Starting phenix.real_space_refine on Sat Aug 23 10:06:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3w_36863/08_2025/8k3w_36863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3w_36863/08_2025/8k3w_36863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3w_36863/08_2025/8k3w_36863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3w_36863/08_2025/8k3w_36863.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3w_36863/08_2025/8k3w_36863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3w_36863/08_2025/8k3w_36863.cif" } resolution = 2.91 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= -0.000 sd= 0.032 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 7143 2.51 5 N 1753 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10916 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5360 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 20, 'TRANS': 673} Chain breaks: 5 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'TRP:plan': 2, 'ASP:plan': 8, 'ASN:plan1': 7, 'TYR:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 163 Chain: "A" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5380 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 20, 'TRANS': 673} Chain breaks: 5 Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TRP:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 7, 'TYR:plan': 1, 'GLU:plan': 11, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {' MG': 1, 'POV': 1, 'UD1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {' MG': 1, 'POV': 1, 'UD1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.46, per 1000 atoms: 0.23 Number of scatterers: 10916 At special positions: 0 Unit cell: (125.19, 97.37, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 6 15.00 Mg 2 11.99 O 1944 8.00 N 1753 7.00 C 7143 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: 0.99 Conformation dependent library (CDL) restraints added in 542.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 64.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 410 through 413 removed outlier: 3.611A pdb=" N PHE B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.863A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 460 through 479 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 5.909A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 669 removed outlier: 3.633A pdb=" N SER B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 716 through 726 removed outlier: 3.579A pdb=" N LEU B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.091A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.564A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.737A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.554A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 894 removed outlier: 3.957A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 932 Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.550A pdb=" N SER B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 948 Processing helix chain 'B' and resid 949 through 955 Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 998 through 1012 removed outlier: 3.741A pdb=" N GLN B1002 " --> pdb=" O SER B 998 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B1005 " --> pdb=" O ILE B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1060 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1091 through 1127 removed outlier: 4.201A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.611A pdb=" N PHE A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.863A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 478 removed outlier: 3.847A pdb=" N LEU A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 5.909A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 669 removed outlier: 3.632A pdb=" N SER A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 711 through 714 Processing helix chain 'A' and resid 715 through 726 removed outlier: 3.797A pdb=" N LEU A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.091A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.564A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.738A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.555A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 894 removed outlier: 3.958A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 932 Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.550A pdb=" N SER A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 949 through 955 Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 998 through 1012 removed outlier: 3.891A pdb=" N GLN A1002 " --> pdb=" O SER A 998 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1060 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1091 through 1127 removed outlier: 4.201A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.692A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE B 493 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N