Starting phenix.real_space_refine on Sat Aug 23 04:53:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3t_36859/08_2025/8k3t_36859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3t_36859/08_2025/8k3t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3t_36859/08_2025/8k3t_36859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3t_36859/08_2025/8k3t_36859.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3t_36859/08_2025/8k3t_36859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3t_36859/08_2025/8k3t_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-2.0-5787/lib/python3.9/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: 2.49, per 1000 atoms: 0.26 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: 1.06 Conformation dependent library (CDL) restraints added in 384.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.36 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: 1.69 Time building geometry restraints manager: 1.33 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: 5282 23.20 - 46.40: 230 46.40 - 69.59: 42 69.59 - 92.79: 24 92.79 - 115.99: 2 Dihedral angle restraints: 5580 sinusoidal: 1878 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 5577 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: 0.02 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.070 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 15.004 115.988 3184 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 aren 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 covalent geometry : bond 0.00935 ( 9642) covalent geometry : angle 0.92936 (13172) hydrogen bonds : bond 0.14551 ( 625) hydrogen bonds : angle 7.05484 ( 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 : 0.380 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: 0.8779 (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: 0.0843 time to fit residues: 19.7110 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 : 0.290 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3955 r_free = 0.3955 target = 0.127554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094350 restraints weight = 19844.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097854 restraints weight = 8689.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100047 restraints weight = 5334.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.100897 restraints weight = 4064.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101949 restraints weight = 3600.257| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9642 Z= 0.147 Angle : 0.562 6.898 13172 Z= 0.305 Chirality : 0.041 0.155 1550 Planarity : 0.004 0.040 1612 Dihedral : 12.851 120.281 1474 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.89 % Allowed : 6.82 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.25), residues: 1234 helix: 1.80 (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 B 713 PHE 0.017 0.001 PHE B 864 TRP 0.011 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9642) covalent geometry : angle 0.56225 (13172) hydrogen bonds : bond 0.05286 ( 625) hydrogen bonds : angle 4.78502 ( 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 : 0.370 Fit side-chains REVERT: A 560 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8460 (tp40) REVERT: A 823 ILE cc_start: 0.9177 (tt) cc_final: 0.8925 (tt) REVERT: A 876 MET cc_start: 0.9012 (tpp) cc_final: 0.8778 (tpp) REVERT: A 879 MET cc_start: 0.8484 (ttp) cc_final: 0.8207 (ttp) REVERT: A 938 MET cc_start: 0.8719 (tpp) cc_final: 0.8492 (tpp) REVERT: B 543 MET cc_start: 0.6737 (pmm) cc_final: 0.6394 (ptp) REVERT: B 560 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8509 (tp40) REVERT: B 823 ILE cc_start: 0.9182 (tt) cc_final: 0.8935 (tt) REVERT: B 876 MET cc_start: 0.9009 (tpp) cc_final: 0.8776 (tpp) REVERT: B 879 MET cc_start: 0.8479 (ttp) cc_final: 0.8202 (ttp) REVERT: B 938 MET cc_start: 0.8735 (tpp) cc_final: 0.8487 (tpp) outliers start: 8 outliers final: 6 residues processed: 144 average time/residue: 0.0719 time to fit residues: 16.5043 Evaluate side-chains 116 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 804 ILE 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: 1.9990 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: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS A 774 HIS B 774 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.122369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089236 restraints weight = 20636.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.092366 restraints weight = 9303.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094341 restraints weight = 5819.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095274 restraints weight = 4467.