550 SER 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 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 573 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 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 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 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: 0.0270 chunk 18 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 203 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 467 HIS ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS E 534 GLN F 414 HIS ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 664 GLN H 500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079105 restraints weight = 55882.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082794 restraints weight = 27582.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.085311 restraints weight = 16336.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.087028 restraints weight = 10901.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.088193 restraints weight = 7943.246| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- 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: 0.7805 moved from start: 0.4021 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= 0.120 Angle : 0.608 10.961 20594 Z= 0.302 Chirality : 0.038 0.140 2546 Planarity : 0.004 0.037 2716 Dihedral : 3.794 16.250 2398 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.20 % Rotamer: Outliers : 5.90 % Allowed : 40.42 % Favored : 53.67 % 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: 1.18 (0.19), residues: 2296 helix: 1.31 (0.13), residues: 1836 sheet: None (None), residues: 0 loop : -1.27 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 464 TYR 0.028 0.001 TYR F 426 PHE 0.039 0.002 PHE D 493 TRP 0.028 0.001 TRP F 448 HIS 0.019 0.001 HIS D 644 Details of bonding type rmsd covalent geometry : bond 0.00265 (14926) covalent geometry : angle 0.60763 (20594) hydrogen bonds : bond 0.02842 ( 1082) hydrogen bonds : angle 3.67183 ( 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 655 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 602 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8817 (t80) cc_final: 0.8215 (t80) REVERT: A 471 LEU cc_start: 0.8807 (tp) cc_final: 0.8530 (tt) REVERT: A 503 THR cc_start: 0.8619 (m) cc_final: 0.8221 (t) REVERT: A 557 MET cc_start: 0.7960 (tmm) cc_final: 0.7702 (tmm) REVERT: A 558 ILE cc_start: 0.8456 (tp) cc_final: 0.8213 (tp) REVERT: A 664 GLN cc_start: 0.8682 (mt0) cc_final: 0.8426 (mt0) REVERT: B 421 VAL cc_start: 0.8635 (p) cc_final: 0.8311 (p) REVERT: B 500 ASN cc_start: 0.8546 (t0) cc_final: 0.8344 (t0) REVERT: B 508 LYS cc_start: 0.8329 (tttp) cc_final: 0.7943 (ttmt) REVERT: B 560 GLN cc_start: 0.8286 (tt0) cc_final: 0.8043 (tt0) REVERT: B 564 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7539 (mm-40) REVERT: B 587 GLN cc_start: 0.8914 (pp30) cc_final: 0.7976 (pp30) REVERT: B 591 HIS cc_start: 0.7879 (m-70) cc_final: 0.6962 (m170) REVERT: B 645 MET cc_start: 0.7657 (mmm) cc_final: 0.7254 (mmm) REVERT: C 473 LEU cc_start: 0.8620 (mt) cc_final: 0.8297 (mm) REVERT: C 541 PHE cc_start: 0.8423 (t80) cc_final: 0.8099 (t80) REVERT: C 566 PHE cc_start: 0.8413 (m-10) cc_final: 0.8051 (m-80) REVERT: C 667 PHE cc_start: 0.8957 (t80) cc_final: 0.8748 (t80) REVERT: D 426 TYR cc_start: 0.7783 (t80) cc_final: 0.7325 (t80) REVERT: D 465 VAL cc_start: 0.8272 (m) cc_final: 0.7851 (p) REVERT: D 489 THR cc_start: 0.8574 (p) cc_final: 0.8328 (m) REVERT: D 504 TYR cc_start: 0.7671 (t80) cc_final: 0.7090 (t80) REVERT: D 508 LYS cc_start: 0.8528 (tttp) cc_final: 0.8013 (ttmt) REVERT: D 536 GLN cc_start: 0.8321 (tt0) cc_final: 0.7949 (tt0) REVERT: D 538 MET cc_start: 0.8222 (mmm) cc_final: 