Starting phenix.real_space_refine on Thu Jul 2 19:04:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k3t_36859/07_2026/8k3t_36859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3t_36859/07_2026/8k3t_36859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k3t_36859/07_2026/8k3t_36859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3t_36859/07_2026/8k3t_36859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3t_36859/07_2026/8k3t_36859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3t_36859/07_2026/8k3t_36859.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8k3t_36859/07_2026/8k3t_36859.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k3t_36859/07_2026/8k3t_36859.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.052 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 4 5.21 5 S 58 5.16 5 C 6178 2.51 5 N 1482 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4630 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 17, 'PHE:plan': 6, 'ARG:plan': 16, 'GLN:plan1': 6, 'ASN:plan1': 7, 'ASP:plan': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 283 Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4630 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 17, 'PHE:plan': 6, 'ARG:plan': 16, 'GLN:plan1': 6, 'ASN:plan1': 7, 'ASP:plan': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 283 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 1.58, per 1000 atoms: 0.17 Number of scatterers: 9410 At special positions: 0 Unit cell: (113.42, 109.18, 100.7, 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 58 16.00 P 6 15.00 Mg 4 11.99 O 1682 8.00 N 1482 7.00 C 6178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 333.6 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 67.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.876A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.538A pdb=" N TYR A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 478 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 516 removed outlier: 4.155A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.617A pdb=" N ARG A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 Processing helix chain 'A' and resid 610 through 618 removed outlier: 3.817A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 3.927A pdb=" N PHE A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 643 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 669 removed outlier: 3.539A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.753A 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 697 removed outlier: 3.748A pdb=" N GLY A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 715 through 726 removed outlier: 4.470A pdb=" N LEU A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.627A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.602A pdb=" N TRP A 779 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.829A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 861 through 893 removed outlier: 3.776A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 933 Processing helix chain 'A' and resid 942 through 955 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 1027 through 1060 removed outlier: 4.176A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1091 through 1130 removed outlier: 4.073A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.875A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.538A pdb=" N TYR B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 516 removed outlier: 4.154A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.615A pdb=" N ARG B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 610 through 618 removed outlier: 3.818A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.927A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 643 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 669 removed outlier: 3.540A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.749A pdb=" N GLY B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 715 through 726 removed outlier: 4.470A pdb=" N LEU B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.626A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.603A pdb=" N TRP B 779 " --> pdb=" O TYR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 Processing helix chain 'B' and resid 807 through 828 Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.829A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 861 through 893 removed outlier: 3.776A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 933 Processing helix chain 'B' and resid 942 through 955 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 1027 through 1060 removed outlier: 4.176A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1091 through 1130 removed outlier: 4.071A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 417 through 421 removed outlier: 