LEU B 568 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 495 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 527 through 528 removed outlier: 6.728A pdb=" N GLU B 527 " --> pdb=" O ILE A 982 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.670A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 981 through 982 removed outlier: 6.406A pdb=" N GLU A 527 " --> pdb=" O ILE B 982 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.693A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 493 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LEU A 568 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 495 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.671A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) 661 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1654 1.31 - 1.43: 3219 1.43 - 1.56: 6189 1.56 - 1.69: 12 1.69 - 1.81: 104 Bond restraints: 11178 Sorted by residual: bond pdb=" C4 UD1 B1503 " pdb=" N3 UD1 B1503 " ideal model delta sigma weight residual 1.386 1.277 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 UD1 A1503 " pdb=" N3 UD1 A1503 " ideal model delta sigma weight residual 1.386 1.278 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C2B UD1 A1503 " pdb=" C3B UD1 A1503 " ideal model delta sigma weight residual 1.533 1.462 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2B UD1 B1503 " pdb=" C3B UD1 B1503 " ideal model delta sigma weight residual 1.533 1.462 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.11e-02 8.12e+03 1.05e+01 ... (remaining 11173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 15073 4.18 - 8.36: 75 8.36 - 12.54: 24 12.54 - 16.72: 6 16.72 - 20.89: 2 Bond angle restraints: 15180 Sorted by residual: angle pdb=" C1B UD1 B1503 " pdb=" C2B UD1 B1503 " pdb=" O2' UD1 B1503 " ideal model delta sigma weight residual 109.46 130.35 -20.89 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C1B UD1 A1503 " pdb=" C2B UD1 A1503 " pdb=" O2' UD1 A1503 " ideal model delta sigma weight residual 109.46 130.35 -20.89 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C MET B 992 " pdb=" CA MET B 992 " pdb=" CB MET B 992 " ideal model delta sigma weight residual 116.54 109.41 7.13 1.15e+00 7.56e-01 3.85e+01 angle pdb=" C MET A 992 " pdb=" CA MET A 992 " pdb=" CB MET A 992 " ideal model delta sigma weight residual 116.63 109.53 7.10 1.16e+00 7.43e-01 3.74e+01 angle pdb=" C2B UD1 B1503 " pdb=" C1B UD1 B1503 " pdb=" O4B UD1 B1503 " ideal model delta sigma weight residual 106.74 91.07 15.67 3.00e+00 1.11e-01 2.73e+01 ... (remaining 15175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 6384 33.90 - 67.80: 188 67.80 - 101.70: 30 101.70 - 135.60: 6 135.60 - 169.51: 2 Dihedral angle restraints: 6610 sinusoidal: 2516 harmonic: 4094 Sorted by residual: dihedral pdb=" C27 POV B1502 " pdb=" C28 POV B1502 " pdb=" C29 POV B1502 " pdb="C210 POV B1502 " ideal model delta sinusoidal sigma weight residual 127.48 -63.01 -169.51 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C27 POV A1502 " pdb=" C28 POV A1502 " pdb=" C29 POV A1502 " pdb="C210 POV A1502 " ideal model delta sinusoidal sigma weight residual 127.48 -63.01 -169.51 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA PRO A 410 " pdb=" C PRO A 410 " pdb=" N ASN A 411 " pdb=" CA ASN A 411 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 6607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1453 0.090 - 0.180: 252 0.180 - 0.271: 20 0.271 - 0.361: 6 0.361 - 0.451: 4 Chirality restraints: 1735 Sorted by residual: chirality pdb=" C2B UD1 A1503 " pdb=" C1B UD1 A1503 " pdb=" C3B UD1 A1503 " pdb=" O2' UD1 A1503 " both_signs ideal model delta sigma weight residual False -2.62 -2.17 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C2B UD1 B1503 " pdb=" C1B UD1 B1503 " pdb=" C3B UD1 B1503 " pdb=" O2' UD1 B1503 " both_signs ideal model delta sigma weight residual False -2.62 -2.17 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C5' UD1 B1503 " pdb=" C4' UD1 B1503 " pdb=" C6' UD1 B1503 " pdb=" O5' UD1 B1503 " both_signs ideal model delta sigma weight residual False -2.52 -2.10 -0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 1732 not shown) Planarity restraints: 1859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2' UD1 B1503 " 0.169 2.00e-02 2.50e+03 1.36e-01 2.32e+02 pdb=" C7' UD1 B1503 " -0.055 2.00e-02 2.50e+03 pdb=" C8' UD1 B1503 " 0.133 2.00e-02 2.50e+03 pdb=" N2' UD1 B1503 " -0.204 2.00e-02 2.50e+03 pdb=" O7' UD1 B1503 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2' UD1 A1503 " 0.169 2.00e-02 2.50e+03 1.36e-01 2.32e+02 pdb=" C7' UD1 A1503 " -0.055 2.00e-02 2.50e+03 pdb=" C8' UD1 A1503 " 0.133 2.00e-02 2.50e+03 pdb=" N2' UD1 A1503 " -0.204 2.00e-02 2.50e+03 pdb=" O7' UD1 A1503 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 696 " -0.016 2.00e-02 2.50e+03 1.62e-02 5.24e+00 pdb=" CG TYR A 696 