Starting phenix.real_space_refine on Fri Feb 14 05:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3t_36859/02_2025/8k3t_36859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3t_36859/02_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_36859/02_2025/8k3t_36859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3t_36859/02_2025/8k3t_36859.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3t_36859/02_2025/8k3t_36859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3t_36859/02_2025/8k3t_36859.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16} 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: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16} 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: 5.76, per 1000 atoms: 0.61 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: 2.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.15 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: 3.41 Time building geometry restraints manager: 3.17 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: 0.05 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: 0.490 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.050 ------------------------------------------------------------------------------- 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= 0.605 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (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 TRP 0.022 0.003 TRP A 806 HIS 0.006 0.002 HIS B 783 PHE 0.021 0.002 PHE A1052 TYR 0.028 0.002 TYR B 878 ARG 0.004 0.001 ARG B 817 *********************** 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 : 0.981 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: 0.1850 time to fit residues: 42.7127 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 : 1.101 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.128853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096052 restraints weight = 19742.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099626 restraints weight = 8677.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.101761 restraints weight = 5294.769| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9642 Z= 0.178 Angle : 0.557 7.063 13172 Z= 0.300 Chirality : 0.041 0.157 1550 Planarity : 0.003 0.037 1612 Dihedral : 12.668 118.092 1474 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.89 % Allowed : 6.49 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1234 helix: 1.83 (0.19), residues: 742 sheet: -0.48 (0.45), residues: 152 loop : -0.59 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1103 HIS 0.004 0.001 HIS A 828 PHE 0.016 0.001 PHE B 864 TYR 0.016 0.002 TYR A 713 ARG 0.003 0.000 ARG B 758 *********************** 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 149 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 1.016 Fit side-chains REVERT: A 560 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8473 (tp40) REVERT: A 823 ILE cc_start: 0.9178 (tt) cc_final: 0.8924 (tt) REVERT: A 876 MET cc_start: 0.9009 (tpp) cc_final: 0.8776 (tpp) REVERT: A 879 MET cc_start: 0.8488 (ttp) cc_final: 0.8223 (ttp) REVERT: A 938 MET cc_start: 0.8741 (tpp) cc_final: 0.8490 (tpp) REVERT: B 543 MET cc_start: 0.6637 (pmm) cc_final: 0.6318 (ptp) REVERT: B 560 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8501 (tp40) REVERT: B 823 ILE cc_start: 0.9177 (tt) cc_final: 0.8930 (tt) REVERT: B 876 MET cc_start: 0.9010 (tpp) cc_final: 0.8778 (tpp) REVERT: B 879 MET cc_start: 0.8477 (ttp) cc_final: 0.8215 (ttp) REVERT: B 938 MET cc_start: 0.8744 (tpp) cc_final: 0.8470 (tpp) outliers start: 8 outliers final: 5 residues processed: 143 average time/residue: 0.1590 time to fit residues: 35.7222 Evaluate side-chains 110 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 68 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 582 HIS B 774 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.126523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093215 restraints weight = 20062.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096638 restraints weight = 8905.