Starting phenix.real_space_refine on Wed May 21 23:31:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh3_37527/05_2025/8wh3_37527.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh3_37527/05_2025/8wh3_37527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wh3_37527/05_2025/8wh3_37527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh3_37527/05_2025/8wh3_37527.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh3_37527/05_2025/8wh3_37527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh3_37527/05_2025/8wh3_37527.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 96 5.16 5 C 14268 2.51 5 N 3768 2.21 5 O 4146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22278 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 13.22, per 1000 atoms: 0.59 Number of scatterers: 22278 At special positions: 0 Unit cell: (128.52, 142.8, 137.76, 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 96 16.00 O 4146 8.00 N 3768 7.00 C 14268 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: 5.72 Conformation dependent library (CDL) restraints added in 2.9 seconds 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 42 sheets defined 46.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.735A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 430 through 435 removed outlier: 4.090A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.697A pdb=" N LYS A 450 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.735A pdb=" N ARG A 619 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 679 Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.915A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 752 through 763 Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 removed outlier: 4.178A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 removed outlier: 3.558A pdb=" N THR B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.623A pdb=" N THR B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.560A pdb=" N ALA B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 577 Processing helix chain 'B' and resid 616 through 619 Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 679 Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.853A pdb=" N GLU B 692 " --> pdb=" O THR B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.523A pdb=" N LEU B 700 " --> pdb=" O PHE B 696 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 715 removed outlier: 3.583A pdb=" N ILE B 714 " --> pdb=" O VAL B 711 " (cutoff:3.500A) Proline residue: B 715 - end of helix Processing helix chain 'B' and resid 716 through 722 removed outlier: 4.285A pdb=" N LYS B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 747 removed outlier: 3.643A pdb=" N PHE B 739 " --> pdb=" O PRO B 735 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 747 " --> pdb=" O ILE B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 removed outlier: 6.862A pdb=" N HIS B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.576A pdb=" N SER C 380 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER C 381 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU C 382 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 384 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.982A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 472 through 474 No H-bonds generated for 'chain 'C' and resid 472 through 474' Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.841A pdb=" N ALA C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 578 removed outlier: 3.708A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 619 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 679 Processing helix chain 'C' and resid 689 through 695 removed outlier: 3.639A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 696 through 703 removed outlier: 3.674A pdb=" N LYS C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 702 " --> pdb=" O PHE C 698 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 703 " --> pdb=" O TYR C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 716 through 724 removed outlier: 4.629A pdb=" N LYS C 722 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS C 723 " --> pdb=" O ASP C 719 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 724 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 747 removed outlier: 4.051A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 747 " --> pdb=" O ILE C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 763 Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'D' and resid 324 through 336 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.964A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.918A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.804A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.545A pdb=" N THR D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 532 removed outlier: 4.238A pdb=" N ILE D 531 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 578 Processing helix chain 'D' and resid 617 through 621 removed outlier: 3.949A pdb=" N ILE D 621 " --> pdb=" O MET D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 696 through 706 Processing helix chain 'D' and resid 710 through 715 Proline residue: D 715 - end of helix Processing helix chain 'D' and resid 716 through 724 Processing helix chain 'D' and resid 735 through 744 Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'D' and resid 779 through 784 Processing helix chain 'E' and resid 324 through 336 Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.916A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 430 through 435 removed outlier: 4.007A pdb=" N LYS E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 