3.683A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 493 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU A 568 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 495 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 629 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.770A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.682A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 493 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU B 568 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 495 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET B 449 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B 601 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 451 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY B 629 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 549 removed outlier: 4.769A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1629 1.32 - 1.45: 2673 1.45 - 1.57: 5244 1.57 - 1.69: 10 1.69 - 1.81: 86 Bond restraints: 9642 Sorted by residual: bond pdb=" O1A UDP B1502 " pdb=" PA UDP B1502 " ideal model delta sigma weight residual 1.482 1.527 -0.045 1.00e-02 1.00e+04 1.99e+01 bond pdb=" O1A UDP A1502 " pdb=" PA UDP A1502 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.92e+01 bond pdb=" N ILE A 493 " pdb=" CA ILE A 493 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N VAL B 533 " pdb=" CA VAL B 533 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.15e-02 7.56e+03 9.53e+00 bond pdb=" N ILE B 493 " pdb=" CA ILE B 493 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.37e+00 ... (remaining 9637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 12580 2.05 - 4.09: 515 4.09 - 6.14: 57 6.14 - 8.18: 16 8.18 - 10.23: 4 Bond angle restraints: 13172 Sorted by residual: angle pdb=" CA PHE B 831 " pdb=" C PHE B 831 " pdb=" N ASN B 832 " ideal model delta sigma weight residual 118.27 108.41 9.86 1.59e+00 3.96e-01 3.84e+01 angle pdb=" CA PHE A 831 " pdb=" C PHE A 831 " pdb=" N ASN A 832 " ideal model delta sigma weight residual 118.27 108.42 9.85 1.59e+00 3.96e-01 3.84e+01 angle pdb=" O5' UDP A1502 " pdb=" PA UDP A1502 " pdb=" O1A UDP A1502 " ideal model delta sigma weight residual 106.70 111.20 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" O5' UDP B1502 " pdb=" PA UDP B1502 " pdb=" O1A UDP B1502 " ideal model delta sigma weight residual 106.70 111.18 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" O2A UDP B1502 " pdb=" PA UDP B1502 " pdb=" O3A UDP B1502 " ideal model delta sigma weight residual 105.97 110.25 -4.28 1.00e+00 1.00e+00 1.83e+01 ... (remaining 13167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 5256 23.20 - 46.40: 210 46.40 - 69.59: 30 69.59 - 92.79: 6 92.79 - 115.99: 2 Dihedral angle restraints: 5504 sinusoidal: 1802 harmonic: 3702 Sorted by residual: dihedral pdb=" C27 POV B1503 " pdb=" C28 POV B1503 " pdb=" C29 POV B1503 " pdb="C210 POV B1503 " ideal model delta sinusoidal sigma weight residual 127.48 -116.53 -115.99 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C27 POV A1503 " pdb=" C28 POV A1503 " pdb=" C29 POV A1503 " pdb="C210 POV A1503 " ideal model delta sinusoidal sigma weight residual 127.48 -116.59 -115.93 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CA PHE A 911 " pdb=" C PHE A 911 " pdb=" N ARG A 912 " pdb=" CA ARG A 912 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 939 0.041 - 0.082: 444 0.082 - 0.124: 128 0.124 - 0.165: 29 0.165 - 0.206: 10 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA ILE B 719 " pdb=" N ILE B 719 " pdb=" C ILE B 719 " pdb=" CB ILE B 719 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 719 " pdb=" N ILE A 719 " pdb=" C ILE A 719 " pdb=" CB ILE A 719 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL A 421 " pdb=" N VAL A 421 " pdb=" C VAL A 421 " pdb=" CB VAL A 421 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1547 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1503 " -0.025 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" C29 POV A1503 " 0.059 2.00e-02 2.50e+03 pdb="C210 POV A1503 " -0.059 2.00e-02 2.50e+03 pdb="C211 POV A1503 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1503 " 0.025 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C29 POV B1503 " -0.059 2.00e-02 2.50e+03 pdb="C210 POV B1503 " 0.059 2.00e-02 2.50e+03 pdb="C211 POV B1503 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 606 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 607 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " 0.026 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1967 2.76 - 3.30: 10068 3.30 - 3.83: 15870 3.83 - 4.36: 17632 4.36 - 4.90: 29939 Nonbonded interactions: 75476 Sorted by model distance: nonbonded pdb=" O ALA A 511 " pdb=" OG SER A 515 " model vdw 2.225 3.040 nonbonded pdb=" O ALA B 511 " pdb=" OG SER B 515 " model vdw 2.225 3.040 nonbonded pdb=" OE2 GLU A1060 " pdb=" OG1 THR A1091 