Starting phenix.real_space_refine on Wed May 14 04:08:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3w_36863/05_2025/8k3w_36863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3w_36863/05_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_36863/05_2025/8k3w_36863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3w_36863/05_2025/8k3w_36863.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3w_36863/05_2025/8k3w_36863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3w_36863/05_2025/8k3w_36863.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} 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: 7.70, per 1000 atoms: 0.71 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: 3.21 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.43 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: 3.46 Time building geometry restraints manager: 3.66 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 1127 or resid 1501 thro \ ugh 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 11 \ 27 or resid 1501 through 1503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.180 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- 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 : 10.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), 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 TRP 0.016 0.002 TRP A 779 HIS 0.004 0.001 HIS B 783 PHE 0.020 0.002 PHE B 885 TYR 0.040 0.002 TYR A 696 ARG 0.004 0.001 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.16243 ( 661) hydrogen bonds : angle 6.81741 ( 1890) covalent geometry : bond 0.00881 (11178) covalent geometry : angle 1.12349 (15180) *********************** 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 : 1.140 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: 1.0137 time to fit residues: 292.5259 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 : 1.128 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3992 r_free = 0.3992 target = 0.172762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139733 restraints weight = 13070.123| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.05 r_work: 0.3477 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11178 Z= 0.123 Angle : 0.527 9.895 15180 Z= 0.279 Chirality : 0.040 0.152 1735 Planarity : 0.004 0.043 1859 Dihedral : 11.212 149.955 1683 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.34 % Allowed : 12.73 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1364 helix: 2.28 (0.19), residues: 760 sheet: -1.01 (0.44), residues: 132 loop : -0.58 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.005 0.001 HIS A 459 PHE 0.019 0.002 PHE A1052 TYR 0.016 0.001 TYR A 827 ARG 0.004 0.001 ARG B 759 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 661) hydrogen bonds : angle 4.30286 ( 1890) covalent geometry : bond 0.00265 (11178) covalent geometry : angle 0.52686 (15180) *********************** 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 195 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.178 Fit side-chains REVERT: B 579 ILE cc_start: 0.8169 (tt) cc_final: 0.7904 (mm) REVERT: B 594 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.8007 (mpt-90) REVERT: B 655 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7537 (mmmt) REVERT: B 700 MET cc_start: 0.2847 (tmm) cc_final: 0.1792 (mmm) REVERT: B 932 TYR cc_start: 0.7351 (t80) cc_final: 0.6906 (t80) REVERT: B 943 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8004 (pt) REVERT: A 579 ILE cc_start: 0.8146 (tt) cc_final: 0.7857 (mm) REVERT: A 594 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.8036 (mpt-90) REVERT: A 655 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7589 (mmmt) REVERT: A 692 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7546 (tp40) REVERT: A 717 ASP cc_start: 0.4091 (t0) cc_final: 0.3635 (t0) REVERT: A 886 MET cc_start: 0.7077 (mtm) cc_final: 0.6210 (mmm) REVERT: A 932 TYR cc_start: 0.7328 (t80) cc_final: 0.6874 (t80) outliers start: 37 outliers final: 9 residues processed: 182 average time/residue: 0.8881 time to fit residues: 178.9199 Evaluate side-chains 141 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 594 ARG 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 594 ARG 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 948 LEU 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 3 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 934 GLN A 398 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.167161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133858 restraints weight = 13295.314| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.07 r_work: 0.3397 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11178 Z= 0.159 Angle : 0.545 6.052 15180 Z= 0.294 Chirality : 0.041 0.157 1735 Planarity : 0.004 0.045 1859 Dihedral : 10.704 137.611 1681 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.78 % Allowed : 13.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1364 helix: 2.40 (0.19), residues: 758 sheet: -0.63 (0.43), residues: 148 loop : -0.64 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 806 HIS 0.004 0.001 HIS B 459 PHE 0.017 0.002 PHE A1052 TYR 0.013 0.002 TYR A 827 ARG 0.004 0.001 ARG B 718 Details of bonding type rmsd hydrogen bonds : bond 0.05846 ( 661) hydrogen bonds : angle 4.15575 ( 1890) covalent geometry : bond 0.00365 (11178) covalent geometry : angle 0.54483 (15180) *********************** 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 196 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 1.374 Fit side-chains REVERT: B 594 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8138 (mpt-90) REVERT: B 631 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7210 (tp) REVERT: B 655 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7518 (mmmt) REVERT: B 932 TYR cc_start: 0.7271 (t80) cc_final: 0.6876 (t80) REVERT: B 943 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8208 (pt) REVERT: A 594 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8117 (mpt-90) REVERT: A 655 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7551 (mmmt) REVERT: A 692 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7553 (tp40) REVERT: A 700 MET cc_start: 0.5206 (OUTLIER) cc_final: 0.4928 (mpt) REVERT: A 932 TYR cc_start: 0.7263 (t80) cc_final: 0.6873 (t80) REVERT: A 982 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6685 (pt) outliers start: 53 outliers final: 24 residues processed: 172 average time/residue: 0.9583 time to fit residues: 181.9011 Evaluate side-chains 161 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 594 ARG Chi-restraints excluded: chain B residue 631 ILE 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 967 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 446 THR Chi-restraints excluded: chain A residue 594 ARG 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 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 967 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 120 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 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 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133438 restraints weight = 13044.030| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.96 r_work: 0.3445 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11178 Z= 0.140 Angle : 0.513 7.719 15180 Z= 0.275 Chirality : 0.040 0.160 1735 Planarity : 0.004 0.044 1859 Dihedral : 10.506 133.163 1681 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.69 % Allowed : 13.81 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1364 helix: 2.51 (0.19), residues: 762 sheet: -0.47 (0.43), residues: 148 loop : -0.62 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 806 HIS 0.004 0.001 HIS B 459 PHE 0.023 0.002 PHE B1124 TYR 0.010 0.001 TYR A 713 ARG 0.003 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.05186 ( 661) hydrogen bonds : angle 3.95722 ( 1890) covalent geometry : bond 0.00325 (11178) covalent geometry : angle 0.51329 (15180) *********************** 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 177 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 523 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.5680 (p90) REVERT: B 655 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7631 (mmmt) REVERT: B 886 MET cc_start: 0.6698 (mtm) cc_final: 0.5828 (mmm) REVERT: B 943 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8238 (pt) REVERT: A 523 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.5659 (p90) REVERT: A 655 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7789 (mtpt) REVERT: A 886 MET cc_start: 0.6727 (mtm) cc_final: 0.5834 (mmm) REVERT: A 982 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6579 (pt) outliers start: 52 outliers final: 26 residues processed: 157 average time/residue: 0.9483 time to fit residues: 164.3695 Evaluate side-chains 156 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 532 LYS 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 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 391 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 535 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 57 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 692 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136186 restraints weight = 13115.605| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.99 r_work: 0.3437 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4386 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= 0.135 Angle : 0.496 6.913 15180 Z= 0.269 Chirality : 0.040 0.157 1735 Planarity : 0.003 0.043 1859 Dihedral : 10.431 132.440 1681 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.33 % Allowed : 14.53 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1364 helix: 2.53 (0.19), residues: 770 sheet: -0.50 (0.43), residues: 148 loop : -0.70 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 806 HIS 0.004 0.001 HIS B 459 PHE 0.017 0.002 PHE A1052 TYR 0.017 0.001 TYR B 827 ARG 0.002 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.05118 ( 661) hydrogen bonds : angle 3.87857 ( 1890) covalent geometry : bond 0.00312 (11178) covalent geometry : angle 0.49630 (15180) *********************** 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 171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 655 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7652 (mmmt) REVERT: B 886 MET cc_start: 0.6721 (mtm) cc_final: 0.5841 (mmm) REVERT: B 943 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8244 (pt) REVERT: A 655 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7713 (mmmt) REVERT: A 700 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4753 (mmt) REVERT: A 886 MET cc_start: 0.6733 (mtm) cc_final: 0.5847 (mmm) REVERT: A 982 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6569 (pt) outliers start: 48 outliers final: 29 residues processed: 156 average time/residue: 0.9524 time to fit residues: 164.4293 Evaluate side-chains 151 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 532 LYS 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 535 MET 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 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 64 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 108 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 0.0170 chunk 13 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN B 545 ASN B 658 ASN B 692 GLN A 545 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.173562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141120 restraints weight = 13167.631| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.04 r_work: 0.3479 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11178 Z= 0.096 Angle : 0.440 6.377 15180 Z= 0.236 Chirality : 0.038 0.152 1735 Planarity : 0.003 0.042 1859 Dihedral : 10.010 128.055 1681 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.79 % Allowed : 16.16 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1364 helix: 2.83 (0.19), residues: 770 sheet: -0.50 (0.42), residues: 152 loop : -0.57 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 806 HIS 0.003 0.001 HIS B 828 PHE 0.013 0.001 PHE A1052 TYR 0.010 0.001 TYR A 713 ARG 0.003 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 661) hydrogen bonds : angle 3.67625 ( 1890) covalent geometry : bond 0.00202 (11178) covalent