541 through 547 removed outlier: 4.142A pdb=" N MET E 547 " --> pdb=" O PHE E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 579 removed outlier: 3.657A pdb=" N THR E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E 579 " --> pdb=" O LYS E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 Processing helix chain 'E' and resid 632 through 637 removed outlier: 4.279A pdb=" N GLU E 637 " --> pdb=" O PRO E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 661 Processing helix chain 'E' and resid 664 through 679 Processing helix chain 'E' and resid 689 through 693 removed outlier: 4.041A pdb=" N GLU E 692 " --> pdb=" O THR E 689 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE E 693 " --> pdb=" O PRO E 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 689 through 693' Processing helix chain 'E' and resid 694 through 704 removed outlier: 4.255A pdb=" N PHE E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 715 No H-bonds generated for 'chain 'E' and resid 713 through 715' Processing helix chain 'E' and resid 716 through 722 removed outlier: 3.808A pdb=" N LYS E 722 " --> pdb=" O THR E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 744 Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 779 through 784 Processing helix chain 'F' and resid 324 through 336 Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.851A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 430 through 435 removed outlier: 4.099A pdb=" N LYS F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 475 through 488 Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 528 through 532 removed outlier: 4.072A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 546 removed outlier: 3.522A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.729A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 620 removed outlier: 3.501A pdb=" N ARG F 619 " --> pdb=" O ALA F 616 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 620 " --> pdb=" O LEU F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 Processing helix chain 'F' and resid 653 through 661 removed outlier: 4.646A pdb=" N GLY F 657 " --> pdb=" O GLU F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 679 Processing helix chain 'F' and resid 689 through 695 removed outlier: 3.806A pdb=" N GLU F 692 " --> pdb=" O THR F 689 " (cutoff:3.500A) Proline residue: F 694 - end of helix Processing helix chain 'F' and resid 696 through 704 removed outlier: 3.572A pdb=" N THR F 704 " --> pdb=" O LEU F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 715 No H-bonds generated for 'chain 'F' and resid 713 through 715' Processing helix chain 'F' and resid 716 through 721 Processing helix chain 'F' and resid 722 through 724 No H-bonds generated for 'chain 'F' and resid 722 through 724' Processing helix chain 'F' and resid 735 through 744 Processing helix chain 'F' and resid 752 through 764 removed outlier: 3.570A pdb=" N LYS F 764 " --> pdb=" O ILE F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 784 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 527 removed outlier: 6.343A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 604 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 removed outlier: 3.872A pdb=" N VAL A 582 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN A 594 " --> pdb=" O VAL A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 630 Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 707 removed outlier: 3.665A pdb=" N ILE A 777 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 728 removed outlier: 3.543A pdb=" N ILE A 726 " --> pdb=" O THR A 733 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 733 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB1, first strand: chain 'B' and resid 524 through 527 removed outlier: 6.394A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 604 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 628 through 631 Processing sheet with id=AB3, first strand: chain 'B' and resid 706 through 708 removed outlier: 3.673A pdb=" N VAL B 707 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 726 through 728 removed outlier: 4.387A pdb=" N ILE B 726 " --> pdb=" O THR B 733 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 733 " --> pdb=" O ILE B 726 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.668A pdb=" N TYR B 773 " --> pdb=" O LYS B 765 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB8, first strand: chain 'C' and resid 524 through 527 removed outlier: 6.198A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 581 through 583 removed outlier: 4.041A pdb=" N VAL C 582 " --> pdb=" O ASN C 594 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN C 594 " --> pdb=" O VAL C 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AC2, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AC3, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AC4, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC5, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC6, first strand: chain 'D' and resid 524 through 527 removed outlier: 6.018A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP D 603 " --> pdb=" O CYS D 555 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 499 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 602 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 581 through 583 removed outlier: 3.634A pdb=" N VAL D 582 " --> pdb=" O ASN D 594 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN D 594 " --> pdb=" O VAL D 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 628 through 631 Processing sheet with id=AC9, first strand: chain 