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096060 restraints weight = 3927.913| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9642 Z= 0.302 Angle : 0.680 6.606 13172 Z= 0.363 Chirality : 0.045 0.166 1550 Planarity : 0.004 0.042 1612 Dihedral : 13.896 148.215 1470 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.24 % Allowed : 12.75 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.24), residues: 1234 helix: 1.52 (0.19), residues: 742 sheet: -0.58 (0.45), residues: 152 loop : -0.84 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 758 TYR 0.016 0.002 TYR A 878 PHE 0.031 0.002 PHE A1052 TRP 0.022 0.002 TRP A 806 HIS 0.005 0.002 HIS B 937 Details of bonding type rmsd covalent geometry : bond 0.00705 ( 9642) covalent geometry : angle 0.67975 (13172) hydrogen bonds : bond 0.05350 ( 625) hydrogen bonds : angle 4.72717 ( 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 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 543 MET cc_start: 0.6743 (pmm) cc_final: 0.6404 (ptp) REVERT: A 560 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8522 (tp40) REVERT: A 646 LEU cc_start: 0.8088 (tp) cc_final: 0.7879 (tp) REVERT: A 1066 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8324 (t70) REVERT: B 476 MET cc_start: 0.8527 (mpp) cc_final: 0.7412 (mpp) REVERT: B 543 MET cc_start: 0.6646 (pmm) cc_final: 0.6335 (ptp) REVERT: B 560 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8535 (tp40) REVERT: B 1066 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8336 (t70) outliers start: 20 outliers final: 11 residues processed: 118 average time/residue: 0.0705 time to fit residues: 13.3502 Evaluate side-chains 116 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 8.9990 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 HIS B 832 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.126405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092967 restraints weight = 20809.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096169 restraints weight = 9585.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.098159 restraints weight = 6047.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099340 restraints weight = 4672.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.099888 restraints weight = 4048.753| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9642 Z= 0.115 Angle : 0.487 6.028 13172 Z= 0.262 Chirality : 0.040 0.187 1550 Planarity : 0.003 0.033 1612 Dihedral : 13.180 145.697 1470 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.90 % Allowed : 14.09 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.25), residues: 1234 helix: 2.18 (0.19), residues: 740 sheet: -0.29 (0.45), residues: 152 loop : -0.77 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 758 TYR 0.012 0.001 TYR B 713 PHE 0.014 0.001 PHE A 864 TRP 0.011 0.001 TRP B 806 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9642) covalent geometry : angle 0.48743 (13172) hydrogen bonds : bond 0.04298 ( 625) hydrogen bonds : angle 4.24525 ( 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 140 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.369 Fit side-chains REVERT: A 437 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7351 (tp-100) REVERT: A 476 MET cc_start: 0.8515 (mpp) cc_final: 0.7386 (mpp) REVERT: A 543 MET cc_start: 0.6952 (pmm) cc_final: 0.6602 (ptp) REVERT: A 560 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8535 (tp40) REVERT: A 876 MET cc_start: 0.9048 (tpp) cc_final: 0.8655 (tpp) REVERT: A 1052 PHE cc_start: 0.8883 (t80) cc_final: 0.8512 (t80) REVERT: B 437 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7545 (tp-100) REVERT: B 476 MET cc_start: 0.8600 (mpp) cc_final: 0.7612 (mpp) REVERT: B 543 MET cc_start: 0.6756 (pmm) cc_final: 0.6445 (ptp) REVERT: B 560 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8515 (tp40) REVERT: B 876 MET cc_start: 0.9035 (tpp) cc_final: 0.8654 (tpp) REVERT: B 1052 PHE cc_start: 0.8881 (t80) cc_final: 0.8519 (t80) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 0.0674 time to fit residues: 14.0044 Evaluate side-chains 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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: 0.0030 chunk 30 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.125964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092753 restraints weight = 20708.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.095922 restraints weight = 9577.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097923 restraints weight = 6054.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.099085 restraints weight = 4668.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.099621 restraints weight = 4046.847| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9642 Z= 0.124 Angle : 0.486 6.382 13172 Z= 0.263 Chirality : 0.040 0.188 1550 Planarity : 0.003 0.033 1612 Dihedral : 12.916 140.096 1470 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.79 % Allowed : 15.88 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.25), residues: 1234 helix: 2.19 (0.19), residues: 750 sheet: -0.20 (0.44), residues: 152 loop : -0.84 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.011 0.001 TYR B 713 PHE 0.016 0.001 PHE A1052 TRP 0.012 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9642) covalent geometry : angle 0.48573 (13172) hydrogen bonds : bond 0.04158 ( 625) hydrogen bonds : angle 4.13688 ( 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 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.415 Fit side-chains REVERT: A 437 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7306 (tp-100) REVERT: A 476 MET cc_start: 0.8508 (mpp) cc_final: 0.7579 (mpp) REVERT: A 543 MET cc_start: 0.6881 (pmm) cc_final: 