geometry : angle 0.43975 (15180) *********************** 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 184 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: B 523 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.5418 (p90) REVERT: B 655 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7732 (mmmt) REVERT: B 943 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8290 (pt) REVERT: A 523 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.5522 (p90) REVERT: A 700 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.4731 (mmt) REVERT: A 982 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6610 (pt) REVERT: A 1086 GLU cc_start: 0.6428 (pm20) cc_final: 0.5677 (mm-30) outliers start: 42 outliers final: 21 residues processed: 169 average time/residue: 0.9100 time to fit residues: 170.6122 Evaluate side-chains 160 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 692 GLN 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 B residue 1061 THR 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 535 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 700 MET 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 98 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.167875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135150 restraints weight = 13396.196| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.02 r_work: 0.3429 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11178 Z= 0.149 Angle : 0.511 6.531 15180 Z= 0.274 Chirality : 0.040 0.156 1735 Planarity : 0.004 0.037 1859 Dihedral : 10.237 133.442 1681 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.24 % Allowed : 16.97 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1364 helix: 2.62 (0.18), residues: 770 sheet: -0.55 (0.42), residues: 152 loop : -0.65 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 806 HIS 0.004 0.001 HIS B 459 PHE 0.017 0.002 PHE B1052 TYR 0.015 0.001 TYR B 827 ARG 0.004 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.05271 ( 661) hydrogen bonds : angle 3.83721 ( 1890) covalent geometry : bond 0.00350 (11178) covalent geometry : angle 0.51128 (15180) *********************** 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 178 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: B 523 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.5373 (p90) REVERT: B 655 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7730 (mmmt) REVERT: B 943 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8270 (pt) REVERT: A 523 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.5597 (p90) REVERT: A 700 MET cc_start: 0.4969 (OUTLIER) cc_final: 0.4597 (mmt) REVERT: A 982 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6613 (pt) REVERT: A 1086 GLU cc_start: 0.6669 (pm20) cc_final: 0.5893 (mm-30) outliers start: 47 outliers final: 30 residues processed: 161 average time/residue: 0.9193 time to fit residues: 163.8124 Evaluate side-chains 164 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 532 LYS 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 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 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 640 VAL Chi-restraints excluded: chain A residue 642 LEU 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 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 50 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1004 ASN A 965 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136215 restraints weight = 13105.751| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.00 r_work: 0.3435 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11178 Z= 0.133 Angle : 0.493 6.348 15180 Z= 0.265 Chirality : 0.040 0.160 1735 Planarity : 0.003 0.037 1859 Dihedral : 10.197 131.734 1681 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.42 % Allowed : 16.70 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1364 helix: 2.64 (0.18), residues: 770 sheet: -0.50 (0.42), residues: 150 loop : -0.68 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 806 HIS 0.003 0.001 HIS B 828 PHE 0.017 0.001 PHE A1052 TYR 0.009 0.001 TYR B 797 ARG 0.004 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 661) hydrogen bonds : angle 3.79711 ( 1890) covalent geometry : bond 0.00308 (11178) covalent geometry : angle 0.49317 (15180) *********************** 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 180 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: B 523 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.5518 (p90) REVERT: B 655 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7698 (mmmt) REVERT: B 692 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: B 876 MET cc_start: 0.7478 (tpp) cc_final: 0.7209 (mmt) REVERT: B 943 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8278 (pt) REVERT: A 476 MET cc_start: 0.7938 (mtm) cc_final: 0.7641 (mtm) REVERT: A 523 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.5598 (p90) REVERT: A 700 MET cc_start: 0.4974 (OUTLIER) cc_final: 0.4619 (mmt) REVERT: A 876 MET cc_start: 0.7455 (tpp) cc_final: 0.7191 (mmt) REVERT: A 982 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6613 (pt) REVERT: A 1086 GLU cc_start: 0.6513 (pm20) cc_final: 0.5805 (mm-30) outliers start: 49 outliers final: 35 residues processed: 159 average time/residue: 0.9947 time to fit residues: 175.1221 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 : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 532 LYS 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 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 386 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 509 SER 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 640 VAL Chi-restraints excluded: chain A residue 642 LEU 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 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 1089 LEU 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 2 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS B 692 GLN B1004 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132969 restraints weight = 13281.765| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.11 r_work: 0.3385 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11178 Z= 0.135 Angle : 0.496 6.493 15180 Z= 0.267 Chirality : 0.040 0.161 1735 Planarity : 0.003 0.037 1859 Dihedral : 10.189 131.421 1681 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.60 % Allowed : 16.