'D' and resid 726 through 728 Processing sheet with id=AD1, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD2, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD3, first strand: chain 'E' and resid 524 through 527 removed outlier: 3.631A pdb=" N SER E 556 " --> pdb=" O THR E 527 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU E 557 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR E 604 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA E 622 " --> pdb=" O LEU E 498 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 581 through 583 removed outlier: 4.321A pdb=" N VAL E 582 " --> pdb=" O ASN E 594 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN E 594 " --> pdb=" O VAL E 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 629 through 630 removed outlier: 6.202A pdb=" N HIS E 629 " --> pdb=" O LYS E 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 726 through 728 Processing sheet with id=AD7, first strand: chain 'E' and resid 765 through 766 Processing sheet with id=AD8, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AD9, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AE1, first strand: chain 'F' and resid 524 through 527 removed outlier: 6.262A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR F 604 " --> pdb=" O PHE F 501 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 581 through 583 removed outlier: 4.221A pdb=" N VAL F 582 " --> pdb=" O ASN F 594 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN F 594 " --> pdb=" O VAL F 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 629 through 631 removed outlier: 6.134A pdb=" N HIS F 629 " --> pdb=" O LYS F 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 706 through 708 removed outlier: 3.631A pdb=" N ILE F 777 " --> pdb=" O VAL F 707 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 726 through 728 removed outlier: 3.706A pdb=" N ILE F 726 " --> pdb=" O THR F 733 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 765 through 766 801 hydrogen bonds defined for protein. 2298 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: 7.81 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7150 1.34 - 1.46: 3752 1.46 - 1.58: 11718 1.58 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 22758 Sorted by residual: bond pdb=" C ILE B 714 " pdb=" N PRO B 715 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.06e+00 bond pdb=" CB PRO F 735 " pdb=" CG PRO F 735 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.16e+00 bond pdb=" CB GLU B 557 " pdb=" CG GLU B 557 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CB PHE D 668 " pdb=" CG PHE D 668 " ideal model delta sigma weight residual 1.502 1.534 -0.032 2.30e-02 1.89e+03 1.90e+00 bond pdb=" CB GLN B 660 " pdb=" CG GLN B 660 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 ... (remaining 22753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 30645 3.27 - 6.53: 115 6.53 - 9.80: 6 9.80 - 13.06: 1 13.06 - 16.33: 1 Bond angle restraints: 30768 Sorted by residual: angle pdb=" CA LEU D 515 " pdb=" CB LEU D 515 " pdb=" CG LEU D 515 " ideal model delta sigma weight residual 116.30 132.63 -16.33 3.50e+00 8.16e-02 2.18e+01 angle pdb=" CA GLU B 557 " pdb=" CB GLU B 557 " pdb=" CG GLU B 557 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" C GLU E 640 " pdb=" N ASN E 641 " pdb=" CA ASN E 641 " ideal model delta sigma weight residual 123.17 118.08 5.09 1.49e+00 4.50e-01 1.17e+01 angle pdb=" CA LYS C 658 " pdb=" CB LYS C 658 " pdb=" CG LYS C 658 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA TYR E 645 " pdb=" CB TYR E 645 " pdb=" CG TYR E 645 " ideal model delta sigma weight residual 113.90 119.83 -5.93 1.80e+00 3.09e-01 1.09e+01 ... (remaining 30763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11668 17.99 - 35.98: 1616 35.98 - 53.97: 460 53.97 - 71.96: 84 71.96 - 89.95: 20 Dihedral angle restraints: 13848 sinusoidal: 5670 harmonic: 8178 Sorted by residual: dihedral pdb=" CA ASP E 643 " pdb=" C ASP E 643 " pdb=" N ALA E 644 " pdb=" CA ALA E 644 " ideal model delta harmonic sigma weight residual -180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASN E 642 " pdb=" C ASN E 642 " pdb=" N ASP E 643 " pdb=" CA ASP E 643 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA HIS C 713 " pdb=" C HIS C 713 " pdb=" N ILE C 714 " pdb=" CA ILE C 714 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 13845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2570 0.043 - 0.087: 670 0.087 - 0.130: 209 0.130 - 0.173: 4 0.173 - 0.217: 3 Chirality restraints: 3456 Sorted by residual: chirality pdb=" CG LEU A 716 " pdb=" CB LEU A 716 " pdb=" CD1 LEU A 716 " pdb=" CD2 LEU A 716 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR B 599 " pdb=" CA THR B 599 " pdb=" OG1 THR B 599 " pdb=" CG2 THR B 599 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CG LEU D 515 " pdb=" CB LEU D 515 " pdb=" CD1 LEU D 515 " pdb=" CD2 LEU D 515 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 3453 not shown) Planarity restraints: 3936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 607 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO F 608 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 608 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 608 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 734 " -0.031 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO F 735 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 735 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 735 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 579 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO F 580 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 