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU B1060 " pdb=" OG1 THR B1091 " model vdw 2.263 3.040 nonbonded pdb=" O1A UDP B1502 " pdb="MG MG B1504 " model vdw 2.287 2.170 ... (remaining 75471 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.630 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 0.081 9642 Z= 0.478 Angle : 0.929 10.229 13172 Z= 0.555 Chirality : 0.052 0.206 1550 Planarity : 0.005 0.047 1612 Dihedral : 13.196 115.988 3108 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.12 % Allowed : 1.34 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1234 helix: 1.11 (0.20), residues: 672 sheet: -0.96 (0.44), residues: 154 loop : -0.47 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 817 TYR 0.028 0.002 TYR B 878 PHE 0.021 0.002 PHE A1052 TRP 0.022 0.003 TRP A 806 HIS 0.006 0.002 HIS B 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00935 / 0.48 ( 9642) covalent geometry : angle 0.92936 / 0.56 (13172) hydrogen bonds : bond 0.14551 / 10.33 ( 625) hydrogen bonds : angle 7.05484 / 4.94 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASN cc_start: 0.3025 (OUTLIER) cc_final: 0.2570 (p0) REVERT: A 437 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8097 (mm110) REVERT: A 560 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8429 (tp40) REVERT: A 568 LEU cc_start: 0.7665 (tt) cc_final: 0.7193 (mp) REVERT: A 823 ILE cc_start: 0.9063 (tt) cc_final: 0.8791 (tt) REVERT: A 886 MET cc_start: 0.8323 (mtt) cc_final: 0.7679 (tmm) REVERT: B 411 ASN cc_start: 0.3117 (OUTLIER) cc_final: 0.2657 (p0) REVERT: B 437 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8137 (mm110) REVERT: B 560 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8454 (tp40) REVERT: B 568 LEU cc_start: 0.7621 (tt) cc_final: 0.7191 (mp) REVERT: B 823 ILE cc_start: 0.9066 (tt) cc_final: 0.8786 (tt) REVERT: B 886 MET cc_start: 0.8316 (mtt) cc_final: 0.7693 (tmm) outliers start: 10 outliers final: 0 residues processed: 157 average time/residue: 0.0648 time to fit residues: 15.3632 Evaluate side-chains 111 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain B residue 411 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN A1051 ASN B 411 ASN B1051 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.127687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094565 restraints weight = 19854.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098078 restraints weight = 8653.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100268 restraints weight = 5306.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101375 restraints weight = 4033.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.102231 restraints weight = 3517.146| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9642 Z= 0.145 Angle : 0.561 7.030 13172 Z= 0.302 Chirality : 0.041 0.157 1550 Planarity : 0.004 0.038 1612 Dihedral : 8.814 120.318 1398 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.89 % Allowed : 7.27 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1234 helix: 1.81 (0.19), residues: 742 sheet: -0.49 (0.45), residues: 152 loop : -0.59 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 758 TYR 0.017 0.002 TYR A 713 PHE 0.016 0.001 PHE B 864 TRP 0.010 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 9642) covalent geometry : angle 0.56071 / 0.30 (13172) hydrogen bonds : bond 0.05172 / 3.56 ( 625) hydrogen bonds : angle 4.73774 / 3.33 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.264 Fit side-chains REVERT: A 560 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8462 (tp40) REVERT: A 823 ILE cc_start: 0.9179 (tt) cc_final: 0.8926 (tt) REVERT: A 876 MET cc_start: 0.9016 (tpp) cc_final: 0.8783 (tpp) REVERT: A 879 MET cc_start: 0.8475 (ttp) cc_final: 0.8194 (ttp) REVERT: A 938 MET cc_start: 0.8740 (tpp) cc_final: 0.8502 (tpp) REVERT: B 543 MET cc_start: 0.6709 (pmm) cc_final: 0.6387 (ptp) REVERT: B 560 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8488 (tp40) REVERT: B 823 ILE cc_start: 0.9180 (tt) cc_final: 0.8932 (tt) REVERT: B 876 MET cc_start: 0.9012 (tpp) cc_final: 0.8780 (tpp) REVERT: B 879 MET cc_start: 0.8508 (ttp) cc_final: 0.8256 (ttp) REVERT: B 938 MET cc_start: 0.8752 (tpp) cc_final: 0.8395 (tpp) outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 0.0551 time to fit residues: 12.7249 Evaluate side-chains 115 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 HIS A 774 HIS B 582 HIS B 774 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.123842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090658 restraints weight = 20412.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.093868 restraints weight = 9125.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095948 restraints weight = 5639.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096867 restraints weight = 4285.