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 696 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 696 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 696 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 696 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 696 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 696 " 0.004 2.00e-02 2.50e+03 ... (remaining 1856 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2899 2.81 - 3.33: 10904 3.33 - 3.85: 17859 3.85 - 4.38: 20609 4.38 - 4.90: 36151 Nonbonded interactions: 88422 Sorted by model distance: nonbonded pdb=" O3' UD1 A1503 " pdb=" O7' UD1 A1503 " model vdw 2.285 3.040 nonbonded pdb=" O3' UD1 B1503 " pdb=" O7' UD1 B1503 " model vdw 2.285 3.040 nonbonded pdb=" O CYS A 845 " pdb=" OG1 THR A 849 " model vdw 2.351 3.040 nonbonded pdb=" O CYS B 845 " pdb=" OG1 THR B 849 " model vdw 2.352 3.040 nonbonded pdb=" O ILE B 844 " pdb=" OG SER B 848 " model vdw 2.356 3.040 ... (remaining 88417 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 381 through 501 or (resid 502 and (name N or name CA or na \ me C or name O or name CB )) or resid 503 or (resid 504 and (name N or name CA o \ r name C or name O or name CB )) or resid 505 through 664 or (resid 665 and (nam \ e N or name CA or name C or name O or name CB )) or resid 666 through 670 or (re \ sid 671 and (name N or name CA or name C or name O or name CB )) or resid 672 th \ rough 716 or (resid 717 and (name N or name CA or name C or name O or name CB )) \ or resid 718 or (resid 719 and (name N or name CA or name C or name O or name C \ B )) or resid 720 through 981 or (resid 982 through 987 and (name N or name CA o \ r name C or name O or name CB )) or (resid 988 through 997 and (name N or name C \ A or name C or name O or name CB )) or resid 998 through 1503)) selection = (chain 'B' and (resid 381 through 449 or (resid 450 through 452 and (name N or n \ ame CA or name C or name O or name CB )) or resid 453 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 through 15 \ 03)) } 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 11.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 0.009 0.109 11178 Z= 0.560 Angle : 1.123 20.895 15180 Z= 0.704 Chirality : 0.070 0.451 1735 Planarity : 0.006 0.136 1859 Dihedral : 17.131 169.506 3962 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.89 % Allowed : 1.81 % Favored : 95.31 % 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 (0.23), residues: 1364 helix: 1.09 (0.19), residues: 772 sheet: -1.74 (0.44), residues: 120 loop : -1.34 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 436 TYR 0.040 0.002 TYR A 696 PHE 0.020 0.002 PHE B 885 TRP 0.016 0.002 TRP A 779 HIS 0.004 0.001 HIS B 783 Details of bonding type rmsd covalent geometry : bond 0.00881 (11178) covalent geometry : angle 1.12349 (15180) hydrogen bonds : bond 0.16243 ( 661) hydrogen bonds : angle 6.81741 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.437 Fit side-chains REVERT: B 579 ILE cc_start: 0.8138 (tt) cc_final: 0.7933 (mm) REVERT: B 700 MET cc_start: 0.2571 (tmm) cc_final: 0.2363 (mmt) REVERT: B 932 TYR cc_start: 0.7042 (t80) cc_final: 0.6832 (t80) REVERT: A 579 ILE cc_start: 0.8100 (tt) cc_final: 0.7876 (mm) REVERT: A 932 TYR cc_start: 0.7027 (t80) cc_final: 0.6817 (t80) REVERT: A 952 TYR cc_start: 0.7335 (m-10) cc_final: 0.7112 (m-10) outliers start: 32 outliers final: 2 residues processed: 265 average time/residue: 0.4619 time to fit residues: 133.1714 Evaluate side-chains 145 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain A residue 394 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 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 540 HIS B1002 GLN B1004 ASN B1013 ASN A 540 HIS A 965 HIS A 977 ASN A1002 GLN A1004 ASN A1013 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138960 restraints weight = 13207.743| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.10 r_work: 0.3459 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11178 Z= 0.133 Angle : 0.546 10.677 15180 Z= 0.287 Chirality : 0.041 0.155 1735 Planarity : 0.004 0.044 1859 Dihedral : 11.227 148.178 1683 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.61 % Allowed : 12.91 % Favored : 83.48 % 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: 1.41 (0.24), residues: 1364 helix: 2.20 (0.19), residues: 760 sheet: -0.97 (0.44), residues: 132 loop : -0.58 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 718 TYR 0.018 0.001 TYR A 827 PHE 0.021 0.002 PHE B1052 TRP 0.013 0.001 TRP B1047 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00284 (11178) covalent geometry : angle 0.54590 (15180) hydrogen bonds : bond 0.05042 ( 661) hydrogen bonds : angle 4.27375 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.399 Fit side-chains REVERT: B 579 ILE cc_start: 0.8187 (tt) cc_final: 0.7946 (mm) REVERT: B 630 GLU cc_start: 0.7179 (tt0) cc_final: 0.6870 (tp30) REVERT: B 655 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7655 (mmmt) REVERT: B 700 MET cc_start: 0.3074 (tmm) cc_final: 0.2319 (mmt) REVERT: B 932 TYR cc_start: 0.7378 (t80) cc_final: 0.6925 (t80) REVERT: B 943 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8102 (pt) REVERT: A 579 ILE cc_start: 0.8145 (tt) cc_final: 0.7877 (mm) REVERT: A 630 GLU cc_start: 0.7215 (tt0) cc_final: 0.6865 (tp30) REVERT: A 655 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7600 (mmmt) REVERT: A 692 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7605 (tp40) REVERT: A 717 ASP cc_start: 0.4578 (t0) cc_final: 0.4161 (t0) REVERT: A 932 TYR cc_start: 0.7348 (t80) cc_final: 0.6861 (t80) outliers start: 40 outliers final: 8 residues processed: 186 average time/residue: 0.3907 time to fit residues: 80.2695 Evaluate side-chains 144 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1090 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 121 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN B 934 GLN A 398 GLN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 934 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.163816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130082 restraints weight = 13404.292| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.12 r_work: 0.3356 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11178 Z= 0.220 Angle : 0.620 8.337 15180 Z= 0.333 Chirality : 0.044 0.164 1735 Planarity : 0.004 0.047 1859 Dihedral : 11.029 135.775 1681 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.87 % Allowed : 13.09 % Favored : 82.04 % 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: 1.26 (0.23), residues: 1364 helix: 2.13 (0.19), residues: 760 sheet: -0.78 (0.42), residues: 148 loop : -0.84 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 594 TYR 0.016 0.002 TYR B 538 PHE 0.017 0.002 PHE B1052 TRP 0.019 0.002 TRP A 806 HIS 0.006 0.002 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00529 (11178) covalent geometry : angle 0.62004 (15180) hydrogen bonds : bond 0.06805 ( 661) hydrogen bonds : angle 4.32730 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 630 GLU cc_start: 0.7413 (tt0) cc_final: 0.7107 (tt0) REVERT: B 655 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7520 (mmmt) REVERT: B 886 MET cc_start: 0.6703 (mtm) cc_final: 0.5772 (mmm) REVERT: B 932 TYR cc_start: 0.7275 (t80) cc_final: 0.6808 (t80) REVERT: B 943 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8213 (pt) REVERT: A 630 GLU cc_start: 0.7403 (tt0) cc_final: 0.7037 (tt0) REVERT: A 692 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7577 (tp40) REVERT: A 700 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4918 (mmt) REVERT: A 932 TYR cc_start: 0.7284 (t80) cc_final: 0.6817 (t80) REVERT: A 936 TRP cc_start: 0.6654 (OUTLIER) cc_final: 0.6005 (m-90) REVERT: A 982 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6657 (pt) outliers start: 54 outliers final: 30 residues processed: 178 average time/residue: 0.4450 time to fit residues: 86.9451 Evaluate side-chains 167 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 936 TRP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN A 545 ASN A 623 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139601 restraints weight = 12992.864| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.77 r_work: 0.3489 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11178 Z= 0.123 Angle : 0.483 7.001 15180 Z= 0.261 Chirality : 0.040 0.157 1735 Planarity : 0.004 0.047 1859 Dihedral : 10.717 131.241 1681 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.88 % Allowed : 13.90 % Favored : 82.22 % 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: 1.73 (0.24), residues: 1364 helix: 2.56 (0.19), residues: 758 sheet: -0.57 (0.42), residues: 148 loop : -0.72 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 594 TYR 0.017 0.001 TYR A 827 PHE 0.021 0.001 PHE B1124 TRP 0.013 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00275 (11178) covalent geometry : angle 0.48339 (15180) hydrogen bonds : bond 0.04947 ( 661) hydrogen bonds : angle 3.90029 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: B 523 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.5613 (p90) REVERT: B 630 GLU cc_start: 0.7406 (tt0) cc_final: 0.7069 (tt0) REVERT: B 655 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7765 (mmmt) REVERT: B 943 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8287 (pt) REVERT: B 1086 GLU cc_start: 0.6775 (pm20) cc_final: 0.5863 (mm-30) REVERT: A 523 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.5666 (p90) REVERT: A 630 GLU cc_start: 0.7377 (tt0) cc_final: 0.6980 (tt0) REVERT: A 655 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7793 (mmmt) REVERT: A 982 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6756 (pt) outliers start: 43 outliers final: 19 residues processed: 