Starting phenix.real_space_refine on Sat Aug 23 07:19:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3x_36864/08_2025/8k3x_36864_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3x_36864/08_2025/8k3x_36864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3x_36864/08_2025/8k3x_36864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3x_36864/08_2025/8k3x_36864.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3x_36864/08_2025/8k3x_36864_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3x_36864/08_2025/8k3x_36864_neut.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.136 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 6738 2.51 5 N 1696 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 10386 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5158 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 20, 'TRANS': 672} Chain breaks: 9 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 408 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASN:plan1': 10, 'PHE:plan': 16, 'ARG:plan': 11, 'GLU:plan': 16, 'GLN:plan1': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 279 Chain: "B" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5158 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 20, 'TRANS': 672} Chain breaks: 9 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 408 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASN:plan1': 10, 'PHE:plan': 16, 'ARG:plan': 11, 'GLU:plan': 16, 'GLN:plan1': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 279 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'BGI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'BGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.00, per 1000 atoms: 0.29 Number of scatterers: 10386 At special positions: 0 Unit cell: (77.38, 136.74, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1888 8.00 N 1696 7.00 C 6738 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: 1.09 Conformation dependent library (CDL) restraints added in 438.8 milliseconds Enol-peptide restraints added in 1.7 microseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 64.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.641A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.522A pdb=" N LYS A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 424 through 428 removed outlier: 4.020A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.590A pdb=" N LEU A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.543A pdb=" N LYS A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.687A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 4.072A pdb=" N ASN A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.536A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 3.734A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.704A pdb=" N PHE A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 3.613A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.756A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 removed outlier: 3.950A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 4.380A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 3.906A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 784 through 807 Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.683A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.523A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 893 Processing helix chain 'A' and resid 917 through 932 Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.781A pdb=" N THR A 940 " --> pdb=" O TRP A 936 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 936 through 941' Processing helix chain 'A' and resid 941 through 948 removed outlier: 3.531A pdb=" N TYR A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 955 Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 997 through 1014 Processing helix chain 'A' and resid 1027 through 1045 removed outlier: 3.526A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1060 removed outlier: 3.811A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 3.523A pdb=" N THR A1075 " --> pdb=" O LYS A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1128 removed outlier: 4.241A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A1109 " --> pdb=" O VAL A1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.641A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.522A pdb=" N LYS B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 424 through 428 removed outlier: 4.020A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.591A pdb=" N LEU B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.543A pdb=" N LYS B 491 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.687A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 588 removed outlier: 4.073A pdb=" N ASN B 580 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.535A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 3.734A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.704A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 660 removed outlier: 3.613A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.755A 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 