580 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 580 " -0.025 5.00e-02 4.00e+02 ... (remaining 3933 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1164 2.73 - 3.27: 21741 3.27 - 3.82: 36109 3.82 - 4.36: 43582 4.36 - 4.90: 73499 Nonbonded interactions: 176095 Sorted by model distance: nonbonded pdb=" NH1 ARG B 389 " pdb=" OD2 ASP F 398 " model vdw 2.188 3.120 nonbonded pdb=" O GLU F 504 " pdb=" OG1 THR F 507 " model vdw 2.191 3.040 nonbonded pdb=" OH TYR D 725 " pdb=" OD2 ASP D 781 " model vdw 2.207 3.040 nonbonded pdb=" O GLU C 504 " pdb=" OG1 THR C 507 " model vdw 2.215 3.040 nonbonded pdb=" N GLU E 378 " pdb=" OE1 GLU E 378 " model vdw 2.228 3.120 ... (remaining 176090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 49.620 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 0.073 22758 Z= 0.128 Angle : 0.568 16.327 30768 Z= 0.305 Chirality : 0.042 0.217 3456 Planarity : 0.004 0.053 3936 Dihedral : 17.915 89.947 8544 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.97 % Allowed : 28.14 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2766 helix: 0.89 (0.16), residues: 1041 sheet: 0.00 (0.32), residues: 314 loop : -0.45 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.009 0.001 HIS D 680 PHE 0.030 0.001 PHE C 759 TYR 0.013 0.001 TYR D 482 ARG 0.011 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.16804 ( 801) hydrogen bonds : angle 5.97239 ( 2298) covalent geometry : bond 0.00297 (22758) covalent geometry : angle 0.56778 (30768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 2.405 Fit side-chains revert: symmetry clash REVERT: A 684 MET cc_start: 0.4625 (OUTLIER) cc_final: 0.2160 (ppp) REVERT: A 775 GLN cc_start: 0.6048 (OUTLIER) cc_final: 0.5668 (mm-40) REVERT: C 603 ASP cc_start: 0.8118 (t0) cc_final: 0.7889 (t70) REVERT: E 484 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.6875 (tptt) outliers start: 49 outliers final: 28 residues processed: 241 average time/residue: 1.2186 time to fit residues: 338.5770 Evaluate side-chains 234 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 484 LYS Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 507 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 5.9990 chunk 209 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 ASN B 469 GLN B 475 ASN B 478 ASN B 529 GLN ** C 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 GLN E 466 ASN E 615 ASN F 680 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.249903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.186511 restraints weight = 26026.799| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 3.56 r_work: 0.3363 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22758 Z= 0.240 Angle : 0.621 10.667 30768 Z= 0.325 Chirality : 0.047 0.188 3456 Planarity : 0.005 0.051 3936 Dihedral : 6.120 124.641 3061 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.51 % Allowed : 25.28 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2766 helix: 0.52 (0.16), residues: 1045 sheet: -0.20 (0.32), residues: 307 loop : -0.48 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 350 HIS 0.008 0.001 HIS D 763 PHE 0.022 0.002 PHE A 524 TYR 0.034 0.001 TYR E 645 ARG 0.007 0.001 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.05663 ( 801) hydrogen bonds : angle 5.13788 ( 2298) covalent geometry : bond 0.00603 (22758) covalent geometry : angle 0.62083 (30768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 226 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7820 (m110) REVERT: A 365 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8376 (m) REVERT: B 529 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: B 699 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: C 334 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8505 (tp) REVERT: C 365 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8386 (p) REVERT: C 625 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7363 (mmm160) REVERT: C 765 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6069 (mttt) REVERT: D 612 ARG cc_start: 0.5816 (mtm180) cc_final: 0.5455 (ttm170) REVERT: D 618 MET cc_start: 0.6766 (pmt) cc_final: 0.6517 (pmm) REVERT: D 632 GLN cc_start: 0.1195 (OUTLIER) cc_final: 0.0668 (tt0) REVERT: E 424 ASP cc_start: 0.7210 (t0) cc_final: 0.6974 (t0) REVERT: F 556 SER cc_start: 0.6570 (OUTLIER) cc_final: 0.5925 (t) REVERT: F 669 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7925 (tt) outliers start: 112 outliers final: 41 residues processed: 314 average time/residue: 1.2381 time to fit residues: 447.1005 Evaluate side-chains 257 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 625 ARG Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 83 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 235 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN C 594 ASN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN E 573 ASN E 615 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.251038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.184590 restraints weight = 25821.991| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.55 r_work: 0.3349 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22758 Z= 0.168 Angle : 0.551 10.431 30768 Z= 0.290 Chirality : 0.044 0.152 3456 Planarity : 0.004 0.044 3936 Dihedral : 5.060 58.029 3030 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.79 % Allowed : 25.44 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2766 helix: 0.61 (0.16), residues: 1057 sheet: -0.19 (0.32), residues: 307 loop : -0.50 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 350 HIS 0.007 0.001 HIS F 680 PHE 0.027 0.001 PHE