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098752 restraints weight = 5472.349| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9642 Z= 0.258 Angle : 0.544 5.825 13172 Z= 0.292 Chirality : 0.041 0.168 1550 Planarity : 0.003 0.033 1612 Dihedral : 12.833 129.827 1470 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.79 % Allowed : 10.40 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1234 helix: 2.01 (0.19), residues: 754 sheet: -0.35 (0.45), residues: 152 loop : -0.59 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 PHE 0.022 0.002 PHE B 772 TYR 0.012 0.001 TYR A 713 ARG 0.004 0.000 ARG A 758 *********************** 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 127 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 459 HIS cc_start: 0.7348 (p-80) cc_final: 0.6587 (p-80) REVERT: A 476 MET cc_start: 0.8584 (mpp) cc_final: 0.7405 (mpp) REVERT: A 543 MET cc_start: 0.6820 (pmm) cc_final: 0.6416 (ptp) REVERT: A 560 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8477 (tp40) REVERT: A 876 MET cc_start: 0.8932 (tpp) cc_final: 0.8608 (tpp) REVERT: A 879 MET cc_start: 0.8543 (ttp) cc_final: 0.8322 (ttp) REVERT: A 938 MET cc_start: 0.8802 (tpp) cc_final: 0.8452 (tpp) REVERT: B 459 HIS cc_start: 0.7388 (p-80) cc_final: 0.6676 (p-80) REVERT: B 543 MET cc_start: 0.6773 (pmm) cc_final: 0.6464 (ptp) REVERT: B 560 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8504 (tp40) REVERT: B 876 MET cc_start: 0.8933 (tpp) cc_final: 0.8607 (tpp) REVERT: B 879 MET cc_start: 0.8539 (ttp) cc_final: 0.8313 (ttp) REVERT: B 938 MET cc_start: 0.8804 (tpp) cc_final: 0.8313 (tpp) outliers start: 16 outliers final: 12 residues processed: 123 average time/residue: 0.1550 time to fit residues: 30.2292 Evaluate side-chains 119 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 65 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.124020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090563 restraints weight = 20761.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093601 restraints weight = 9713.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.095518 restraints weight = 6225.174| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9642 Z= 0.306 Angle : 0.555 6.125 13172 Z= 0.299 Chirality : 0.042 0.192 1550 Planarity : 0.004 0.034 1612 Dihedral : 13.369 141.602 1470 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.35 % Allowed : 13.09 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1234 helix: 1.96 (0.19), residues: 752 sheet: -0.43 (0.45), residues: 152 loop : -0.82 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 806 HIS 0.005 0.001 HIS A 828 PHE 0.024 0.002 PHE B1052 TYR 0.014 0.002 TYR A 878 ARG 0.006 0.001 ARG A 758 *********************** 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 133 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7462 (tp-100) REVERT: A 476 MET cc_start: 0.8537 (mpp) cc_final: 0.7578 (mpp) REVERT: A 543 MET cc_start: 0.6858 (pmm) cc_final: 0.6544 (ptp) REVERT: A 560 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8548 (tp40) REVERT: A 606 MET cc_start: 0.6083 (mpp) cc_final: 0.5754 (mtt) REVERT: A 1066 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8217 (t70) REVERT: B 437 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7565 (tp-100) REVERT: B 543 MET cc_start: 0.6628 (pmm) cc_final: 0.6377 (ptp) REVERT: B 560 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8526 (tp40) outliers start: 21 outliers final: 14 residues processed: 121 average time/residue: 0.1574 time to fit residues: 30.1443 Evaluate side-chains 124 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 717 ASP Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN B 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.125483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092153 restraints weight = 20430.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095273 restraints weight = 9495.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.097167 restraints weight = 6046.831| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9642 Z= 0.200 Angle : 0.498 6.096 13172 Z= 0.266 Chirality : 0.040 0.199 1550 Planarity : 0.003 0.034 1612 Dihedral : 13.066 142.303 1470 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.46 % Allowed : 14.88 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1234 helix: 2.15 (0.19), residues: 752 sheet: -0.29 (0.45), residues: 152 loop : -0.75 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 806 HIS 0.004 0.001 HIS A 828 PHE 0.016 0.001 PHE A 864 TYR 0.010 0.001 TYR B 713 ARG 0.003 0.000 ARG A 436 *********************** 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 137 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7281 (tp-100) REVERT: A 476 MET cc_start: 0.8498 (mpp) cc_final: 0.8284 (mpp) REVERT: A 543 MET cc_start: 0.6786 (pmm) cc_final: 0.6485 (ptp) REVERT: A 560 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8547 (tp40) REVERT: A 876 MET cc_start: 0.8954 (tpp) cc_final: 0.8556 (tpp) REVERT: A 886 MET cc_start: 0.8362 (ttp) cc_final: 0.7525 (tmm) REVERT: A 938 MET cc_start: 0.8709 (tpp) cc_final: 0.7801 (tpp) REVERT: A 1066 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8154 (t70) REVERT: B 437 