Starting phenix.real_space_refine on Sun Oct 12 06:54:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh3_37527/10_2025/8wh3_37527.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh3_37527/10_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_37527/10_2025/8wh3_37527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh3_37527/10_2025/8wh3_37527.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh3_37527/10_2025/8wh3_37527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh3_37527/10_2025/8wh3_37527.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 5.77, per 1000 atoms: 0.26 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.93 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: 4.88 Time building geometry restraints manager: 2.54 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: 0.02 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.780 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.000 ARG A 625 TYR 0.013 0.001 TYR D 482 PHE 0.030 0.001 PHE C 759 TRP 0.008 0.001 TRP B 350 HIS 0.009 0.001 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00297 (22758) covalent geometry : angle 0.56778 (30768) hydrogen bonds : bond 0.16804 ( 801) hydrogen bonds : angle 5.97239 ( 2298) *********************** 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 : 1.091 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: 0.6005 time to fit residues: 167.0363 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 : 0.943 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 GLN E 466 ASN E 615 ASN ** F 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.251327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.185243 restraints weight = 26201.658| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.61 r_work: 0.3392 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22758 Z= 0.163 Angle : 0.553 10.546 30768 Z= 0.291 Chirality : 0.044 0.167 3456 Planarity : 0.004 0.047 3936 Dihedral : 5.899 124.907 3061 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.78 % Allowed : 25.81 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.16), residues: 2766 helix: 0.75 (0.16), residues: 1044 sheet: -0.12 (0.32), residues: 314 loop : -0.42 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.034 0.001 TYR E 645 PHE 0.017 0.001 PHE A 524 TRP 0.011 0.001 TRP B 350 HIS 0.007 0.001 HIS D 763 Details of bonding type rmsd covalent geometry : bond 0.00403 (22758) covalent geometry : angle 0.55331 (30768) hydrogen bonds : bond 0.04764 ( 801) hydrogen bonds : angle 5.01012 ( 2298) *********************** 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 322 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 228 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 324 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7625 (m110) REVERT: B 529 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: B 557 GLU cc_start: 0.7675 (pp20) cc_final: 0.7456 (pp20) REVERT: C 334 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8538 (tp) REVERT: C 365 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 625 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7307 (mmm160) REVERT: C 764 LYS cc_start: 0.7379 (pttm) cc_final: 0.7050 (pttm) REVERT: C 765 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6037 (mttt) REVERT: D 618 MET cc_start: 0.6812 (pmt) cc_final: 0.6549 (pmm) REVERT: D 632 GLN cc_start: 0.1206 (OUTLIER) cc_final: 0.0657 (tt0) REVERT: D 759 PHE cc_start: 0.5688 (t80) cc_final: 0.4772 (t80) REVERT: E 424 ASP cc_start: 0.7095 (t0) cc_final: 0.6886 (t0) REVERT: F 669 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7899 (tt) outliers start: 94 outliers final: 37 residues processed: 300 average time/residue: 0.5887 time to fit residues: 203.8381 Evaluate side-chains 250 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 618 MET 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 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 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 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 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 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 669 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 142 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 198 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 264 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 148 optimal weight: 9.9990 chunk 267 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 529 GLN E 573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.254075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.188361 restraints weight = 26350.121| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.68 r_work: 0.3427 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22758 Z= 0.101 Angle : 0.493 10.171 30768 Z= 0.260 Chirality : 0.041 0.144 3456 Planarity : 0.004 0.041 3936 Dihedral : 4.604 55.659 3027 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.30 % Allowed : 26.17 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 2766 helix: 0.93 (0.16), residues: 1084 sheet: -0.03 (0.32), residues: 305 loop : -0.47 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 