162 average time/residue: 0.4160 time to fit residues: 74.1910 Evaluate side-chains 156 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 133 optimal weight: 0.3980 chunk 126 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.167667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135171 restraints weight = 13208.698| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.01 r_work: 0.3423 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11178 Z= 0.141 Angle : 0.503 6.732 15180 Z= 0.273 Chirality : 0.040 0.158 1735 Planarity : 0.004 0.044 1859 Dihedral : 10.621 132.308 1681 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.05 % Allowed : 13.90 % Favored : 81.05 % 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: 1.64 (0.24), residues: 1364 helix: 2.48 (0.19), residues: 766 sheet: -0.77 (0.41), residues: 152 loop : -0.74 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 594 TYR 0.015 0.001 TYR A 827 PHE 0.018 0.002 PHE A1052 TRP 0.015 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00324 (11178) covalent geometry : angle 0.50341 (15180) hydrogen bonds : bond 0.05337 ( 661) hydrogen bonds : angle 3.87715 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 131 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: B 523 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.5612 (p90) REVERT: B 630 GLU cc_start: 0.7506 (tt0) cc_final: 0.7193 (tt0) REVERT: B 655 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7708 (mtpt) REVERT: B 661 ASP cc_start: 0.7749 (m-30) cc_final: 0.7481 (m-30) REVERT: B 886 MET cc_start: 0.6711 (mtm) cc_final: 0.5797 (mmm) REVERT: B 943 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8243 (pt) REVERT: A 523 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.5628 (p90) REVERT: A 630 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: A 655 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7639 (mmmt) REVERT: A 700 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4800 (mmt) REVERT: A 886 MET cc_start: 0.6738 (mtm) cc_final: 0.5814 (mmm) REVERT: A 982 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6656 (pt) REVERT: A 1086 GLU cc_start: 0.6539 (pm20) cc_final: 0.5855 (mm-30) outliers start: 56 outliers final: 32 residues processed: 168 average time/residue: 0.3970 time to fit residues: 73.2006 Evaluate side-chains 172 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 GLN A 692 GLN A 965 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135924 restraints weight = 13171.371| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.02 r_work: 0.3431 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11178 Z= 0.127 Angle : 0.482 6.389 15180 Z= 0.260 Chirality : 0.040 0.162 1735 Planarity : 0.003 0.044 1859 Dihedral : 10.463 131.556 1681 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.60 % Allowed : 15.25 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.24), residues: 1364 helix: 2.59 (0.19), residues: 770 sheet: -0.67 (0.41), residues: 152 loop : -0.79 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 594 TYR 0.010 0.001 TYR A 959 PHE 0.017 0.001 PHE A1052 TRP 0.014 0.001 TRP B 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00290 (11178) covalent geometry : angle 0.48191 (15180) hydrogen bonds : bond 0.04926 ( 661) hydrogen bonds : angle 3.78486 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.265 Fit side-chains REVERT: B 523 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.5681 (p90) REVERT: B 630 GLU cc_start: 0.7431 (tt0) cc_final: 0.7100 (tt0) REVERT: B 655 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7600 (mmmt) REVERT: B 692 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7033 (mp-120) REVERT: B 886 MET cc_start: 0.6579 (mtm) cc_final: 0.5725 (mmm) REVERT: B 943 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8241 (pt) REVERT: B 1086 GLU cc_start: 0.6631 (pm20) cc_final: 0.5984 (mm-30) REVERT: A 523 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.5571 (p90) REVERT: A 630 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: A 655 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7663 (mmmt) REVERT: A 700 MET cc_start: 0.4971 (OUTLIER) cc_final: 0.4603 (mmt) REVERT: A 886 MET cc_start: 0.6596 (mtm) cc_final: 0.5728 (mmm) REVERT: A 982 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6680 (pt) REVERT: A 1086 GLU cc_start: 0.6562 (pm20) cc_final: 0.5866 (mm-30) outliers start: 51 outliers final: 34 residues processed: 171 average time/residue: 0.3745 time to fit residues: 71.0119 Evaluate side-chains 174 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.4426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.170121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138411 restraints weight = 13141.884| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.98 r_work: 0.3454 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11178 Z= 0.104 