0.7973 (tpp) REVERT: D 566 PHE cc_start: 0.8420 (m-80) cc_final: 0.7656 (m-80) REVERT: D 630 TRP cc_start: 0.7775 (m100) cc_final: 0.7291 (m100) REVERT: D 680 TYR cc_start: 0.8599 (t80) cc_final: 0.8335 (t80) REVERT: D 689 HIS cc_start: 0.7898 (m-70) cc_final: 0.7590 (m-70) REVERT: D 693 ARG cc_start: 0.7559 (mtt90) cc_final: 0.7236 (mtt90) REVERT: E 441 PHE cc_start: 0.8826 (t80) cc_final: 0.8341 (t80) REVERT: E 471 LEU cc_start: 0.8840 (tp) cc_final: 0.8552 (tt) REVERT: E 503 THR cc_start: 0.8647 (m) cc_final: 0.8238 (t) REVERT: E 541 PHE cc_start: 0.8426 (t80) cc_final: 0.8143 (t80) REVERT: E 630 TRP cc_start: 0.7808 (m100) cc_final: 0.7360 (m100) REVERT: E 667 PHE cc_start: 0.9188 (t80) cc_final: 0.8816 (t80) REVERT: F 415 ILE cc_start: 0.8297 (mm) cc_final: 0.7507 (tp) REVERT: F 464 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7522 (ttm110) REVERT: F 493 PHE cc_start: 0.8520 (m-80) cc_final: 0.8244 (m-10) REVERT: F 508 LYS cc_start: 0.8262 (tttp) cc_final: 0.7830 (ttmt) REVERT: F 538 MET cc_start: 0.7690 (mmm) cc_final: 0.7373 (mmm) REVERT: F 564 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7470 (mm-40) REVERT: F 587 GLN cc_start: 0.8884 (pp30) cc_final: 0.8116 (pp30) REVERT: F 591 HIS cc_start: 0.8009 (m-70) cc_final: 0.7210 (m170) REVERT: F 645 MET cc_start: 0.7837 (mmm) cc_final: 0.7598 (mmm) REVERT: F 680 TYR cc_start: 0.8795 (t80) cc_final: 0.8178 (t80) REVERT: G 473 LEU cc_start: 0.8554 (mt) cc_final: 0.8224 (mm) REVERT: G 534 GLN cc_start: 0.7547 (tt0) cc_final: 0.7248 (tt0) REVERT: G 541 PHE cc_start: 0.8427 (t80) cc_final: 0.8177 (t80) REVERT: G 630 TRP cc_start: 0.7259 (m-10) cc_final: 0.6939 (m-10) REVERT: G 639 HIS cc_start: 0.7888 (m-70) cc_final: 0.7661 (m-70) REVERT: H 426 TYR cc_start: 0.7861 (t80) cc_final: 0.7588 (t80) REVERT: H 493 PHE cc_start: 0.8504 (m-80) cc_final: 0.8199 (m-10) REVERT: H 508 LYS cc_start: 0.8570 (tttp) cc_final: 0.8101 (ttmt) REVERT: H 630 TRP cc_start: 0.7899 (m100) cc_final: 0.7521 (m100) outliers start: 53 outliers final: 48 residues processed: 611 average time/residue: 0.0919 time to fit residues: 88.0804 Evaluate side-chains 649 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 601 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 636 HIS 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 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 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 705 SER Chi-restraints excluded: chain D residue 451 VAL 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 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 510 ILE Chi-restraints excluded: chain E residue 550 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 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 573 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 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 510 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 59 optimal weight: 0.0980 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 142 optimal weight: 0.0020 chunk 222 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS E 534 GLN E 664 GLN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 664 GLN H 500 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.077090 restraints weight = 73560.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081212 restraints weight = 33432.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.084024 restraints weight = 18998.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.085942 restraints weight = 12298.