0.6562 (ptp) REVERT: A 560 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8533 (tp40) REVERT: A 1066 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8215 (t70) REVERT: B 437 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7371 (tp-100) REVERT: B 476 MET cc_start: 0.8551 (mpp) cc_final: 0.7630 (mpp) REVERT: B 543 MET cc_start: 0.6756 (pmm) cc_final: 0.6540 (ptp) REVERT: B 560 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8512 (tp40) REVERT: B 606 MET cc_start: 0.5754 (mtm) cc_final: 0.5151 (mtt) REVERT: B 800 PHE cc_start: 0.8241 (t80) cc_final: 0.7765 (t80) REVERT: B 1066 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8249 (t70) outliers start: 16 outliers final: 11 residues processed: 119 average time/residue: 0.0701 time to fit residues: 13.3595 Evaluate side-chains 121 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU 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 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.129381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096682 restraints weight = 20072.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100400 restraints weight = 8538.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102678 restraints weight = 5111.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104074 restraints weight = 3809.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104390 restraints weight = 3233.543| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3026 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= 0.104 Angle : 0.484 7.676 13172 Z= 0.256 Chirality : 0.039 0.191 1550 Planarity : 0.003 0.033 1612 Dihedral : 12.450 136.953 1470 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.24 % Allowed : 16.22 % Favored : 81.54 % 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 aren not related in a simple way. whole: 1.85 (0.25), residues: 1234 helix: 2.41 (0.19), residues: 744 sheet: -0.13 (0.45), residues: 152 loop : -0.83 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 758 TYR 0.020 0.001 TYR A 455 PHE 0.013 0.001 PHE A 864 TRP 0.011 0.001 TRP B 806 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9642) covalent geometry : angle 0.48411 (13172) hydrogen bonds : bond 0.03826 ( 625) hydrogen bonds : angle 4.00209 ( 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 139 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.394 Fit side-chains REVERT: A 437 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7279 (tp-100) REVERT: A 476 MET cc_start: 0.8618 (mpp) cc_final: 0.7857 (mpp) REVERT: A 543 MET cc_start: 0.6821 (pmm) cc_final: 0.6539 (ptp) REVERT: A 560 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8544 (tp40) REVERT: A 800 PHE cc_start: 0.8056 (t80) cc_final: 0.7757 (t80) REVERT: A 876 MET cc_start: 0.8985 (tpp) cc_final: 0.8692 (tpp) REVERT: A 925 TYR cc_start: 0.8136 (m-10) cc_final: 0.7897 (m-80) REVERT: A 938 MET cc_start: 0.8425 (tpp) cc_final: 0.7826 (tpp) REVERT: A 1052 PHE cc_start: 0.8886 (t80) cc_final: 0.8599 (t80) REVERT: A 1066 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8320 (t70) REVERT: B 437 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7355 (tp-100) REVERT: B 560 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8558 (tp40) REVERT: B 800 PHE cc_start: 0.8077 (t80) cc_final: 0.7637 (t80) REVERT: B 876 MET cc_start: 0.8983 (tpp) cc_final: 0.8692 (tpp) REVERT: B 925 TYR cc_start: 0.8077 (m-10) cc_final: 0.7833 (m-80) REVERT: B 938 MET cc_start: 0.8407 (tpp) cc_final: 0.7830 (tpp) REVERT: B 1052 PHE cc_start: 0.8889 (t80) cc_final: 0.8605 (t80) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.0787 time to fit residues: 15.5727 Evaluate side-chains 131 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 653 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.125963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.092976 restraints weight = 20382.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096354 restraints weight = 9062.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098318 restraints weight = 5593.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.099647 restraints weight = 4307.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.100255 restraints weight = 3689.214| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9642 Z= 0.141 Angle : 0.502 7.101 13172 Z= 0.270 Chirality : 0.040 0.189 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.080 132.798 1470 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.46 % Allowed : 17.11 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.25), residues: 1234 helix: 2.32 (0.19), residues: 756 sheet: -0.18 (0.44), residues: 152 loop : -0.82 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.014 0.001 TYR A 455 PHE 0.018 0.001 PHE A1052 TRP 0.014 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9642) covalent geometry : angle 0.50219 (13172) hydrogen bonds : bond 0.03976 ( 625) hydrogen bonds : angle 4.02044 ( 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 138 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.366 Fit side-chains REVERT: A 437 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7285 (tp-100) REVERT: A 476 MET cc_start: 0.8539 (mpp) cc_final: 0.7745 (mpp) REVERT: A 543 MET cc_start: 0.6834 (pmm) cc_final: 0.6602 (ptp) REVERT: A 560 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8534 (tp40) REVERT: A 800 PHE cc_start: 0.8128 (t80) cc_final: 0.7835 (t80) REVERT: A 886 MET cc_start: 0.8197 (ttp) cc_final: 0.7527 (tmm) REVERT: B 437 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7343 (tp-100) REVERT: B 476 MET cc_start: 0.8243 (mpp) cc_final: 0.7372 (mpp) REVERT: B 560 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8552 (tp40) REVERT: B 810 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8580 (m) REVERT: B 886 MET cc_start: 0.8196 (ttp) cc_final: 0.7521 (tmm) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.0761 time to fit residues: 14.7417 Evaluate side-chains 127 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG 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 673 VAL 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 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: 1.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 0.0770 chunk 69 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.124056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090652 restraints weight = 20887.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093775 restraints weight = 9666.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.095705 restraints weight = 6129.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096714 restraints weight = 4742.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097429 restraints weight = 4153.450| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9642 Z= 0.179 Angle : 0.551 7.928 13172 Z= 0.290 Chirality : 0.041 0.180 1550 Planarity : 0.003 0.032 1612 Dihedral : 11.321 125.497 1470 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.24 % Allowed : 18.34 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.25), residues: 1234 helix: 2.26 (0.19), residues: 746 sheet: -0.32 (0.44), residues: 152 loop : -0.81 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 758 TYR 0.020 0.002 TYR B 925 PHE 0.023 0.002 PHE A1052 TRP 0.015 0.001 TRP A 806 HIS 0.005 0.001 HIS B 937 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9642) covalent geometry : angle 0.55127 (13172) hydrogen bonds : bond 0.04331 ( 625) hydrogen bonds : angle 4.13678 ( 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 124 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.368 Fit side-chains REVERT: A 437 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7244 (tp-100) REVERT: A 476 MET cc_start: 0.8428 (mpp) cc_final: 0.7671 (mpp) REVERT: A 543 MET cc_start: 0.6809 (pmm) cc_final: 0.6566 (ptp) REVERT: A 560 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8535 (tp40) REVERT: A 606 MET cc_start: 0.5979 (mtm) cc_final: 0.5283 (mtt) REVERT: A 810 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8646 (m) REVERT: A 876 MET cc_start: 0.9004 (tpp) cc_final: 0.8747 (tpp) REVERT: A 886 MET cc_start: 0.8180 (ttp) cc_final: 0.7486 (tmm) REVERT: A 1070 MET cc_start: 0.8235 (tmm) cc_final: 0.7793 (tmm) REVERT: B 437 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7341 (tp-100) REVERT: B 476 MET cc_start: 0.8259 (mpp) cc_final: 0.8035 (mpp) REVERT: B 560 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8549 (tp40) REVERT: B 606 MET cc_start: 0.6021 (mtm) cc_final: 0.5323 (mtt) REVERT: B 810 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8641 (m) REVERT: B 876 MET cc_start: 0.9005 (tpp) cc_final: 0.8747 (tpp) REVERT: B 886 MET cc_start: 0.8178 (ttp) cc_final: 0.7480 (tmm) outliers start: 20 outliers final: 16 residues processed: 114 average time/residue: 0.0744 time to fit residues: 13.4005 Evaluate side-chains 122 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG 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 673 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.127994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094579 restraints weight = 20087.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098241 restraints weight = 8696.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100485 restraints weight = 5247.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101759 restraints weight = 3932.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102565 restraints weight = 3376.817| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9642 Z= 0.112 Angle : 0.502 7.068 13172 Z= 0.257 Chirality : 0.039 0.176 1550 Planarity : 0.003 0.032 1612 Dihedral : 10.875 119.641 1470 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.24 % Allowed : 18.46 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.25), residues: 1234 helix: 2.40 (0.19), residues: 746 sheet: -0.28 (0.44), residues: 152 loop : -0.79 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 758 TYR 0.018 0.001 TYR B 925 PHE 0.017 0.001 PHE B 772 TRP 0.011 0.001 TRP B 806 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9642) covalent geometry : angle 0.50191 (13172) hydrogen bonds : bond 0.03876 ( 625) hydrogen bonds : angle 3.99748 ( 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 133 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7308 (tp-100) REVERT: A 476 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7917 (mpp) REVERT: A 543 MET cc_start: 0.6792 (pmm) cc_final: 0.6572 (ptp) REVERT: A 606 MET cc_start: 0.5673 (mtm) cc_final: 0.5023 (mtt) REVERT: A 876 MET cc_start: 0.8969 (tpp) cc_final: 0.8673 (tpp) REVERT: A 886 MET cc_start: 0.8202 (ttp) cc_final: 0.7308 (tmm) REVERT: A 1070 MET cc_start: 0.8190 (tmm) cc_final: 0.7811 (tmm) REVERT: B 437 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7389 (tp-100) REVERT: B 560 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8544 (tp40) REVERT: B 606 MET cc_start: 0.5709 (mtm) cc_final: 0.5069 (mtt) REVERT: B 810 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8506 (m) REVERT: B 876 MET cc_start: 0.8960 (tpp) cc_final: 0.8663 (tpp) REVERT: B 886 MET cc_start: 0.8207 (ttp) cc_final: 0.7514 (tmm) outliers start: 20 outliers final: 16 residues processed: 122 average time/residue: 0.0709 time to fit residues: 13.6897 Evaluate side-chains 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 MET 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 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 612 ILE Chi-restraints excluded: chain B residue 673 VAL 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 948 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.125312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.092530 restraints weight = 20289.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.095815 restraints weight = 9086.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.097895 restraints weight = 5630.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099086 restraints weight = 4281.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.099792 restraints weight = 3688.347| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9642 Z= 0.160 Angle : 0.530 6.975 13172 Z= 0.276 Chirality : 0.040 0.177 1550 Planarity : 0.003 0.032 1612 Dihedral : 10.346 97.886 1470 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.24 % Allowed : 18.68 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.24), residues: 1234 helix: 2.39 (0.19), residues: 744 sheet: -0.37 (0.44), residues: 152 loop : -0.79 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 758 TYR 0.018 0.001 TYR B 925 PHE 0.020 0.001 PHE B1052 TRP 0.015 0.001 TRP B 806 HIS 0.003 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9642) covalent geometry : angle 0.52984 (13172) hydrogen bonds : bond 0.04106 ( 625) hydrogen bonds : angle 4.04248 ( 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 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7265 (tp-100) REVERT: A 476 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7843 (mpp) REVERT: A 606 MET cc_start: 0.5771 (mtm) cc_final: 0.5091 (mtt) REVERT: A 810 SER cc_start: 0.9168 (OUTLIER) cc_final: 0.8566 (m) REVERT: A 876 MET cc_start: 0.8976 (tpp) cc_final: 0.8653 (tpp) REVERT: A 886 MET cc_start: 0.8184 (ttp) cc_final: 0.7502 (tmm) REVERT: A 1070 MET cc_start: 0.8341 (tmm) cc_final: 0.8001 (tmm) REVERT: B 437 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7419 (tp-100) REVERT: B 560 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8520 (tp40) REVERT: B 606 MET cc_start: 0.5739 (mtm) cc_final: 0.5057 (mtt) REVERT: B 810 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 876 MET cc_start: 0.9011 (tpp) cc_final: 0.8685 (tpp) REVERT: B 886 MET cc_start: 0.8182 (ttp) cc_final: 0.7502 (tmm) outliers start: 20 outliers final: 15 residues processed: 118 average time/residue: 0.0734 time to fit residues: 13.7323 Evaluate side-chains 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 MET 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 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 612 ILE Chi-restraints excluded: chain B residue 673 VAL 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 948 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 chunk 106 optimal weight: 0.5980 chunk 10 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.128388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095156 restraints weight = 20154.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098806 restraints weight = 8697.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100907 restraints weight = 5264.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.102358 restraints weight = 4006.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.103015 restraints weight = 3391.758| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9642 Z= 0.109 Angle : 0.499 7.387 13172 Z= 0.257 Chirality : 0.039 0.171 1550 Planarity : 0.003 0.032 1612 Dihedral : 9.948 83.724 1470 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.13 % Allowed : 19.02 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.24), residues: 1234 helix: 2.48 (0.19), residues: 744 sheet: -0.30 (0.44), residues: 152 loop : -0.77 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.017 0.001 TYR B 925 PHE 0.023 0.001 PHE B1052 TRP 0.012 0.001 TRP B 806 HIS 0.005 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9642) covalent geometry : angle 0.49895 (13172) hydrogen bonds : bond 0.03807 ( 625) hydrogen bonds : angle 3.97597 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.61 seconds wall clock time: 31 minutes 10.96 seconds (1870.96 seconds total)