625 TYR 0.013 0.001 TYR A 670 PHE 0.026 0.001 PHE D 668 TRP 0.007 0.001 TRP E 350 HIS 0.006 0.001 HIS D 763 Details of bonding type rmsd covalent geometry : bond 0.00236 (22758) covalent geometry : angle 0.49316 (30768) hydrogen bonds : bond 0.03269 ( 801) hydrogen bonds : angle 4.68991 ( 2298) *********************** 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 307 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 225 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7581 (mm-30) REVERT: A 699 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: B 450 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7304 (mttt) REVERT: B 557 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7287 (pp20) REVERT: C 334 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8462 (tp) REVERT: C 764 LYS cc_start: 0.7232 (pttm) cc_final: 0.7028 (ptpp) REVERT: C 765 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.6070 (mttt) REVERT: D 420 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7843 (tt) REVERT: D 501 PHE cc_start: 0.5497 (OUTLIER) cc_final: 0.5008 (m-10) REVERT: D 547 MET cc_start: 0.8032 (mtm) cc_final: 0.7463 (ppp) REVERT: D 632 GLN cc_start: 0.1367 (OUTLIER) cc_final: 0.0857 (tt0) REVERT: E 615 ASN cc_start: 0.8050 (p0) cc_final: 0.7110 (t0) REVERT: F 465 ILE cc_start: 0.8081 (mm) cc_final: 0.7824 (tp) outliers start: 82 outliers final: 24 residues processed: 288 average time/residue: 0.5613 time to fit residues: 187.3624 Evaluate side-chains 239 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE 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 450 LYS Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 557 GLU 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 C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 765 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 501 PHE 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 465 ILE 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 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 423 VAL Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 726 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 172 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 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 = 0.250996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185903 restraints weight = 26146.245| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.67 r_work: 0.3354 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22758 Z= 0.188 Angle : 0.562 10.621 30768 Z= 0.293 Chirality : 0.045 0.174 3456 Planarity : 0.005 0.069 3936 Dihedral : 4.598 57.891 3018 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.07 % Allowed : 26.21 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.16), residues: 2766 helix: 0.73 (0.16), residues: 1058 sheet: -0.11 (0.32), residues: 313 loop : -0.44 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 750 TYR 0.017 0.001 TYR C 482 PHE 0.029 0.002 PHE D 668 TRP 0.011 0.001 TRP B 350 HIS 0.012 0.001 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00471 (22758) covalent geometry : angle 0.56189 (30768) hydrogen bonds : bond 0.04894 ( 801) hydrogen bonds : angle 4.75380 ( 2298) *********************** 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 324 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 223 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7905 (t0) REVERT: A 365 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 557 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7613 (mm-30) REVERT: A 684 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.1498 (ppp) REVERT: B 450 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7222 (mttt) REVERT: B 529 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: B 557 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7273 (pp20) REVERT: B 699 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: C 334 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8547 (tp) REVERT: C 365 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8438 (p) REVERT: C 764 LYS cc_start: 0.7466 (pttm) cc_final: 0.7076 (ptpp) REVERT: C 765 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6110 (mttt) REVERT: D 501 PHE cc_start: 0.5471 (OUTLIER) cc_final: 0.5033 (m-10) REVERT: D 547 MET cc_start: 0.8070 (mtm) cc_final: 0.7440 (ppp) REVERT: D 618 MET cc_start: 0.6832 (pmt) cc_final: 0.6571 (pmm) REVERT: D 632 GLN cc_start: 0.1399 (OUTLIER) cc_final: 0.0938 (tt0) REVERT: E 407 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: E 424 ASP cc_start: 0.7227 (t0) cc_final: 0.7013 (t0) REVERT: E 615 ASN cc_start: 0.7956 (p0) cc_final: 0.7048 (t0) REVERT: E 619 ARG cc_start: 0.7624 (ptt180) cc_final: 0.7416 (pmm-80) REVERT: F 556 SER cc_start: 0.6486 (OUTLIER) cc_final: 0.5914 (t) REVERT: F 669 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8041 (tt) outliers start: 101 outliers final: 42 residues processed: 303 average time/residue: 0.5557 time to fit residues: 195.4727 Evaluate side-chains 268 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 505 THR Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 557 GLU 