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1364 helix: 2.63 (0.18), residues: 770 sheet: -0.53 (0.42), residues: 150 loop : -0.69 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.003 0.001 HIS B 828 PHE 0.017 0.002 PHE A1052 TYR 0.017 0.001 TYR B 827 ARG 0.005 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 661) hydrogen bonds : angle 3.79353 ( 1890) covalent geometry : bond 0.00313 (11178) covalent geometry : angle 0.49611 (15180) *********************** 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 180 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 1.222 Fit side-chains REVERT: B 523 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.5449 (p90) REVERT: B 655 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7567 (mmmt) REVERT: B 876 MET cc_start: 0.7414 (tpp) cc_final: 0.7109 (mmt) REVERT: B 943 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8183 (pt) REVERT: B 1086 GLU cc_start: 0.6662 (pm20) cc_final: 0.5963 (mm-30) REVERT: A 523 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.5587 (p90) REVERT: A 700 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4820 (mmt) REVERT: A 876 MET cc_start: 0.7425 (tpp) cc_final: 0.7123 (mmt) REVERT: A 982 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6519 (pt) REVERT: A 1086 GLU cc_start: 0.6672 (pm20) cc_final: 0.6000 (mm-30) outliers start: 51 outliers final: 40 residues processed: 162 average time/residue: 0.8907 time to fit residues: 160.2197 Evaluate side-chains 171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 532 LYS 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 784 ASN Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 914 ILE 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 509 SER 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 640 VAL Chi-restraints excluded: chain A residue 642 LEU 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 745 ASP 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 914 ILE 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 1089 LEU 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 72 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1004 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132717 restraints weight = 13147.586| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.13 r_work: 0.3381 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 11178 Z= 0.200 Angle : 0.835 59.200 15180 Z= 0.480 Chirality : 0.041 0.203 1735 Planarity : 0.004 0.098 1859 Dihedral : 10.194 131.564 1681 Min Nonbonded Distance : 1.391 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.06 % Allowed : 16.52 % Favored : 79.42 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.23), residues: 1364 helix: 2.62 (0.18), residues: 770 sheet: -0.53 (0.42), residues: 150 loop : -0.71 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 806 HIS 0.003 0.001 HIS B 828 PHE 0.017 0.002 PHE A1052 TYR 0.011 0.001 TYR A 827 ARG 0.005 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 661) hydrogen bonds : angle 3.80760 ( 1890) covalent geometry : bond 0.00453 (11178) covalent geometry : angle 0.83502 (15180) ********************** 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 171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 1.192 Fit side-chains REVERT: B 523 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.5468 (p90) REVERT: B 655 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7561 (mmmt) REVERT: B 876 MET cc_start: 0.7417 (tpp) cc_final: 0.7116 (mmt) REVERT: B 943 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8181 (pt) REVERT: B 1086 GLU cc_start: 0.6662 (pm20) cc_final: 0.5959 (mm-30) REVERT: A 523 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.5594 (p90) REVERT: A 700 MET cc_start: 0.5143 (OUTLIER) cc_final: 0.4814 (mmt) REVERT: A 876 MET cc_start: 0.7429 (tpp) cc_final: 0.7130 (mmt) REVERT: A 982 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6529 (pt) REVERT: A 1086 GLU cc_start: 0.6664 (pm20) cc_final: 0.5984 (mm-30) outliers start: 45 outliers final: 36 residues processed: 156 average time/residue: 0.8963 time to fit residues: 155.4760 Evaluate side-chains 167 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 532 LYS 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 914 ILE 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 509 SER 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 640 VAL Chi-restraints excluded: chain A residue 642 LEU 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 745 ASP 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 914 ILE 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 1089 LEU 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 104 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 93 optimal weight: 0.0870 chunk 84 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1004 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132763 restraints weight = 13078.753| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.11 r_work: 0.3383 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 11178 Z= 0.200 Angle : 0.835 59.200 15180 Z= 0.480 Chirality : 0.041 0.203 1735 Planarity : 0.004 0.098 1859 Dihedral : 10.194 131.564 1681 Min Nonbonded Distance : 1.391 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.88 % Allowed : 16.79 % Favored : 79.33 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.23), residues: 1364 helix: 2.62 (0.18), residues: 770 sheet: -0.53 (0.42), residues: 150 loop : -0.71 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 806 HIS 0.003 0.001 HIS B 828 PHE 0.017 0.002 PHE A1052 TYR 0.011 0.001 TYR A 827 ARG 0.005 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 661) hydrogen bonds : angle 3.80760 ( 1890) covalent geometry : bond 0.00453 (11178) covalent geometry : angle 0.83502 (15180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7746.94 seconds wall clock time: 134 minutes 14.65 seconds (8054.65 seconds total)