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087228 restraints weight = 8760.787| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 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 = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4109 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= 0.135 Angle : 0.619 11.510 20594 Z= 0.310 Chirality : 0.039 0.147 2546 Planarity : 0.004 0.051 2716 Dihedral : 3.758 16.178 2398 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.84 % Favored : 94.98 % Rotamer: Outliers : 5.57 % Allowed : 41.65 % Favored : 52.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 2296 helix: 1.39 (0.13), residues: 1836 sheet: None (None), residues: 0 loop : -1.24 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 464 TYR 0.023 0.001 TYR F 426 PHE 0.037 0.002 PHE D 493 TRP 0.058 0.002 TRP A 630 HIS 0.018 0.001 HIS D 644 Details of bonding type rmsd covalent geometry : bond 0.00289 (14926) covalent geometry : angle 0.61864 (20594) hydrogen bonds : bond 0.02826 ( 1082) hydrogen bonds : angle 3.71208 ( 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 658 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 608 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 PHE cc_start: 0.8821 (t80) cc_final: 0.8219 (t80) REVERT: A 471 LEU cc_start: 0.8815 (tp) cc_final: 0.8520 (tt) REVERT: A 500 ASN cc_start: 0.8456 (t0) cc_final: 0.8228 (t0) REVERT: A 503 THR cc_start: 0.8605 (m) cc_final: 0.8234 (t) REVERT: A 555 TYR cc_start: 0.8741 (m-80) cc_final: 0.8383 (m-80) REVERT: A 557 MET cc_start: 0.7993 (tmm) cc_final: 0.7675 (tmm) REVERT: A 558 ILE cc_start: 0.8455 (tp) cc_final: 0.8219 (tp) REVERT: A 630 TRP cc_start: 0.7548 (m100) cc_final: 0.7127 (m100) REVERT: A 664 GLN cc_start: 0.8647 (mt0) cc_final: 0.8335 (mt0) REVERT: B 500 ASN cc_start: 0.8506 (t0) cc_final: 0.8203 (t0) REVERT: B 508 LYS cc_start: 0.8343 (tttp) cc_final: 0.7962 (ttmt) REVERT: B 560 GLN cc_start: 0.8298 (tt0) cc_final: 0.8056 (tt0) REVERT: B 564 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7562 (mm-40) REVERT: B 587 GLN cc_start: 0.8923 (pp30) cc_final: 0.7975 (pp30) REVERT: B 591 HIS cc_start: 0.7898 (m-70) cc_final: 0.6939 (m170) REVERT: B 608 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8138 (mm-40) REVERT: B 645 MET cc_start: 0.7658 (mmm) cc_final: 0.7354 (mmm) REVERT: C 473 LEU cc_start: 0.8646 (mt) cc_final: 0.8316 (mm) REVERT: C 541 PHE cc_start: 0.8415 (t80) cc_final: 0.8113 (t80) REVERT: C 566 PHE cc_start: 0.8424 (m-10) cc_final: 0.8066 (m-80) REVERT: D 426 TYR cc_start: 0.7766 (t80) cc_final: 0.7262 (t80) REVERT: D 465 VAL cc_start: 0.8282 (m) cc_final: 0.7839 (p) REVERT: D 489 THR cc_start: 0.8578 (p) cc_final: 0.8297 (m) REVERT: D 504 TYR cc_start: 0.7675 (t80) cc_final: 0.7092 (t80) REVERT: D 508 LYS cc_start: 0.8540 (tttp) cc_final: 0.8011 (ttmt) REVERT: D 536 GLN cc_start: 0.8328 (tt0) cc_final: 0.7975 (tt0) REVERT: D 538 MET cc_start: 0.8230 (mmm) cc_final: 0.7996 (tpp) REVERT: D 566 PHE cc_start: 0.8413 (m-80) cc_final: 0.7710 (m-80) REVERT: D 599 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: D 630 TRP cc_start: 0.7800 (m100) cc_final: 0.7385 (m100) REVERT: D 680 TYR cc_start: 0.8603 (t80) cc_final: 0.8323 (t80) REVERT: D 689 HIS cc_start: 0.7881 (m-70) cc_final: 0.7545 (m-70) REVERT: D 693 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7327 (mtt90) REVERT: E 441 PHE cc_start: 0.8813 (t80) cc_final: 0.8347 (t80) REVERT: E 471 LEU cc_start: 0.8818 (tp) cc_final: 0.8521 (tt) REVERT: E 503 THR cc_start: 0.8644 (m) cc_final: 0.8234 (t) REVERT: E 534 GLN cc_start: 0.7856 (tm130) cc_final: 0.7606 (tp40) REVERT: E 541 PHE cc_start: 0.8432 (t80) cc_final: 0.8192 (t80) REVERT: E 630 TRP cc_start: 0.7798 (m100) cc_final: 0.7471 (m100) REVERT: E 667 PHE cc_start: 0.9181 (t80) cc_final: 0.8779 (t80) REVERT: F 464 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7650 (ttm110) REVERT: F 493 PHE cc_start: 0.8492 (m-80) cc_final: 