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 525 VAL Chi-restraints excluded: chain C residue 531 ILE 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 363 LEU Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 501 PHE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 632 GLN 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 411 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 669 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 72 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 chunk 156 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN E 466 ASN F 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.248554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.182158 restraints weight = 25917.689| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.66 r_work: 0.3297 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 22758 Z= 0.311 Angle : 0.678 10.095 30768 Z= 0.353 Chirality : 0.050 0.247 3456 Planarity : 0.005 0.052 3936 Dihedral : 5.006 59.970 3016 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.60 % Allowed : 25.12 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.16), residues: 2766 helix: 0.30 (0.16), residues: 1055 sheet: -0.21 (0.31), residues: 322 loop : -0.64 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 625 TYR 0.023 0.002 TYR C 482 PHE 0.033 0.002 PHE D 668 TRP 0.014 0.002 TRP B 350 HIS 0.007 0.001 HIS D 763 Details of bonding type rmsd covalent geometry : bond 0.00789 (22758) covalent geometry : angle 0.67797 (30768) hydrogen bonds : bond 0.06360 ( 801) hydrogen bonds : angle 5.05173 ( 2298) *********************** 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 360 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 221 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7900 (m110) REVERT: A 365 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8468 (m) REVERT: A 477 LYS cc_start: 0.8129 (mptp) cc_final: 0.7850 (mptt) REVERT: A 557 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7625 (mm-30) REVERT: A 678 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7664 (ttpp) REVERT: B 547 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6723 (ppp) REVERT: B 551 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8321 (mtt-85) REVERT: B 557 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: B 699 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: C 334 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8627 (tp) REVERT: C 365 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8542 (p) REVERT: C 660 GLN cc_start: 0.8370 (mp10) cc_final: 0.7984 (mp10) REVERT: C 764 LYS cc_start: 0.7768 (pttm) cc_final: 0.7359 (pttm) REVERT: C 765 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.6217 (mttt) REVERT: D 501 PHE cc_start: 0.5506 (OUTLIER) cc_final: 0.5180 (m-10) REVERT: D 547 MET cc_start: 0.8015 (mtm) cc_final: 0.7383 (ppp) REVERT: D 664 TYR cc_start: 0.4614 (OUTLIER) cc_final: 0.4282 (m-10) REVERT: E 407 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: E 435 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8255 (mtmm) REVERT: E 615 ASN cc_start: 0.7926 (p0) cc_final: 0.6981 (t0) REVERT: E 619 ARG cc_start: 0.7626 (ptt180) cc_final: 0.7397 (pmm-80) REVERT: F 556 SER cc_start: 0.6520 (OUTLIER) cc_final: 0.5931 (t) REVERT: F 592 ILE cc_start: 0.0654 (OUTLIER) cc_final: 0.0443 (mm) REVERT: F 669 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8112 (tt) REVERT: F 680 HIS cc_start: 0.5908 (OUTLIER) cc_final: 0.5389 (p-80) outliers start: 139 outliers final: 60 residues processed: 326 average time/residue: 0.5890 time to fit residues: 221.8578 Evaluate side-chains 285 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 207 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 505 THR Chi-restraints excluded: chain A residue 558 LEU 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 684 MET Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 408 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 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 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 477 LYS 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 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 501 PHE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 628 THR 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 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 411 ASP Chi-restraints excluded: chain E residue 426 MET 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 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 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 507 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 680 HIS 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 130 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 268 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN C 594 ASN D 629 HIS 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 = 0.4648 r_free = 0.4648 target = 0.250001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.185542 restraints weight = 26132.776| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.54 r_work: 0.3344 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22758 