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096867 restraints weight = 3756.542| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9642 Z= 0.245 Angle : 0.616 6.403 13172 Z= 0.327 Chirality : 0.043 0.170 1550 Planarity : 0.004 0.036 1612 Dihedral : 9.749 143.067 1394 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.24 % Allowed : 11.97 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1234 helix: 1.85 (0.19), residues: 730 sheet: -0.43 (0.45), residues: 152 loop : -0.71 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 758 TYR 0.013 0.002 TYR A 878 PHE 0.027 0.002 PHE A1052 TRP 0.019 0.002 TRP A 806 HIS 0.004 0.001 HIS B 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 ( 9642) covalent geometry : angle 0.61558 / 0.33 (13172) hydrogen bonds : bond 0.05034 / 3.48 ( 625) hydrogen bonds : angle 4.55749 / 3.21 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 HIS cc_start: 0.7388 (p-80) cc_final: 0.6615 (p-80) REVERT: A 476 MET cc_start: 0.8519 (mpp) cc_final: 0.7321 (mpp) REVERT: A 543 MET cc_start: 0.6752 (pmm) cc_final: 0.6411 (ptp) REVERT: A 560 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8522 (tp40) REVERT: A 1066 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8308 (t70) REVERT: B 543 MET cc_start: 0.6753 (pmm) cc_final: 0.6425 (ptp) REVERT: B 560 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8532 (tp40) REVERT: B 1066 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8313 (t70) outliers start: 20 outliers final: 11 residues processed: 117 average time/residue: 0.0480 time to fit residues: 9.2230 Evaluate side-chains 114 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.124994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.091420 restraints weight = 20888.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.094546 restraints weight = 9640.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096504 restraints weight = 6094.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097678 restraints weight = 4711.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098211 restraints weight = 4077.401| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9642 Z= 0.143 Angle : 0.503 5.916 13172 Z= 0.270 Chirality : 0.040 0.181 1550 Planarity : 0.003 0.035 1612 Dihedral : 9.642 141.917 1394 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.90 % Allowed : 13.87 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.25), residues: 1234 helix: 2.15 (0.19), residues: 740 sheet: -0.33 (0.45), residues: 152 loop : -0.78 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 436 TYR 0.012 0.001 TYR B 713 PHE 0.015 0.001 PHE A 864 TRP 0.014 0.001 TRP A 806 HIS 0.005 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9642) covalent geometry : angle 0.50294 / 0.27 (13172) hydrogen bonds : bond 0.04473 / 3.08 ( 625) hydrogen bonds : angle 4.29221 / 3.02 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7226 (tp-100) REVERT: A 543 MET cc_start: 0.6912 (pmm) cc_final: 0.6568 (ptp) REVERT: A 560 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8539 (tp40) REVERT: A 876 MET cc_start: 0.8986 (tpp) cc_final: 0.8590 (tpp) REVERT: A 1066 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8251 (t70) REVERT: B 437 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7552 (tp-100) REVERT: B 543 MET cc_start: 0.6722 (pmm) cc_final: 0.6416 (ptp) REVERT: B 560 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8521 (tp40) REVERT: B 876 MET cc_start: 0.8984 (tpp) cc_final: 0.8588 (tpp) REVERT: B 1066 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8243 (t70) outliers start: 17 outliers final: 12 residues processed: 122 average time/residue: 0.0546 time to fit residues: 10.9139 Evaluate side-chains 122 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 717 ASP Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.123887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090477 restraints weight = 20950.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093586 restraints weight = 9713.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.095548 restraints weight = 6138.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.096562 restraints weight = 4746.