Angle : 0.450 6.351 15180 Z= 0.242 Chirality : 0.039 0.157 1735 Planarity : 0.003 0.042 1859 Dihedral : 10.113 129.512 1681 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.60 % Allowed : 15.79 % Favored : 79.60 % 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: 1.95 (0.24), residues: 1364 helix: 2.74 (0.19), residues: 770 sheet: -0.43 (0.41), residues: 150 loop : -0.74 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.018 0.001 TYR A 827 PHE 0.014 0.001 PHE A1052 TRP 0.011 0.001 TRP A 806 HIS 0.003 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00221 (11178) covalent geometry : angle 0.45049 (15180) hydrogen bonds : bond 0.04311 ( 661) hydrogen bonds : angle 3.68430 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.316 Fit side-chains REVERT: B 523 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.5535 (p90) REVERT: B 630 GLU cc_start: 0.7440 (tt0) cc_final: 0.7117 (tt0) REVERT: B 655 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7651 (mmmt) REVERT: B 661 ASP cc_start: 0.7736 (m-30) cc_final: 0.7488 (m-30) REVERT: B 886 MET cc_start: 0.6675 (mtm) cc_final: 0.5836 (mmm) REVERT: B 943 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8289 (pt) REVERT: B 1086 GLU cc_start: 0.6618 (pm20) cc_final: 0.6022 (mm-30) REVERT: A 476 MET cc_start: 0.8071 (mtm) cc_final: 0.7763 (mtm) REVERT: A 523 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.5413 (p90) REVERT: A 630 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: A 655 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7664 (mmmt) REVERT: A 700 MET cc_start: 0.4928 (OUTLIER) cc_final: 0.4586 (mmt) REVERT: A 886 MET cc_start: 0.6714 (mtm) cc_final: 0.5861 (mmm) REVERT: A 982 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6694 (pt) REVERT: A 1086 GLU cc_start: 0.6559 (pm20) cc_final: 0.5903 (mm-30) outliers start: 51 outliers final: 30 residues processed: 176 average time/residue: 0.3570 time to fit residues: 69.6056 Evaluate side-chains 173 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 78 optimal weight: 0.0980 chunk 71 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1004 ASN A 692 GLN A1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133644 restraints weight = 13050.273| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.08 r_work: 0.3399 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11178 Z= 0.114 Angle : 0.463 6.384 15180 Z= 0.248 Chirality : 0.039 0.167 1735 Planarity : 0.003 0.039 1859 Dihedral : 10.031 130.860 1681 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.78 % Allowed : 15.79 % Favored : 79.42 % 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: 1.98 (0.23), residues: 1364 helix: 2.75 (0.18), residues: 770 sheet: -0.36 (0.41), residues: 150 loop : -0.73 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.011 0.001 TYR A 959 PHE 0.016 0.001 PHE A1052 TRP 0.013 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00254 (11178) covalent geometry : angle 0.46293 (15180) hydrogen bonds : bond 0.04537 ( 661) hydrogen bonds : angle 3.69135 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 0.436 Fit side-chains REVERT: B 523 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.5586 (p90) REVERT: B 630 GLU cc_start: 0.7400 (tt0) cc_final: 0.7065 (tt0) REVERT: B 655 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7554 (mmmt) REVERT: B 661 ASP cc_start: 0.7726 (m-30) cc_final: 0.7461 (m-30) REVERT: B 943 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8179 (pt) REVERT: B 1086 GLU cc_start: 0.6583 (pm20) cc_final: 0.5990 (mm-30) REVERT: A 476 MET cc_start: 0.8071 (mtm) cc_final: 0.7763 (mtm) REVERT: A 523 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.5575 (p90) REVERT: A 630 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: A 655 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7587 (mmmt) REVERT: A 700 MET cc_start: 0.5035 (OUTLIER) cc_final: 0.4684 (mmt) REVERT: A 876 MET cc_start: 0.7491 (tpp) cc_final: 0.7054 (mmt) REVERT: A 982 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6595 (pt) REVERT: A 1086 GLU cc_start: 0.6556 (pm20) cc_final: 0.5858 (mm-30) outliers start: 53 outliers final: 38 residues processed: 167 average time/residue: 0.4450 time to fit residues: 81.9075 Evaluate side-chains 178 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 92 optimal weight: 0.0040 chunk 128 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 GLN B1004 ASN A 692 GLN A1004 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135091 restraints weight = 13031.435| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.05 r_work: 0.3422 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11178 Z= 0.102 Angle : 0.448 6.389 15180 Z= 0.240 Chirality : 0.039 0.158 1735 Planarity : 0.003 0.039 1859 Dihedral : 9.895 128.965 1681 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.33 % Allowed : 16.16 % Favored : 79.51 % 