0.8276 (m-10) REVERT: F 508 LYS cc_start: 0.8263 (tttp) cc_final: 0.7752 (ttmt) REVERT: F 538 MET cc_start: 0.7670 (mmm) cc_final: 0.7385 (mmm) REVERT: F 564 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7491 (mm-40) REVERT: F 587 GLN cc_start: 0.8899 (pp30) cc_final: 0.8124 (pp30) REVERT: F 591 HIS cc_start: 0.8023 (m-70) cc_final: 0.7219 (m170) REVERT: F 645 MET cc_start: 0.7820 (mmm) cc_final: 0.7572 (mmm) REVERT: F 680 TYR cc_start: 0.8830 (t80) cc_final: 0.8267 (t80) REVERT: G 429 ILE cc_start: 0.8900 (pt) cc_final: 0.8644 (mp) REVERT: G 473 LEU cc_start: 0.8550 (mt) cc_final: 0.8254 (mm) REVERT: G 534 GLN cc_start: 0.7540 (tt0) cc_final: 0.7266 (tt0) REVERT: G 541 PHE cc_start: 0.8463 (t80) cc_final: 0.8218 (t80) REVERT: G 630 TRP cc_start: 0.7223 (m-10) cc_final: 0.6896 (m-10) REVERT: G 639 HIS cc_start: 0.7899 (m-70) cc_final: 0.7677 (m-70) REVERT: H 426 TYR cc_start: 0.7867 (t80) cc_final: 0.7558 (t80) REVERT: H 448 TRP cc_start: 0.7994 (m-10) cc_final: 0.7751 (m-10) REVERT: H 493 PHE cc_start: 0.8521 (m-80) cc_final: 0.8278 (m-10) REVERT: H 508 LYS cc_start: 0.8574 (tttp) cc_final: 0.8110 (ttmt) REVERT: H 630 TRP cc_start: 0.7893 (m100) cc_final: 0.7519 (m100) outliers start: 50 outliers final: 46 residues processed: 616 average time/residue: 0.0940 time to fit residues: 91.8581 Evaluate side-chains 654 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 608 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 636 HIS 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 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 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 451 VAL 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 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 510 ILE 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 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 573 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 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 510 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: 1.9990 chunk 183 optimal weight: 0.5980 chunk 204 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 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 467 HIS ** 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** G 664 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077869 restraints weight = 59487.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.081631 restraints weight = 28870.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084189 restraints weight = 16960.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085977 restraints weight = 11269.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087198 restraints weight = 8144.504| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 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 = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14926 Z= 0.147 Angle : 0.622 11.370 20594 Z= 0.313 Chirality : 0.039 0.142 2546 Planarity : 0.004 0.039 2716 Dihedral : 3.763 16.025 2398 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.97 % Favored : 94.85 % Rotamer: Outliers : 6.12 % Allowed : 41.20 % Favored : 52.67 % 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: 1.39 (0.19), residues: 2296 helix: 1.48 (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 0.009 0.001 ARG B 464 TYR 0.020 0.001 TYR F 426 PHE 0.035 0.002 PHE D 493 TRP 0.036 0.002 TRP A 630 HIS 0.025 0.001 HIS D 644 Details of bonding type rmsd covalent geometry : bond 0.00309 (14926) covalent geometry : angle 0.62229 (20594) hydrogen bonds : bond 0.02879 ( 1082) hydrogen bonds : angle 3.73791 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2788.42 seconds wall clock time: 48 minutes 26.58 seconds (2906.58 seconds total)