Z= 0.205 Angle : 0.588 10.414 30768 Z= 0.308 Chirality : 0.045 0.194 3456 Planarity : 0.005 0.064 3936 Dihedral : 4.824 58.771 3014 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.91 % Allowed : 25.89 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2766 helix: 0.44 (0.16), residues: 1053 sheet: -0.30 (0.30), residues: 333 loop : -0.58 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 625 TYR 0.019 0.001 TYR A 670 PHE 0.026 0.002 PHE A 759 TRP 0.011 0.002 TRP E 350 HIS 0.007 0.001 HIS D 763 Details of bonding type rmsd covalent geometry : bond 0.00518 (22758) covalent geometry : angle 0.58828 (30768) hydrogen bonds : bond 0.05026 ( 801) hydrogen bonds : angle 4.86041 ( 2298) *********************** 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 338 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 216 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 557 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7632 (mm-30) REVERT: A 684 MET cc_start: 0.5090 (OUTLIER) cc_final: 0.1520 (pp-130) REVERT: A 699 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.6714 (m-80) REVERT: B 547 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6614 (ppp) REVERT: B 551 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8375 (mtt-85) REVERT: B 557 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: B 612 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6410 (ttm110) REVERT: C 334 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8532 (tp) REVERT: C 365 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8539 (p) REVERT: C 612 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7337 (ttp80) REVERT: C 764 LYS cc_start: 0.7691 (pttm) cc_final: 0.7227 (pttm) REVERT: C 765 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6236 (mttt) REVERT: D 501 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.5177 (m-10) REVERT: D 547 MET cc_start: 0.8034 (mtm) cc_final: 0.7319 (pp-130) REVERT: D 618 MET cc_start: 0.6521 (pmt) cc_final: 0.6262 (pmm) REVERT: D 664 TYR cc_start: 0.4565 (OUTLIER) cc_final: 0.4197 (m-10) REVERT: E 407 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: E 435 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8204 (mtmm) REVERT: E 615 ASN cc_start: 0.7963 (p0) cc_final: 0.6943 (t0) REVERT: E 619 ARG cc_start: 0.7660 (ptt180) cc_final: 0.7419 (pmm-80) REVERT: F 556 SER cc_start: 0.6397 (OUTLIER) cc_final: 0.5806 (t) REVERT: F 592 ILE cc_start: 0.0536 (OUTLIER) cc_final: 0.0306 (mm) REVERT: F 669 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7984 (tt) REVERT: F 680 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5461 (p-80) outliers start: 122 outliers final: 60 residues processed: 314 average time/residue: 0.5693 time to fit residues: 207.4412 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 : 0.798 ------------------------------------------------------------------------------- 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 684 MET 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 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 612 ARG Chi-restraints excluded: chain B residue 614 ASP 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 334 LEU 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 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 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR 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 501 PHE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 628 THR 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 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 411 ASP Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 505 THR 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 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 363 LEU 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 574 ILE Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 732 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 0 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 128 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 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 = 0.251968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.185217 restraints weight = 26086.638| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.67 r_work: 0.3374 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22758 Z= 0.134 Angle : 0.538 10.160 30768 Z= 0.282 Chirality : 0.042 0.183 3456 Planarity : 0.004 0.051 3936 Dihedral : 4.610 57.931 3014 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.82 % Allowed : 27.05 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2766 helix: 0.68 (0.16), residues: 1057 sheet: -0.33 (0.31), residues: 330 loop : -0.57 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 625 TYR 0.016 0.001 TYR A 670 PHE 0.029 0.001 PHE D 668 TRP 0.010 0.001 TRP E 350 HIS 0.007 0.001 HIS D 763 Details of bonding type rmsd covalent geometry : bond 0.00332 (22758) covalent geometry : angle 0.53772 (30768) hydrogen bonds : bond 0.03934 ( 801) hydrogen bonds : angle 4.69734 ( 2298) *********************** 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 311 