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7365 (tp-100) REVERT: B 543 MET cc_start: 0.6640 (pmm) cc_final: 0.6416 (ptp) REVERT: B 560 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8568 (tp40) REVERT: B 876 MET cc_start: 0.8953 (tpp) cc_final: 0.8556 (tpp) REVERT: B 886 MET cc_start: 0.8352 (ttp) cc_final: 0.7523 (tmm) REVERT: B 938 MET cc_start: 0.8696 (tpp) cc_final: 0.7788 (tpp) outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 0.1583 time to fit residues: 30.0683 Evaluate side-chains 128 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ILE 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 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 717 ASP Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.124881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091507 restraints weight = 20693.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.094681 restraints weight = 9579.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096643 restraints weight = 6057.746| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9642 Z= 0.222 Angle : 0.507 6.983 13172 Z= 0.271 Chirality : 0.041 0.194 1550 Planarity : 0.003 0.033 1612 Dihedral : 12.877 140.567 1470 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.46 % Allowed : 16.67 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1234 helix: 2.22 (0.19), residues: 756 sheet: -0.26 (0.45), residues: 152 loop : -0.86 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 PHE 0.019 0.001 PHE B1052 TYR 0.018 0.001 TYR A 455 ARG 0.004 0.000 ARG A 758 *********************** 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 136 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7271 (tp-100) REVERT: A 543 MET cc_start: 0.6820 (pmm) cc_final: 0.6539 (ptp) REVERT: A 560 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8546 (tp40) REVERT: A 606 MET cc_start: 0.5964 (mtm) cc_final: 0.5280 (mtt) REVERT: A 876 MET cc_start: 0.8928 (tpp) cc_final: 0.8477 (tpp) REVERT: A 886 MET cc_start: 0.8414 (ttp) cc_final: 0.8194 (tmm) REVERT: A 1066 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8336 (t70) REVERT: B 437 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7283 (tp-100) REVERT: B 476 MET cc_start: 0.8429 (mpp) cc_final: 0.7359 (mpp) REVERT: B 560 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8564 (tp40) REVERT: B 606 MET cc_start: 0.5830 (mtm) cc_final: 0.5204 (mtt) REVERT: B 810 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8654 (m) REVERT: B 876 MET cc_start: 0.8933 (tpp) cc_final: 0.8484 (tpp) REVERT: B 886 MET cc_start: 0.8415 (ttp) cc_final: 0.8186 (tmm) outliers start: 22 outliers final: 14 residues processed: 121 average time/residue: 0.1661 time to fit residues: 31.0442 Evaluate side-chains 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 717 ASP 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 459 HIS Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.126321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.093105 restraints weight = 20647.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.096418 restraints weight = 9425.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.098431 restraints weight = 5893.727| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9642 Z= 0.161 Angle : 0.489 6.541 13172 Z= 0.261 Chirality : 0.040 0.198 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.580 139.075 1470 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.68 % Allowed : 17.00 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1234 helix: 2.29 (0.19), residues: 756 sheet: -0.19 (0.45), residues: 152 loop : -0.80 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 PHE 0.024 0.001 PHE A 772 TYR 0.017 0.001 TYR A 455 ARG 0.002 0.000 ARG A 758 *********************** 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 139 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.5011 (tmm) REVERT: A 437 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7289 (tp-100) REVERT: A 543 MET cc_start: 0.6801 (pmm) cc_final: 0.6546 (ptp) REVERT: A 560 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8545 (tp40) REVERT: A 606 MET cc_start: 0.5826 (mtm) cc_final: 0.5158 (mtt) REVERT: A 800 PHE cc_start: 0.8119 (t80) cc_final: 0.7822 (t80) REVERT: A 876 MET cc_start: 0.8933 (tpp) cc_final: 0.8466 (tpp) REVERT: A 886 MET cc_start: 0.8394 (ttp) cc_final: 0.8178 (tmm) REVERT: A 1052 PHE cc_start: 0.8924 (t80) cc_final: 0.8502 (t80) REVERT: A 1066 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8345 (t70) REVERT: B 437 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7298 (tp-100) REVERT: B 476 MET cc_start: 0.8462 (mpp) cc_final: 0.7545 (mpp) REVERT: B 560 