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: 2.11 (0.23), residues: 1364 helix: 2.87 (0.18), residues: 770 sheet: -0.27 (0.42), residues: 150 loop : -0.70 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.017 0.001 TYR A 827 PHE 0.014 0.001 PHE A1052 TRP 0.011 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00222 (11178) covalent geometry : angle 0.44814 (15180) hydrogen bonds : bond 0.04157 ( 661) hydrogen bonds : angle 3.63512 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.449 Fit side-chains REVERT: B 523 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.5391 (p90) REVERT: B 630 GLU cc_start: 0.7407 (tt0) cc_final: 0.7087 (tt0) REVERT: B 655 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7691 (mmmt) REVERT: B 943 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8201 (pt) REVERT: B 1086 GLU cc_start: 0.6539 (pm20) cc_final: 0.5978 (mm-30) REVERT: A 476 MET cc_start: 0.8130 (mtm) cc_final: 0.7796 (mtm) REVERT: A 523 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.5438 (p90) REVERT: A 630 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6907 (tt0) REVERT: A 655 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7725 (mmmt) REVERT: A 700 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4758 (mmt) REVERT: A 982 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6601 (pt) REVERT: A 1086 GLU cc_start: 0.6526 (pm20) cc_final: 0.5970 (mm-30) REVERT: A 1124 PHE cc_start: 0.7844 (t80) cc_final: 0.7637 (t80) outliers start: 48 outliers final: 35 residues processed: 172 average time/residue: 0.4025 time to fit residues: 76.1394 Evaluate side-chains 178 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1004 ASN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130453 restraints weight = 13312.474| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.12 r_work: 0.3353 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11178 Z= 0.183 Angle : 0.560 9.603 15180 Z= 0.300 Chirality : 0.042 0.175 1735 Planarity : 0.004 0.038 1859 Dihedral : 10.459 133.006 1681 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.42 % Allowed : 16.25 % Favored : 79.33 % 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: 1.65 (0.23), residues: 1364 helix: 2.48 (0.18), residues: 770 sheet: -0.45 (0.41), residues: 150 loop : -0.86 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 594 TYR 0.017 0.002 TYR A 959 PHE 0.016 0.002 PHE A1052 TRP 0.019 0.002 TRP B 806 HIS 0.006 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00443 (11178) covalent geometry : angle 0.55958 (15180) hydrogen bonds : bond 0.05876 ( 661) hydrogen bonds : angle 3.93426 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 0.436 Fit side-chains REVERT: B 523 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.5859 (p90) REVERT: B 630 GLU cc_start: 0.7381 (tt0) cc_final: 0.7035 (tt0) REVERT: B 655 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7547 (mmmt) REVERT: B 943 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8135 (pt) REVERT: B 1086 GLU cc_start: 0.6682 (pm20) cc_final: 0.6105 (mm-30) REVERT: A 523 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.5828 (p90) REVERT: A 630 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: A 655 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7630 (mtpt) REVERT: A 700 MET cc_start: 0.5250 (OUTLIER) cc_final: 0.4952 (mmt) REVERT: A 712 MET cc_start: 0.8631 (mtp) cc_final: 0.8372 (mtm) REVERT: A 876 MET cc_start: 0.7446 (tpp) cc_final: 0.7122 (mmt) REVERT: A 982 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6543 (pt) REVERT: A 1086 GLU cc_start: 0.6655 (pm20) cc_final: 0.6085 (mm-30) outliers start: 49 outliers final: 34 residues processed: 165 average time/residue: 0.4728 time to fit residues: 85.9966 Evaluate side-chains 171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1004 ASN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131886 restraints weight = 13277.310| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.12 r_work: 0.3371 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11178 Z= 0.142 Angle : 0.508 10.409 15180 Z= 0.272 Chirality : 0.041 0.168 1735 Planarity : 0.004 0.039 1859 Dihedral : 10.356 131.471 1681 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.42 % Allowed : 16.43 % Favored : 79.15 % 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: 1.73 (0.23), residues: 1364 helix: 2.56 (0.18), residues: 770 sheet: -0.45 (0.41), residues: 150 loop : -0.86 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 594 TYR 0.017 0.001 TYR B 827 PHE 0.017 0.002 PHE A1052 TRP 0.015 0.001 TRP B 806 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00333 (11178) covalent geometry : angle 0.50803 (15180) hydrogen bonds : bond 0.05158 ( 661) hydrogen bonds : angle 3.83475 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.97 seconds wall clock time: 62 minutes 7.95 seconds (3727.95 seconds total)