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.097296 restraints weight = 4158.622| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9642 Z= 0.166 Angle : 0.514 5.898 13172 Z= 0.276 Chirality : 0.040 0.190 1550 Planarity : 0.003 0.034 1612 Dihedral : 9.559 140.043 1394 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.24 % Allowed : 15.66 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.25), residues: 1234 helix: 2.10 (0.19), residues: 752 sheet: -0.27 (0.44), residues: 152 loop : -0.83 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 758 TYR 0.010 0.001 TYR A 613 PHE 0.020 0.001 PHE B1052 TRP 0.016 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 9642) covalent geometry : angle 0.51404 / 0.28 (13172) hydrogen bonds : bond 0.04411 / 3.05 ( 625) hydrogen bonds : angle 4.23801 / 2.97 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7238 (tp-100) REVERT: A 476 MET cc_start: 0.8528 (mpp) cc_final: 0.7641 (mpp) REVERT: A 543 MET cc_start: 0.6828 (pmm) cc_final: 0.6515 (ptp) REVERT: A 560 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8544 (tp40) REVERT: A 606 MET cc_start: 0.5872 (mtm) cc_final: 0.5186 (mtt) REVERT: A 938 MET cc_start: 0.8693 (tpp) cc_final: 0.7674 (tpp) REVERT: A 1066 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8168 (t70) REVERT: B 437 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7333 (tp-100) REVERT: B 543 MET cc_start: 0.6701 (pmm) cc_final: 0.6489 (ptp) REVERT: B 560 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8559 (tp40) REVERT: B 606 MET cc_start: 0.5897 (mtm) cc_final: 0.5230 (mtt) REVERT: B 646 LEU cc_start: 0.7880 (tp) cc_final: 0.7651 (tp) REVERT: B 938 MET cc_start: 0.8702 (tpp) cc_final: 0.7685 (tpp) outliers start: 20 outliers final: 15 residues processed: 121 average time/residue: 0.0637 time to fit residues: 12.2087 Evaluate side-chains 125 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 81 optimal weight: 0.0980 chunk 88 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 30.0000 chunk 83 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.127572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094194 restraints weight = 20589.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097449 restraints weight = 9519.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099513 restraints weight = 6035.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100734 restraints weight = 4640.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101214 restraints weight = 4012.697| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9642 Z= 0.101 Angle : 0.469 6.967 13172 Z= 0.247 Chirality : 0.039 0.198 1550 Planarity : 0.003 0.032 1612 Dihedral : 9.212 137.412 1394 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.35 % Allowed : 17.11 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1234 helix: 2.21 (0.19), residues: 756 sheet: -0.17 (0.45), residues: 152 loop : -0.83 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 758 TYR 0.010 0.001 TYR B 713 PHE 0.012 0.001 PHE A 864 TRP 0.010 0.001 TRP B 806 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 ( 9642) covalent geometry : angle 0.46932 / 0.25 (13172) hydrogen bonds : bond 0.03899 / 2.67 ( 625) hydrogen bonds : angle 4.05520 / 2.84 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7238 (tp-100) REVERT: A 476 MET cc_start: 0.8507 (mpp) cc_final: 0.7687 (mpp) REVERT: A 543 MET cc_start: 0.6900 (pmm) cc_final: 0.6614 (ptp) REVERT: A 560 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8533 (tp40) REVERT: A 606 MET cc_start: 0.5911 (mtm) cc_final: 0.5238 (mtt) REVERT: A 800 PHE cc_start: 0.8132 (t80) cc_final: 0.7831 (t80) REVERT: A 876 MET cc_start: 0.9024 (tpp) cc_final: 0.8741 (tpp) REVERT: A 886 MET cc_start: 0.7958 (tmm) cc_final: 0.7425 (tmm) REVERT: A 938 MET cc_start: 0.8693 (tpp) cc_final: 0.7771 (tpp) REVERT: A 1052 PHE cc_start: 0.8846 (t80) cc_final: 0.8464 (t80) REVERT: A 1066 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8249 (t70) REVERT: B 437 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7324 (tp-100) REVERT: B 476 MET cc_start: 0.8454 (mpp) cc_final: 0.7476 (mpp) REVERT: B 560 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8547 (tp40) REVERT: B 810 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8620 (m) REVERT: B 876 MET cc_start: 0.9016 (tpp) cc_final: 0.8737 (tpp) REVERT: B 938 MET cc_start: 0.8665 (tpp) cc_final: 0.7702 (tpp) REVERT: B 1052 PHE cc_start: 0.8849 (t80) cc_final: 0.8486 (t80) outliers start: 21 outliers final: 13 residues processed: 132 average time/residue: 0.0667 time to fit residues: 13.7034 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.124364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091198 restraints weight = 20958.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.094372 restraints weight = 9672.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096320 restraints weight = 6074.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.097517 restraints weight = 4686.