D 668 TYR 0.015 0.001 TYR A 670 ARG 0.008 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 801) hydrogen bonds : angle 4.89851 ( 2298) covalent geometry : bond 0.00419 (22758) covalent geometry : angle 0.55099 (30768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 227 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7608 (mm-30) REVERT: A 699 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: B 699 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: C 365 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8464 (p) REVERT: C 625 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7301 (mtm180) REVERT: C 649 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.5979 (tppt) REVERT: C 660 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: C 764 LYS cc_start: 0.7395 (pttm) cc_final: 0.6882 (ptpp) REVERT: C 765 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6159 (mttt) REVERT: D 351 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7307 (mt) REVERT: D 632 GLN cc_start: 0.1401 (OUTLIER) cc_final: 0.0936 (tt0) REVERT: E 481 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7211 (tm) REVERT: F 556 SER cc_start: 0.6642 (OUTLIER) cc_final: 0.6030 (t) REVERT: F 669 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7995 (tt) REVERT: F 777 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5726 (tt) outliers start: 119 outliers final: 42 residues processed: 321 average time/residue: 1.2150 time to fit residues: 450.6433 Evaluate side-chains 263 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 625 ARG Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 777 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 130 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 188 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN B 529 GLN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.252920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.188994 restraints weight = 26262.939| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 3.61 r_work: 0.3409 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22758 Z= 0.109 Angle : 0.507 10.618 30768 Z= 0.266 Chirality : 0.041 0.144 3456 Planarity : 0.004 0.045 3936 Dihedral : 4.674 59.512 3023 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.34 % Allowed : 26.65 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2766 helix: 0.84 (0.16), residues: 1065 sheet: -0.07 (0.32), residues: 310 loop : -0.44 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.015 0.001 HIS D 680 PHE 0.028 0.001 PHE D 668 TYR 0.013 0.001 TYR A 670 ARG 0.009 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 801) hydrogen bonds : angle 4.66006 ( 2298) covalent geometry : bond 0.00261 (22758) covalent geometry : angle 0.50658 (30768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 221 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7659 (mm-30) REVERT: A 699 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: B 551 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8397 (mtt-85) REVERT: B 557 GLU cc_start: 0.7599 (pp20) cc_final: 0.7382 (pp20) REVERT: B 699 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: C 764 LYS cc_start: 0.7351 (pttm) cc_final: 0.6918 (ptpp) REVERT: C 765 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6131 (mttt) REVERT: D 618 MET cc_start: 0.6714 (pmt) cc_final: 0.6485 (pmm) REVERT: E 529 GLN cc_start: 0.7492 (tt0) cc_final: 0.7252 (tt0) REVERT: F 669 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7977 (tt) outliers start: 83 outliers final: 33 residues processed: 284 average time/residue: 1.1841 time to fit residues: 394.0795 Evaluate side-chains 252 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 551 ARG Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 501 PHE Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 726 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 182 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN B 529 GLN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.252150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.186938 restraints weight = 26228.142| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.72 r_work: 0.3386 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22758 Z= 0.122 Angle : 0.510 10.219 30768 Z= 0.267 Chirality : 0.042 0.170 3456 Planarity : 0.004 0.054 3936 Dihedral : 4.492 59.904 3018 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.95 % Allowed : 26.45 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2766 helix: 0.87 (0.16), residues: 1059 sheet: -0.12 (0.32), residues: 309 loop : -0.44 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.006 0.001 HIS F 680 PHE 0.028 0.001 PHE D 668 TYR 0.014 0.001 TYR A 670 ARG 0.009 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 801) hydrogen bonds : angle 4.61417 ( 2298) covalent geometry : bond 0.00298 (22758) covalent geometry : angle 0.50952 (30768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 219 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8133 (p) REVERT: A 557 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7690 (mm-30) REVERT: A 678 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7755 (ttpp) REVERT: B 529 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: B 551 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8406 (mtt-85) REVERT: B 557 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7376 (pp20) REVERT: B 612 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6306 (ttm110) REVERT: B 699 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: C 365 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8378 (p) REVERT: C 764 LYS