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8559 (tp40) REVERT: B 606 MET cc_start: 0.5838 (mtm) cc_final: 0.5175 (mtt) REVERT: B 810 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8630 (m) REVERT: B 876 MET cc_start: 0.8939 (tpp) cc_final: 0.8480 (tpp) REVERT: B 886 MET cc_start: 0.8394 (ttp) cc_final: 0.8163 (tmm) outliers start: 24 outliers final: 17 residues processed: 122 average time/residue: 0.1642 time to fit residues: 30.8364 Evaluate side-chains 132 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 653 GLU 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 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP 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 100 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.123529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.090192 restraints weight = 21149.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.093317 restraints weight = 9741.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095260 restraints weight = 6151.477| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9642 Z= 0.288 Angle : 0.556 6.386 13172 Z= 0.298 Chirality : 0.041 0.192 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.506 133.825 1470 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.80 % Allowed : 17.56 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1234 helix: 2.25 (0.19), residues: 746 sheet: -0.40 (0.44), residues: 152 loop : -0.80 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 806 HIS 0.004 0.001 HIS A 937 PHE 0.025 0.002 PHE B1052 TYR 0.021 0.002 TYR B 925 ARG 0.005 0.001 ARG A 758 *********************** 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 134 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.5551 (OUTLIER) cc_final: 0.5245 (tmm) REVERT: A 437 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7269 (tp-100) REVERT: A 543 MET cc_start: 0.6816 (pmm) cc_final: 0.6566 (ptp) REVERT: A 560 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8542 (tp40) REVERT: A 606 MET cc_start: 0.5921 (mtm) cc_final: 0.5240 (mtt) REVERT: A 810 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8681 (m) REVERT: A 886 MET cc_start: 0.8480 (ttp) cc_final: 0.8152 (tmm) REVERT: A 938 MET cc_start: 0.8419 (tpp) cc_final: 0.7873 (tpp) REVERT: B 437 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7339 (tp-100) REVERT: B 476 MET cc_start: 0.8380 (mpp) cc_final: 0.7470 (mpp) REVERT: B 560 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8554 (tp40) REVERT: B 606 MET cc_start: 0.5993 (mtm) cc_final: 0.5270 (mtt) REVERT: B 810 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8682 (m) REVERT: B 886 MET cc_start: 0.8479 (ttp) cc_final: 0.7923 (tmm) REVERT: B 938 MET cc_start: 0.8364 (tpp) cc_final: 0.7840 (tpp) outliers start: 25 outliers final: 17 residues processed: 118 average time/residue: 0.1741 time to fit residues: 31.2801 Evaluate side-chains 125 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 612 ILE 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 1046 PHE Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 459 HIS 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 32 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.125076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092218 restraints weight = 20293.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.095573 restraints weight = 9020.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.097617 restraints weight = 5561.902| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9642 Z= 0.218 Angle : 0.535 9.240 13172 Z= 0.281 Chirality : 0.040 0.184 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.000 128.632 1470 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.35 % Allowed : 18.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.25), residues: 1234 helix: 2.32 (0.19), residues: 746 sheet: -0.42 (0.44), residues: 152 loop : -0.77 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 PHE 0.020 0.001 PHE B 772 TYR 0.020 0.001 TYR B 925 ARG 0.004 0.000 ARG A 758 *********************** 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 128 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7264 (tp-100) REVERT: A 543 MET cc_start: 0.6810 (pmm) cc_final: 0.6595 (ptp) REVERT: A 560 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8546 (tp40) REVERT: A 606 MET cc_start: 0.5745 (mtm) cc_final: 0.5069 (mtt) REVERT: A 800 PHE cc_start: 0.8140 (t80) cc_final: 0.7848 (t80) REVERT: A 810 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8617 (m) REVERT: A 876 MET cc_start: 0.8978 (tpp) cc_final: 0.8699 (tpp) REVERT: A 886 MET cc_start: 0.8485 (ttp) cc_final: 0.7929 (tmm) REVERT: A 938 MET cc_start: 0.8485 (tpp) cc_final: 0.7875 (tpp) REVERT: B 437 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7352 (tp-100) REVERT: B 476 MET cc_start: 0.8443 (mpp) cc_final: 0.7423 (mpp) REVERT: B 560 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8554 (tp40) REVERT: B 606 MET cc_start: 0.5915 (mtm) cc_final: 0.5249 (mtt) REVERT: B 800 PHE cc_start: 0.8141 (t80) cc_final: 0.7845 (t80) REVERT: B 810 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8611 (m) REVERT: B 876 MET cc_start: 0.8971 (tpp) cc_final: 0.8700 (tpp) REVERT: B 886 MET cc_start: 0.8487 (ttp) cc_final: 0.7895 (tmm) REVERT: B 938 MET cc_start: 0.8471 (tpp) cc_final: 0.7852 (tpp) outliers start: 21 outliers final: 18 residues processed: 116 average time/residue: 0.1651 time to fit residues: 29.7558 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 : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ILE 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 1046 PHE Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 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 14 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 59 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 79 optimal weight: 0.3980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.127499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094368 restraints weight = 20317.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098004 restraints weight = 8761.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100195 restraints weight = 5293.097| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9642 Z= 0.175 Angle : 0.520 10.346 13172 Z= 0.264 Chirality : 0.040 0.189 1550 Planarity : 0.003 0.032 1612 Dihedral : 11.016 122.019 1470 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.13 % Allowed : 18.90 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.25), residues: 1234 helix: 2.42 (0.19), residues: 744 sheet: -0.38 (0.44), residues: 152 loop : -0.69 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 PHE 0.018 0.001 PHE B 772 TYR 0.019 0.001 TYR B 925 ARG 0.004 0.000 ARG A 758 ********************** 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 132 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7293 (tp-100) REVERT: A 586 PHE cc_start: 0.9016 (m-80) cc_final: 0.8748 (m-10) REVERT: A 606 MET cc_start: 0.5638 (mtm) cc_final: 0.4991 (mtt) REVERT: A 800 PHE cc_start: 0.8060 (t80) cc_final: 0.7770 (t80) REVERT: A 810 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8541 (m) REVERT: A 876 MET cc_start: 0.8962 (tpp) cc_final: 0.8714 (tpp) REVERT: A 886 MET cc_start: 0.8505 (ttp) cc_final: 0.8160 (tmm) REVERT: A 938 MET cc_start: 0.8468 (tpp) cc_final: 0.7918 (tpp) REVERT: B 437 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7358 (tp-100) REVERT: B 476 MET cc_start: 0.8373 (mpp) cc_final: 0.7381 (mpp) REVERT: B 560 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8535 (tp40) REVERT: B 606 MET cc_start: 0.5817 (mtm) cc_final: 0.5187 (mtt) REVERT: B 810 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8544 (m) REVERT: B 876 MET cc_start: 0.8977 (tpp) cc_final: 0.8731 (tpp) REVERT: B 886 MET cc_start: 0.8503 (ttp) cc_final: 0.8157 (tmm) REVERT: B 938 MET cc_start: 0.8432 (tpp) cc_final: 0.7861 (tpp) outliers start: 19 outliers final: 16 residues processed: 120 average time/residue: 0.1653 time to fit residues: 30.6808 Evaluate side-chains 124 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 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 54 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 0.0470 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.125905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092631 restraints weight = 20380.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096184 restraints weight = 8884.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098398 restraints weight = 5376.763| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3418 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= 0.271 Angle : 0.564 8.226 13172 Z= 0.292 Chirality : 0.041 0.180 1550 Planarity : 0.003 0.033 1612 Dihedral : 10.427 98.883 1470 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.46 % Allowed : 19.02 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1234 helix: 2.36 (0.19), residues: 744 sheet: -0.43 (0.44), residues: 152 loop : -0.72 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 806 HIS 0.003 0.001 HIS B 828 PHE 0.023 0.002 PHE B1052 TYR 0.018 0.001 TYR B 925 ARG 0.005 0.001 ARG A 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.52 seconds wall clock time: 51 minutes 8.01 seconds (3068.01 seconds total)