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 216 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8309 (p) REVERT: A 557 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7558 (mm-30) REVERT: A 684 MET cc_start: 0.5109 (OUTLIER) cc_final: 0.1457 (pp-130) REVERT: A 699 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: B 529 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: B 547 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6667 (ppp) REVERT: B 551 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8385 (mtt-85) REVERT: B 557 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7378 (pp20) REVERT: B 612 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6448 (ttm110) REVERT: C 334 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8555 (tp) REVERT: C 365 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8498 (p) REVERT: C 660 GLN cc_start: 0.8278 (mp10) cc_final: 0.8061 (mp10) REVERT: C 764 LYS cc_start: 0.7658 (pttm) cc_final: 0.7302 (ptpp) REVERT: C 765 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6214 (mttt) REVERT: D 501 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.5143 (m-10) REVERT: D 547 MET cc_start: 0.7997 (mtm) cc_final: 0.7311 (pp-130) REVERT: E 435 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8226 (mtmm) REVERT: E 615 ASN cc_start: 0.7986 (p0) cc_final: 0.6979 (t0) REVERT: F 453 GLU cc_start: 0.6689 (tm-30) cc_final: 0.6396 (tp30) REVERT: F 556 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5756 (t) REVERT: F 592 ILE cc_start: 0.0416 (OUTLIER) cc_final: 0.0204 (mm) REVERT: F 669 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8021 (tt) REVERT: F 680 HIS cc_start: 0.5806 (OUTLIER) cc_final: 0.5394 (p-80) REVERT: F 760 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.7115 (tp) outliers start: 95 outliers final: 51 residues processed: 292 average time/residue: 0.5530 time to fit residues: 187.8252 Evaluate side-chains 274 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 205 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 630 PHE Chi-restraints excluded: chain A residue 684 MET 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 529 GLN 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 C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU 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 527 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 351 ILE 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 501 PHE Chi-restraints excluded: chain D residue 662 ASN 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 411 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 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 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 592 ILE Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 760 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 91 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 148 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 161 optimal weight: 0.0470 chunk 100 optimal weight: 0.2980 chunk 190 optimal weight: 0.7980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN B 529 GLN 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 = 0.4675 r_free = 0.4675 target = 0.253766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.190364 restraints weight = 26051.236| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.56 r_work: 0.3425 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1989 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= 0.103 Angle : 0.513 11.196 30768 Z= 0.269 Chirality : 0.041 0.155 3456 Planarity : 0.004 0.065 3936 Dihedral : 4.367 56.642 3013 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.86 % Allowed : 27.86 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 2766 helix: 0.91 (0.16), residues: 1064 sheet: -0.30 (0.31), residues: 329 loop : -0.50 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.013 0.001 TYR A 670 PHE 0.028 0.001 PHE A 759 TRP 0.008 0.001 TRP E 350 HIS 0.006 0.001 HIS D 629 Details of bonding type rmsd covalent geometry : bond 0.00241 (22758) covalent geometry : angle 0.51287 (30768) hydrogen bonds : bond 0.03036 ( 801) hydrogen bonds : angle 4.51860 ( 2298) *********************** 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 288 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8129 (p) REVERT: A 684 MET cc_start: 0.4928 (OUTLIER) cc_final: 0.1351 (pp-130) REVERT: A 699 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: B 478 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7062 (t0) REVERT: B 547 MET cc_start: 0.6837 (pp-130) cc_final: 0.6593 (ppp) REVERT: B 551 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8336 (mtt-85) REVERT: B 557 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7289 (pp20) REVERT: B 612 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6359 (ttm110) REVERT: C 334 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8463 (tp) REVERT: C 660 GLN cc_start: 0.8275 (mp10) cc_final: 0.8032 (mp10) REVERT: C 764 LYS cc_start: 0.7550 (pttm) cc_final: 0.7045 (pttm) REVERT: C 765 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6236 (mttt) REVERT: D 501 PHE cc_start: 0.5458 (OUTLIER) cc_final: 