cc_start: 0.7302 (pttm) cc_final: 0.7038 (ptpp) REVERT: C 765 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6203 (mttt) REVERT: D 501 PHE cc_start: 0.5434 (OUTLIER) cc_final: 0.4968 (m-10) REVERT: E 407 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: E 529 GLN cc_start: 0.7394 (tt0) cc_final: 0.7147 (tt0) REVERT: F 465 ILE cc_start: 0.8134 (mm) cc_final: 0.7864 (tp) REVERT: F 556 SER cc_start: 0.6547 (OUTLIER) cc_final: 0.5975 (t) REVERT: F 669 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8025 (tt) outliers start: 98 outliers final: 46 residues processed: 298 average time/residue: 1.1842 time to fit residues: 408.0991 Evaluate side-chains 265 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 551 ARG Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 501 PHE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 407 ASP Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 726 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 53 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 28 optimal weight: 0.4980 chunk 135 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN B 529 GLN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN E 466 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.251426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185928 restraints weight = 26035.614| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.66 r_work: 0.3367 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22758 Z= 0.171 Angle : 0.552 10.091 30768 Z= 0.288 Chirality : 0.044 0.174 3456 Planarity : 0.004 0.048 3936 Dihedral : 4.599 59.816 3016 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.43 % Allowed : 26.25 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2766 helix: 0.73 (0.16), residues: 1059 sheet: -0.13 (0.32), residues: 309 loop : -0.49 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 350 HIS 0.007 0.001 HIS D 763 PHE 0.029 0.002 PHE D 668 TYR 0.016 0.001 TYR C 482 ARG 0.009 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 801) hydrogen bonds : angle 4.71076 ( 2298) covalent geometry : bond 0.00432 (22758) covalent geometry : angle 0.55151 (30768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 211 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8382 (p) REVERT: A 557 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7652 (mm-30) REVERT: A 678 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7740 (ttpp) REVERT: B 547 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6596 (ppp) REVERT: B 551 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8477 (mtt-85) REVERT: B 557 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7330 (pp20) REVERT: B 612 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6365 (ttm110) REVERT: B 699 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: C 365 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8472 (p) REVERT: C 764 LYS cc_start: 0.7488 (pttm) cc_final: 0.7107 (ptpp) REVERT: C 765 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6197 (mttt) REVERT: D 501 PHE cc_start: 0.5453 (OUTLIER) cc_final: 0.5003 (m-10) REVERT: D 618 MET cc_start: 0.6598 (pmt) cc_final: 0.6354 (pmm) REVERT: D 664 TYR cc_start: 0.4597 (OUTLIER) cc_final: 0.4222 (m-10) REVERT: E 407 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: E 435 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8276 (mtmm) REVERT: F 465 ILE cc_start: 0.8113 (mm) cc_final: 0.7857 (tp) REVERT: F 556 SER cc_start: 0.6490 (OUTLIER) cc_final: 0.5848 (t) REVERT: F 669 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8056 (tt) outliers start: 110 outliers final: 52 residues processed: 296 average time/residue: 1.1422 time to fit residues: 391.4657 Evaluate side-chains 271 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 204 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 551 ARG Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 501 PHE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 630 PHE Chi-restraints excluded: chain D residue 664 TYR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 407 ASP Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 726 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 259 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN B 529 GLN C 660 GLN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.249272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.183172 restraints weight = 26105.208| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.68 r_work: 0.3321 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 22758 Z= 0.268 Angle : 0.641 10.233 30768 Z= 0.334 Chirality : 0.048 0.214 3456 Planarity : 0.005 0.053 3936 Dihedral : 4.945 59.073 3016 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.59 % Allowed : 26.09 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2766 helix: 0.44 (0.16), residues: 1052 sheet: -0.25 (0.30), residues: 336 loop : -0.60 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 350 HIS 0.008 0.001 HIS D 763 PHE 0.036 0.002 PHE D 668 TYR 0.022 0.002 TYR C 482 ARG 0.008 0.001 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.05851 ( 801) hydrogen bonds : angle 4.91766 ( 2298) covalent geometry : bond 0.00678 (22758) covalent geometry : angle 0.64052 (30768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 214 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8437 (m) REVERT: A 557 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7556 (mm-30) REVERT: A 678 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7564 (ttpp) REVERT: A 699 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: B 547 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6756 (ppp) REVERT: B 551 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8400 (mtt-85) REVERT: B 557 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7317 (pp20) REVERT: B 612 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6443 (ttm110) REVERT: B 699 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: C 365 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8511 (p) REVERT: C 764 LYS cc_start: 0.7677 (pttm) cc_final: 0.7302 (pttm) REVERT: C 765 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6239 (mttt) REVERT: D 618 MET cc_start: 0.6620 (pmt) cc_final: 0.6387 (pmm) REVERT: D 664 TYR cc_start: 0.4505 (OUTLIER) cc_final: 0.4152 (m-10) REVERT: D 747 PHE cc_start: 0.3519 (m-10) cc_final: 0.3288 (m-10) REVERT: E 407 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: E 435 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8300 (mtmm) REVERT: F 556 SER cc_start: 0.6498 (OUTLIER) cc_final: 0.5905 (t) REVERT: F 669 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8092 (tt) outliers start: 114 outliers final: 63 residues processed: 303 average time/residue: 1.2176 time to fit residues: 425.7520 Evaluate side-chains 287 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 209 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 551 ARG Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 630 PHE Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 664 TYR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 343 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 407 ASP Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 360 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 726 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 90 optimal weight: 20.0000 chunk 233 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 198 optimal weight: 10.0000 chunk 12 optimal weight: 0.0870 chunk 229 optimal weight: 40.0000 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 177 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN B 529 GLN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.252053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186285 restraints weight = 26209.484| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.51 r_work: 0.3390 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22758 Z= 0.129 Angle : 0.535 10.934 30768 Z= 0.282 Chirality : 0.042 0.155 3456 Planarity : 0.004 0.067 3936 Dihedral : 4.653 57.503 3016 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.46 % Allowed : 27.01 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2766 helix: 0.67 (0.16), residues: 1059 sheet: -0.32 (0.31), residues: 329 loop : -0.52 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 350 HIS 0.006 0.001 HIS D 763 PHE 0.028 0.001 PHE A 759 TYR 0.014 0.001 TYR A 670 ARG 0.010 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 801) hydrogen bonds : angle 4.65064 ( 2298) covalent geometry : bond 0.00316 (22758) covalent geometry : angle 0.53520 (30768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 217 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7545 (mm-30) REVERT: B 478 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7064 (t0) REVERT: B 547 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6637 (ppp) REVERT: B 551 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8414 (mtt-85) REVERT: B 557 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7316 (pp20) REVERT: B 612 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6416 (ttm110) REVERT: B 699 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6848 (m-10) REVERT: C 365 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8472 (p) REVERT: C 764 LYS cc_start: 0.7524 (pttm) cc_final: 0.6951 (ptpp) REVERT: C 765 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6207 (mttt) REVERT: D 664 TYR cc_start: 0.4495 (OUTLIER) cc_final: 0.4139 (m-10) REVERT: E 480 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: E 575 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7330 (ptpp) REVERT: F 465 ILE cc_start: 0.8203 (mm) cc_final: 0.7912 (tp) REVERT: F 556 SER cc_start: 0.6419 (OUTLIER) cc_final: 0.5803 (t) REVERT: F 669 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8026 (tt) outliers start: 86 outliers final: 52 residues processed: 284 average time/residue: 1.2087 time to fit residues: 394.7165 Evaluate side-chains 272 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 551 ARG Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 750 ARG Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 630 PHE Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 664 TYR Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 575 LYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 360 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 726 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 0.0570 chunk 54 optimal weight: 5.9990 chunk 223 optimal weight: 0.1980 chunk 60 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.253735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.191434 restraints weight = 26118.054| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.54 r_work: 0.3427 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22758 Z= 0.102 Angle : 0.513 11.987 30768 Z= 0.270 Chirality : 0.041 0.156 3456 Planarity : 0.004 0.069 3936 Dihedral : 4.388 56.576 3016 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.86 % Allowed : 27.90 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2766 helix: 0.91 (0.16), residues: 1073 sheet: -0.29 (0.31), residues: 330 loop : -0.47 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 350 HIS 0.005 0.001 HIS D 763 PHE 0.029 0.001 