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.098046 restraints weight = 4053.203| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9642 Z= 0.179 Angle : 0.541 7.608 13172 Z= 0.284 Chirality : 0.041 0.188 1550 Planarity : 0.003 0.033 1612 Dihedral : 9.317 133.380 1394 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.46 % Allowed : 17.90 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.25), residues: 1234 helix: 2.20 (0.19), residues: 756 sheet: -0.30 (0.45), residues: 152 loop : -0.86 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 758 TYR 0.019 0.001 TYR B 455 PHE 0.023 0.002 PHE B1052 TRP 0.016 0.001 TRP A 806 HIS 0.003 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 9642) covalent geometry : angle 0.54053 / 0.28 (13172) hydrogen bonds : bond 0.04214 / 2.90 ( 625) hydrogen bonds : angle 4.15384 / 2.92 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7245 (tp-100) REVERT: A 476 MET cc_start: 0.8490 (mpp) cc_final: 0.7631 (mpp) REVERT: A 543 MET cc_start: 0.6854 (pmm) cc_final: 0.6595 (ptp) REVERT: A 560 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8538 (tp40) REVERT: A 606 MET cc_start: 0.5933 (mtm) cc_final: 0.5238 (mtt) REVERT: A 886 MET cc_start: 0.7954 (tmm) cc_final: 0.7401 (tmm) REVERT: A 938 MET cc_start: 0.8773 (tpp) cc_final: 0.7894 (tpp) REVERT: B 437 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7291 (tp-100) REVERT: B 476 MET cc_start: 0.8366 (mpp) cc_final: 0.7266 (mpp) REVERT: B 560 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8553 (tp40) REVERT: B 606 MET cc_start: 0.6012 (mtm) cc_final: 0.5311 (mtt) REVERT: B 810 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8622 (m) REVERT: B 886 MET cc_start: 0.8089 (ttp) cc_final: 0.7568 (tmm) REVERT: B 925 TYR cc_start: 0.8135 (m-10) cc_final: 0.7928 (m-80) outliers start: 22 outliers final: 18 residues processed: 118 average time/residue: 0.0618 time to fit residues: 11.5994 Evaluate side-chains 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090780 restraints weight = 20894.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.093885 restraints weight = 9684.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.095887 restraints weight = 6136.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096829 restraints weight = 4736.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097663 restraints weight = 4167.304| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9642 Z= 0.163 Angle : 0.526 6.491 13172 Z= 0.277 Chirality : 0.040 0.181 1550 Planarity : 0.003 0.032 1612 Dihedral : 9.199 127.143 1394 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.68 % Allowed : 18.34 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1234 helix: 2.29 (0.19), residues: 746 sheet: -0.37 (0.44), residues: 152 loop : -0.79 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 758 TYR 0.016 0.001 TYR B 455 PHE 0.022 0.001 PHE B 772 TRP 0.015 0.001 TRP A 806 HIS 0.003 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9642) covalent geometry : angle 0.52567 / 0.28 (13172) hydrogen bonds : bond 0.04243 / 2.92 ( 625) hydrogen bonds : angle 4.13237 / 2.90 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7258 (tp-100) REVERT: A 476 MET cc_start: 0.8472 (mpp) cc_final: 0.7714 (mpp) REVERT: A 543 MET cc_start: 0.6830 (pmm) cc_final: 0.6580 (ptp) REVERT: A 560 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8512 (tp40) REVERT: A 810 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8634 (m) REVERT: A 876 MET cc_start: 0.9026 (tpp) cc_final: 0.8778 (tpp) REVERT: A 886 MET cc_start: 0.7935 (tmm) cc_final: 0.7370 (tmm) REVERT: A 938 MET cc_start: 0.8790 (tpp) cc_final: 0.7861 (tpp) REVERT: B 437 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7304 (tp-100) REVERT: B 560 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8542 (tp40) REVERT: B 606 MET cc_start: 0.5761 (mtm) cc_final: 0.5081 (mtt) REVERT: B 810 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8637 (m) REVERT: B 876 MET cc_start: 0.9029 (tpp) cc_final: 0.8784 (tpp) REVERT: B 886 MET cc_start: 0.8082 (ttp) cc_final: 0.7669 (tmm) REVERT: B 925 TYR cc_start: 0.8214 (m-10) cc_final: 0.7942 (m-80) REVERT: B 938 MET cc_start: 0.8426 (tpp) cc_final: 0.7521 (tpp) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.0650 time to fit residues: 12.7088 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.125120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.091676 restraints weight = 20672.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094849 restraints weight = 9527.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096784 restraints weight = 6040.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097950 restraints weight = 4694.