0.5178 (m-10) REVERT: D 534 ASP cc_start: 0.5304 (t0) cc_final: 0.5039 (m-30) REVERT: D 547 MET cc_start: 0.7951 (mtm) cc_final: 0.7272 (pp-130) REVERT: D 618 MET cc_start: 0.6540 (pmt) cc_final: 0.6336 (pmm) REVERT: E 480 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: E 615 ASN cc_start: 0.7915 (p0) cc_final: 0.6916 (t0) REVERT: F 465 ILE cc_start: 0.8131 (mm) cc_final: 0.7868 (tp) REVERT: F 576 LYS cc_start: 0.7580 (ttmm) cc_final: 0.6876 (ptpt) REVERT: F 680 HIS cc_start: 0.5759 (OUTLIER) cc_final: 0.5353 (p-80) REVERT: F 760 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6960 (pp) outliers start: 71 outliers final: 39 residues processed: 271 average time/residue: 0.6118 time to fit residues: 190.5247 Evaluate side-chains 258 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 568 LYS Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 684 MET 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 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 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 334 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 525 VAL 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 501 PHE Chi-restraints excluded: chain D residue 630 PHE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain E residue 343 GLU 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 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 423 VAL 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 680 HIS Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 760 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 216 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.0670 chunk 190 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 269 optimal weight: 0.0870 chunk 80 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** D 469 GLN ** 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 = 0.4678 r_free = 0.4678 target = 0.254028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.188805 restraints weight = 26229.814| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.65 r_work: 0.3424 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22758 Z= 0.102 Angle : 0.516 12.857 30768 Z= 0.268 Chirality : 0.041 0.158 3456 Planarity : 0.004 0.051 3936 Dihedral : 4.239 56.169 3013 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.62 % Allowed : 28.34 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 2766 helix: 1.02 (0.16), residues: 1067 sheet: -0.32 (0.31), residues: 332 loop : -0.46 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.012 0.001 TYR A 670 PHE 0.038 0.001 PHE D 698 TRP 0.008 0.001 TRP C 350 HIS 0.006 0.001 HIS D 763 Details of bonding type rmsd covalent geometry : bond 0.00237 (22758) covalent geometry : angle 0.51559 (30768) hydrogen bonds : bond 0.02942 ( 801) hydrogen bonds : angle 4.45721 ( 2298) *********************** 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 276 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 211 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8109 (p) REVERT: A 684 MET cc_start: 0.4865 (OUTLIER) cc_final: 0.1347 (pp-130) REVERT: A 699 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: B 478 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7054 (t0) REVERT: B 547 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6571 (ppp) REVERT: B 551 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8354 (mtt-85) REVERT: B 557 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: B 612 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6356 (ttm110) REVERT: C 334 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 764 LYS cc_start: 0.7477 (pttm) cc_final: 0.7018 (ptpp) REVERT: C 765 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6274 (mttt) REVERT: D 351 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7108 (mt) REVERT: D 420 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7865 (tt) REVERT: D 501 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.5104 (m-10) REVERT: D 534 ASP cc_start: 0.5246 (t0) cc_final: 0.4972 (m-30) REVERT: E 480 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: E 615 ASN cc_start: 0.7822 (p0) cc_final: 0.6864 (t0) REVERT: F 514 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7502 (mpp-170) REVERT: F 576 LYS cc_start: 0.7596 (ttmm) cc_final: 0.6893 (ptpt) REVERT: F 680 HIS cc_start: 0.5707 (OUTLIER) cc_final: 0.5193 (p90) REVERT: F 760 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6958 (pp) outliers start: 65 outliers final: 39 residues processed: 262 average time/residue: 0.5947 time to fit residues: 179.9040 Evaluate side-chains 257 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 684 MET 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 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 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 C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 525 VAL 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 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 420 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 343 GLU 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 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 