PHE A 759 TYR 0.012 0.001 TYR A 670 ARG 0.009 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 801) hydrogen bonds : angle 4.49000 ( 2298) covalent geometry : bond 0.00237 (22758) covalent geometry : angle 0.51328 (30768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 214 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7623 (ttpp) REVERT: B 478 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.6956 (t0) REVERT: B 551 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8372 (mtt-85) REVERT: B 557 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: B 612 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6385 (ttm110) REVERT: C 365 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8243 (p) REVERT: C 764 LYS cc_start: 0.7341 (pttm) cc_final: 0.6868 (ptpp) REVERT: C 765 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6242 (mttt) REVERT: D 501 PHE cc_start: 0.5421 (OUTLIER) cc_final: 0.5038 (m-10) REVERT: E 480 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7188 (pp20) REVERT: E 575 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7338 (ptpp) REVERT: F 465 ILE cc_start: 0.8148 (mm) cc_final: 0.7869 (tp) REVERT: F 547 MET cc_start: 0.8151 (ppp) cc_final: 0.7830 (ppp) outliers start: 71 outliers final: 41 residues processed: 267 average time/residue: 1.2147 time to fit residues: 373.8363 Evaluate side-chains 253 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 551 ARG Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 501 PHE Chi-restraints excluded: chain D residue 630 PHE Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 575 LYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 726 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 136 optimal weight: 6.9990 chunk 152 optimal weight: 0.0050 chunk 158 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 615 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.251296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.185859 restraints weight = 26221.395| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.54 r_work: 0.3369 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22758 Z= 0.169 Angle : 0.578 19.100 30768 Z= 0.298 Chirality : 0.044 0.157 3456 Planarity : 0.005 0.066 3936 Dihedral : 4.439 57.389 3013 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.66 % Allowed : 28.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2766 helix: 0.79 (0.16), residues: 1055 sheet: -0.29 (0.31), residues: 332 loop : -0.49 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 350 HIS 0.006 0.001 HIS D 763 PHE 0.048 0.002 PHE D 698 TYR 0.015 0.001 TYR C 482 ARG 0.006 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 801) hydrogen bonds : angle 4.62126 ( 2298) covalent geometry : bond 0.00424 (22758) covalent geometry : angle 0.57844 (30768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 205 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7646 (ttpp) REVERT: B 478 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7086 (t0) REVERT: B 551 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8464 (mtt-85) REVERT: B 557 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: B 612 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6349 (ttm110) REVERT: C 365 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 764 LYS cc_start: 0.7523 (pttm) cc_final: 0.7010 (ptpp) REVERT: C 765 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6280 (mttt) REVERT: D 501 PHE cc_start: 0.5427 (OUTLIER) cc_final: 0.5042 (m-10) REVERT: D 534 ASP cc_start: 0.5258 (t0) cc_final: 0.5004 (m-30) REVERT: E 480 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7273 (pp20) REVERT: E 575 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7376 (ptpp) REVERT: F 465 ILE cc_start: 0.8200 (mm) cc_final: 0.7919 (tp) REVERT: F 556 SER cc_start: 0.6334 (OUTLIER) cc_final: 0.5750 (t) outliers start: 66 outliers final: 44 residues processed: 258 average time/residue: 1.2271 time to fit residues: 367.1488 Evaluate side-chains 252 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 551 ARG Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 645 TYR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 501 PHE Chi-restraints excluded: chain D residue 630 PHE Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 575 LYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 360 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 726 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 171 optimal weight: 6.9990 chunk 274 optimal weight: 0.5980 chunk 202 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.250071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.183249 restraints weight = 25942.518| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.71 r_work: 0.3329 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22758 Z= 0.221 Angle : 0.624 18.437 30768 Z= 0.322 Chirality : 0.046 0.211 3456 Planarity : 0.005 0.067 3936 Dihedral : 4.640 57.997 3013 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.86 % Allowed : 28.26 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2766 helix: 0.58 (0.16), residues: 1052 sheet: -0.32 (0.30), residues: 347 loop : -0.52 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 350 HIS 0.006 0.001 HIS D 763 PHE 0.030 0.002 PHE A 759 TYR 0.019 0.001 TYR C 482 ARG 0.006 0.001 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.05171 ( 801) hydrogen bonds : angle 4.75497 ( 2298) covalent geometry : bond 0.00560 (22758) covalent geometry : angle 0.62428 (30768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16706.28 seconds wall clock time: 287 minutes 55.86 seconds (17275.86 seconds total)