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.098489 restraints weight = 4084.910| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9642 Z= 0.139 Angle : 0.529 10.021 13172 Z= 0.272 Chirality : 0.040 0.177 1550 Planarity : 0.003 0.033 1612 Dihedral : 9.067 122.146 1394 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.36 % Allowed : 18.12 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1234 helix: 2.30 (0.19), residues: 746 sheet: -0.47 (0.44), residues: 152 loop : -0.79 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 758 TYR 0.017 0.001 TYR B 455 PHE 0.019 0.001 PHE B 772 TRP 0.014 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9642) covalent geometry : angle 0.52932 / 0.27 (13172) hydrogen bonds : bond 0.04144 / 2.84 ( 625) hydrogen bonds : angle 4.13021 / 2.90 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7259 (tp-100) REVERT: A 476 MET cc_start: 0.8477 (mpp) cc_final: 0.7709 (mpp) REVERT: A 543 MET cc_start: 0.6864 (pmm) cc_final: 0.6614 (ptp) REVERT: A 606 MET cc_start: 0.5925 (mtm) cc_final: 0.5230 (mtt) REVERT: A 800 PHE cc_start: 0.8168 (t80) cc_final: 0.7861 (t80) REVERT: A 810 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8622 (m) REVERT: A 876 MET cc_start: 0.8997 (tpp) cc_final: 0.8715 (tpp) REVERT: A 886 MET cc_start: 0.7962 (tmm) cc_final: 0.7391 (tmm) REVERT: B 437 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7324 (tp-100) REVERT: B 560 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8541 (tp40) REVERT: B 606 MET cc_start: 0.5688 (mtm) cc_final: 0.5020 (mtt) REVERT: B 800 PHE cc_start: 0.8139 (t80) cc_final: 0.7849 (t80) REVERT: B 810 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8622 (m) REVERT: B 876 MET cc_start: 0.8995 (tpp) cc_final: 0.8717 (tpp) REVERT: B 886 MET cc_start: 0.8151 (ttp) cc_final: 0.7697 (tmm) outliers start: 30 outliers final: 26 residues processed: 126 average time/residue: 0.0556 time to fit residues: 11.1179 Evaluate side-chains 135 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.129261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096284 restraints weight = 20137.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099998 restraints weight = 8756.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102281 restraints weight = 5279.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.103666 restraints weight = 3941.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104285 restraints weight = 3358.086| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9642 Z= 0.103 Angle : 0.491 7.036 13172 Z= 0.253 Chirality : 0.039 0.183 1550 Planarity : 0.003 0.032 1612 Dihedral : 8.686 112.207 1394 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.01 % Allowed : 19.35 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1234 helix: 2.40 (0.19), residues: 744 sheet: -0.37 (0.44), residues: 152 loop : -0.72 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.023 0.001 TYR B 925 PHE 0.016 0.001 PHE B 772 TRP 0.012 0.001 TRP A 806 HIS 0.007 0.001 HIS B 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 9642) covalent geometry : angle 0.49148 / 0.25 (13172) hydrogen bonds : bond 0.03685 / 2.52 ( 625) hydrogen bonds : angle 3.97214 / 2.79 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.5248 (tpt) cc_final: 0.4937 (tmm) REVERT: A 437 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7267 (tp-100) REVERT: A 606 MET cc_start: 0.5800 (mtm) cc_final: 0.5114 (mtt) REVERT: A 800 PHE cc_start: 0.8027 (t80) cc_final: 0.7726 (t80) REVERT: A 886 MET cc_start: 0.8019 (tmm) cc_final: 0.7450 (tmm) REVERT: A 938 MET cc_start: 0.8347 (tpp) cc_final: 0.7813 (tpp) REVERT: B 437 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7356 (tp-100) REVERT: B 560 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8517 (tp40) REVERT: B 606 MET cc_start: 0.5459 (mtm) cc_final: 0.4860 (mtt) REVERT: B 886 MET cc_start: 0.8188 (ttp) cc_final: 0.7729 (tmm) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 0.0581 time to fit residues: 11.2815 Evaluate side-chains 120 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1046 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 106 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 44 optimal weight: 0.0670 chunk 70 optimal weight: 7.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.129345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.096667 restraints weight = 20223.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100326 restraints weight = 8810.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102605 restraints weight = 5362.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103945 restraints weight = 4016.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104506 restraints weight = 3417.535| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9642 Z= 0.113 Angle : 0.516 7.328 13172 Z= 0.263 Chirality : 0.039 0.179 1550 Planarity : 0.003 0.032 1612 Dihedral : 7.768 87.918 1394 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.57 % Allowed : 20.58 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1234 helix: 2.34 (0.19), residues: 748 sheet: -0.34 (0.43), residues: 152 loop : -0.63 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.034 0.001 TYR B 925 PHE 0.020 0.001 PHE B1052 TRP 0.013 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9642) covalent geometry : angle 0.51628 / 0.26 (13172) hydrogen bonds : bond 0.03785 / 2.61 ( 625) hydrogen bonds : angle 3.98141 / 2.79 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.25 seconds wall clock time: 25 minutes 5.49 seconds (1505.49 seconds total)