423 VAL Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 760 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 86 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 238 optimal weight: 0.0470 chunk 39 optimal weight: 0.0770 chunk 231 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** D 469 GLN ** 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 = 0.253716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.187906 restraints weight = 26258.630| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 3.61 r_work: 0.3416 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22758 Z= 0.107 Angle : 0.519 12.405 30768 Z= 0.269 Chirality : 0.041 0.155 3456 Planarity : 0.004 0.067 3936 Dihedral : 4.201 56.849 3013 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.78 % Allowed : 28.38 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.16), residues: 2766 helix: 1.04 (0.16), residues: 1068 sheet: -0.31 (0.31), residues: 332 loop : -0.45 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 625 TYR 0.011 0.001 TYR A 670 PHE 0.029 0.001 PHE A 759 TRP 0.007 0.001 TRP C 350 HIS 0.005 0.001 HIS D 763 Details of bonding type rmsd covalent geometry : bond 0.00257 (22758) covalent geometry : angle 0.51872 (30768) hydrogen bonds : bond 0.03193 ( 801) hydrogen bonds : angle 4.43557 ( 2298) ********************** 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 276 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8124 (p) REVERT: A 658 LYS cc_start: 0.7247 (mtpp) cc_final: 0.6908 (mtpp) REVERT: A 684 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.1344 (pp-130) REVERT: A 699 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: B 477 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6896 (ttpt) REVERT: B 547 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6591 (ppp) REVERT: B 551 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8381 (mtt-85) REVERT: B 557 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7330 (pp20) REVERT: B 612 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6358 (ttm110) REVERT: C 570 ARG cc_start: 0.6698 (mtp-110) cc_final: 0.6314 (mpt-90) REVERT: C 764 LYS cc_start: 0.7514 (pttm) cc_final: 0.7038 (ptpp) REVERT: C 765 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6247 (mttt) REVERT: D 351 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7115 (mt) REVERT: D 501 PHE cc_start: 0.5382 (OUTLIER) cc_final: 0.5072 (m-10) REVERT: E 480 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7210 (pp20) REVERT: E 575 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7388 (ptpp) REVERT: E 615 ASN cc_start: 0.7790 (p0) cc_final: 0.6851 (t0) REVERT: F 556 SER cc_start: 0.6445 (OUTLIER) cc_final: 0.5833 (t) REVERT: F 576 LYS cc_start: 0.7631 (ttmm) cc_final: 0.6929 (ptpt) REVERT: F 680 HIS cc_start: 0.5714 (OUTLIER) cc_final: 0.5228 (p90) REVERT: F 760 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6942 (pp) outliers start: 69 outliers final: 40 residues processed: 263 average time/residue: 0.6216 time to fit residues: 187.8145 Evaluate side-chains 258 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 684 MET 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 477 LYS 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 C residue 324 ASN Chi-restraints excluded: chain C residue 525 VAL 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 351 ILE Chi-restraints excluded: chain D residue 359 SER 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 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 423 VAL 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 680 HIS Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 760 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 36 optimal weight: 0.0030 chunk 13 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 258 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 68 optimal weight: 0.0980 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 0.0970 chunk 167 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.254568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.189269 restraints weight = 26293.651| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 3.68 r_work: 0.3425 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2190 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= 0.097 Angle : 0.519 11.831 30768 Z= 0.268 Chirality : 0.041 0.157 3456 Planarity : 0.004 0.071 3936 Dihedral : 4.111 55.915 3013 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.29 % Allowed : 28.95 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.16), residues: 2766 helix: 1.19 (0.17), residues: 1065 sheet: -0.25 (0.32), residues: 322 loop : -0.44 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 625 TYR 0.010 0.001 TYR A 670 PHE 0.046 0.001 PHE D 698 TRP 0.007 0.001 TRP C 350 HIS 0.005 0.001 HIS D 763 Details of bonding type rmsd covalent geometry : bond 0.00228 (22758) covalent geometry : angle 0.51904 (30768) hydrogen bonds : bond 0.02755 ( 801) hydrogen bonds : angle 4.36701 ( 2298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8558.69 seconds wall clock time: 146 minutes 19.73 seconds (8779.73 seconds total)