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 removed outlier: 3.950A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 4.381A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 3.906A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 784 through 807 Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.683A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 824 " --> pdb=" O THR B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.522A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 893 Processing helix chain 'B' and resid 917 through 932 Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.781A pdb=" N THR B 940 " --> pdb=" O TRP B 936 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 936 through 941' Processing helix chain 'B' and resid 941 through 948 removed outlier: 3.531A pdb=" N TYR B 945 " --> pdb=" O SER B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 955 Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 997 through 1014 Processing helix chain 'B' and resid 1027 through 1045 removed outlier: 3.525A pdb=" N SER B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1060 removed outlier: 3.811A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1075 removed outlier: 3.524A pdb=" N THR B1075 " --> pdb=" O LYS B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1128 removed outlier: 4.241A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER B1108 " --> pdb=" O LEU B1104 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B1109 " --> pdb=" O VAL B1105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 388 through 390 removed outlier: 6.164A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.927A pdb=" N THR A 453 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 629 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.818A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 388 through 390 removed outlier: 6.164A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.926A pdb=" N THR B 453 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 629 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.818A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1728 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: 1.88 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1634 1.30 - 1.43: 2967 1.43 - 1.55: 5921 1.55 - 1.68: 6 1.68 - 1.80: 96 Bond restraints: 10624 Sorted by residual: bond pdb=" C28 BGI A1201 " pdb=" N27 BGI A1201 " ideal model delta sigma weight residual 1.371 1.518 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C28 BGI B1201 " pdb=" N27 BGI B1201 " ideal model delta sigma weight residual 1.371 1.517 -0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" C28 BGI A1201 " pdb=" N22 BGI A1201 " ideal model delta sigma weight residual 1.382 1.515 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C28 BGI B1201 " pdb=" N22 BGI B1201 " ideal model delta sigma weight residual 1.382 1.514 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C13 BGI B1201 " pdb=" N15 BGI B1201 " ideal model delta sigma weight residual 1.343 1.472 -0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 10619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 13435 1.65 - 3.30: 851 3.30 - 4.95: 144 4.95 - 6.61: 42 6.61 - 8.26: 16 Bond angle restraints: 14488 Sorted by residual: angle pdb=" N LEU B 642 " pdb=" CA LEU B 642 " pdb=" C LEU B 642 " ideal model delta sigma weight residual 113.02 106.05 6.97 1.20e+00 6.94e-01 3.38e+01 angle pdb=" N LEU A 642 " pdb=" CA LEU A 642 " pdb=" C LEU A 642 " ideal model delta sigma weight residual 113.02 106.05 6.97 1.20e+00 6.94e-01 3.37e+01 angle pdb=" N THR B 422 " pdb=" CA THR B 422 " pdb=" C THR B 422 " ideal model delta sigma weight residual 114.56 107.87 6.69 1.27e+00 6.20e-01 2.78e+01 angle pdb=" N THR A 422 " pdb=" CA THR A 422 " pdb=" C THR A 422 " ideal model delta sigma weight residual 114.56 107.92 6.64 1.27e+00 6.20e-01 2.74e+01 angle pdb=" N TYR A 952 " pdb=" CA TYR A 952 " pdb=" C TYR A 952 " ideal model delta sigma weight residual 112.89 107.00 5.89 1.24e+00 6.50e-01 2.25e+01 ... (remaining 14483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 5702 15.94 - 31.88: 407 31.88 - 47.83: 85 47.83 - 63.77: 16 63.77 - 79.71: 16 Dihedral angle restraints: 6226 sinusoidal: 2144 harmonic: 4082 Sorted by residual: dihedral pdb=" CA ALA B 715 " pdb=" C ALA B 715 " pdb=" N GLU B 716 " pdb=" CA GLU B 716 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ALA A 715 " pdb=" C ALA A 715 " pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta harmonic sigma weight residual 180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA HIS B 828 " pdb=" C HIS B 828 " pdb=" N SER B 829 " pdb=" CA SER B 829 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1551 0.100 - 0.199: 135 0.199 - 0.299: 10 0.299 - 0.399: 0 0.399 - 0.498: 2 Chirality restraints: 1698 Sorted by residual: chirality pdb=" C19 BGI A1201 " pdb=" C18 BGI A1201 " pdb=" C20 BGI A1201 " pdb=" O30 BGI A1201 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" C19 BGI B1201 " pdb=" C18 BGI B1201 " pdb=" C20 BGI B1201 " pdb=" O30 BGI B1201 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA MET A 416 " pdb=" N MET A 416 " pdb=" C MET A 416 " pdb=" CB MET A 416 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1695 not shown) Planarity restraints: 1798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 539 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" C GLU A 539 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 539 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 540 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 539 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C GLU B 539 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU B 539 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS B 540 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1025 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO A1026 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A1026 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1026 " -0.031 5.00e-02 4.00e+02 ... (remaining 1795 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1319 2.74 - 3.28: 10267 3.28 - 3.82: 16541 3.82 - 4.36: 19582 4.36 - 4.90: 34528 Nonbonded interactions: 82237 Sorted by model distance: nonbonded pdb=" OD1 ASP B 602 " pdb=" O31 BGI B1201 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP B 602 " pdb=" N15 BGI B1201 " model vdw 2.283 3.120 nonbonded pdb=" O ILE A 818 " pdb=" OG SER A 822 " model vdw 2.334 3.040 nonbonded pdb=" O ILE B 818 " pdb=" OG SER B 822 " model vdw 2.334 3.040 nonbonded pdb=" OG SER B 997 " pdb=" OE1 GLU B1000 " model vdw 2.371 3.040 ... (remaining 82232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.012 0.147 10624 Z= 0.567 Angle : 0.935 8.257 14488 Z= 0.580 Chirality : 0.061 0.498 1698 Planarity : 0.005 0.056 1798 Dihedral : 12.853 79.710 3582 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.20 % Allowed : 0.60 % Favored : 99.20 % 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: -0.82 (0.22), residues: 1346 helix: 0.48 (0.19), residues: 736 sheet: -2.28 (0.33), residues: 150 loop : -1.49 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 817 TYR 0.020 0.002 TYR A1008 PHE 0.021 0.002 PHE B 864 TRP 0.019 0.002 TRP A 806 HIS 0.005 0.002 HIS B 965 Details of bonding type rmsd covalent geometry : bond 0.01199 (10624) covalent geometry : angle 0.93513 (14488) hydrogen bonds : bond 0.13632 ( 604) hydrogen bonds : angle 6.62650 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.261 Fit side-chains REVERT: A 458 ASP cc_start: 0.8416 (p0) cc_final: 0.7894 (p0) REVERT: A 466 LEU cc_start: 0.8415 (mt) cc_final: 0.8022 (mm) REVERT: A 514 SER cc_start: 0.8389 (t) cc_final: 0.8011 (p) REVERT: A 538 TYR cc_start: 0.7880 (m-80) cc_final: 0.7265 (m-80) REVERT: A 548 ASN cc_start: 0.7618 (t0) cc_final: 0.6465 (p0) REVERT: A 555 SER cc_start: 0.7594 (m) cc_final: 0.6852 (p) REVERT: A 653 GLU cc_start: 0.8261 (tt0) cc_final: 0.8031 (tt0) REVERT: A 745 ASP cc_start: 0.7872 (p0) cc_final: 0.7658 (p0) REVERT: A 766 PHE cc_start: 0.7460 (m-10) cc_final: 0.7021 (t80) REVERT: A 862 GLU cc_start: 0.8301 (tt0) cc_final: 0.8026 (tt0) REVERT: A 936 TRP cc_start: 0.7925 (m100) cc_final: 0.7704 (m100) REVERT: A 1067 TYR cc_start: 0.8317 (t80) cc_final: 0.7941 (t80) REVERT: A 1088 PRO cc_start: 0.8397 (Cg_endo) cc_final: 0.8177 (Cg_exo) REVERT: A 1103 TRP cc_start: 0.7698 (m100) cc_final: 0.7479 (m100) REVERT: B 428 LEU cc_start: 0.8171 (mm) cc_final: 0.7961 (mm) REVERT: B 433 PHE cc_start: 0.6810 (m-80) cc_final: 0.6371 (m-80) REVERT: B 466 LEU cc_start: 0.8343 (mt) cc_final: 0.8101 (mp) REVERT: B 471 ASP cc_start: 0.8134 (m-30) cc_final: 0.7594 (m-30) REVERT: B 514 SER cc_start: 0.8419 (t) cc_final: 0.7770 (p) REVERT: B 889 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7568 (mptt) REVERT: B 1114 ILE cc_start: 0.8393 (mt) cc_final: 0.8144 (mm) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.3956 time to fit residues: 98.3834 Evaluate side-chains 143 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 459 HIS A 520 GLN A 614 GLN A 644 ASN A 783 HIS A 828 HIS A 892 GLN A 977 ASN B 419 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 HIS B 828 HIS B 977 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123284 restraints weight = 12955.920| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.09 r_work: 0.3273 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10624 Z= 0.115 Angle : 0.479 6.308 14488 Z= 0.262 Chirality : 0.040 0.175 1698 Planarity : 0.004 0.061 1798 Dihedral : 5.208 33.122 1562 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.29 % Allowed : 9.34 % Favored : 88.37 % 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: 0.31 (0.23), residues: 1346 helix: 1.44 (0.19), residues: 770 sheet: -1.42 (0.38), residues: 144 loop : -1.45 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 759 TYR 0.020 0.001 TYR B 827 PHE 0.014 0.001 PHE A 864 TRP 0.008 0.001 TRP A 840 HIS 0.008 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00249 (10624) covalent geometry : angle 0.47923 (14488) hydrogen bonds : bond 0.03920 ( 604) hydrogen bonds : angle 4.61753 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.7166 (ttp) cc_final: 0.6920 (ttt) REVERT: A 466 LEU cc_start: 0.8372 (mt) cc_final: 0.8107 (mm) REVERT: A 514 SER cc_start: 0.8613 (t) cc_final: 0.8318 (p) REVERT: A 538 TYR cc_start: 0.8500 (m-80) cc_final: 0.7739 (m-80) REVERT: A 548 ASN cc_start: 0.7988 (t0) cc_final: 0.6606 (p0) REVERT: A 555 SER cc_start: 0.7645 (m) cc_final: 0.6659 (p) REVERT: A 766 PHE cc_start: 0.7826 (m-10) cc_final: 0.6975 (t80) REVERT: A 963 ASN cc_start: 0.8767 (m-40) cc_final: 0.8558 (m-40) REVERT: A 977 ASN cc_start: 0.4718 (OUTLIER) cc_final: 0.3511 (t0) REVERT: A 1060 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: A 1067 TYR cc_start: 0.8586 (t80) cc_final: 0.8269 (t80) REVERT: A 1088 PRO cc_start: 0.8467 (Cg_endo) cc_final: 0.8249 (Cg_exo) REVERT: B 428 LEU cc_start: 0.8130 (mm) cc_final: 0.7881 (mm) REVERT: B 433 PHE cc_start: 0.7038 (m-80) cc_final: 0.6625 (m-80) REVERT: B 454 MET cc_start: 0.8632 (ptm) cc_final: 0.8415 (ptm) REVERT: B 466 LEU cc_start: 0.8140 (mt) cc_final: 0.7867 (mm) REVERT: B 488 ASP cc_start: 0.8444 (p0) cc_final: 0.8235 (p0) REVERT: B 553 GLU cc_start: 0.7595 (pt0) cc_final: 0.7291 (pp20) REVERT: B 735 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8408 (ttmt) REVERT: B 977 ASN cc_start: 0.4986 (OUTLIER) cc_final: 0.4498 (t0) REVERT: B 1105 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7475 (p) outliers start: 23 outliers final: 7 residues processed: 176 average time/residue: 0.3454 time to fit residues: 67.7756 Evaluate side-chains 135 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 977 ASN Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 977 ASN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 81 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN A 892 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116241 restraints weight = 13057.742| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.07 r_work: 0.3248 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10624 Z= 0.176 Angle : 0.506 9.153 14488 Z= 0.275 Chirality : 0.040 0.164 1698 Planarity : 0.004 0.050 1798 Dihedral : 5.313 41.816 1562 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.78 % Allowed : 12.62 % Favored : 84.59 % 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: 0.59 (0.23), residues: 1346 helix: 1.56 (0.19), residues: 784 sheet: -0.78 (0.41), residues: 142 loop : -1.42 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 759 TYR 0.021 0.001 TYR B 827 PHE 0.018 0.002 PHE A1113 TRP 0.009 0.001 TRP A 779 HIS 0.008 0.002 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00403 (10624) covalent geometry : angle 0.50630 (14488) hydrogen bonds : bond 0.04380 ( 604) hydrogen bonds : angle 4.44314 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.7636 (ttp) cc_final: 0.7428 (ttt) REVERT: A 466 LEU cc_start: 0.8718 (mt) cc_final: 0.8513 (mm) REVERT: A 514 SER cc_start: 0.8774 (t) cc_final: 0.8505 (p) REVERT: A 548 ASN cc_start: 0.8437 (t0) cc_final: 0.7106 (p0) REVERT: A 555 SER cc_start: 0.7714 (m) cc_final: 0.6960 (p) REVERT: A 766 PHE cc_start: 0.7985 (m-10) cc_final: 0.7287 (t80) REVERT: A 892 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6749 (mt0) REVERT: A 1067 TYR cc_start: 0.8793 (t80) cc_final: 0.8580 (t80) REVERT: A 1071 LYS cc_start: 0.7997 (mttt) cc_final: 0.7794 (mttt) REVERT: A 1088 PRO cc_start: 0.8451 (Cg_endo) cc_final: 0.8177 (Cg_exo) REVERT: B 466 LEU cc_start: 0.8524 (mt) cc_final: 0.8285 (mm) REVERT: B 471 ASP cc_start: 0.8528 (m-30) cc_final: 0.8113 (m-30) REVERT: B 553 GLU cc_start: 0.7939 (pt0) cc_final: 0.7469 (pp20) REVERT: B 934 GLN cc_start: 0.8074 (tt0) cc_final: 0.7784 (tt0) REVERT: B 1067 TYR cc_start: 0.8704 (t80) cc_final: 0.8413 (t80) outliers start: 28 outliers final: 12 residues processed: 143 average time/residue: 0.3489 time to fit residues: 55.3013 Evaluate side-chains 127 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 121 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 HIS ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116984 restraints weight = 13057.975| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.05 r_work: 0.3211 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10624 Z= 0.132 Angle : 0.455 7.027 14488 Z= 0.246 Chirality : 0.039 0.168 1698 Planarity : 0.003 0.050 1798 Dihedral : 4.937 36.778 1562 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.38 % Allowed : 12.92 % Favored : 83.70 % 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: 0.90 (0.23), residues: 1346 helix: 1.79 (0.19), residues: 784 sheet: -0.49 (0.40), residues: 142 loop : -1.31 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 464 TYR 0.019 0.001 TYR B 827 PHE 0.016 0.001 PHE B 766 TRP 0.008 0.001 TRP A 779 HIS 0.006 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00297 (10624) covalent geometry : angle 0.45467 (14488) hydrogen bonds : bond 0.03862 ( 604) hydrogen bonds : angle 4.22723 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7271 (ttt) REVERT: A 440 TYR cc_start: 0.7541 (m-80) cc_final: 0.7208 (m-10) REVERT: A 466 LEU cc_start: 0.8510 (mt) cc_final: 0.8278 (mm) REVERT: A 514 SER cc_start: 0.8728 (t) cc_final: 0.8458 (p) REVERT: A 548 ASN cc_start: 0.8433 (t0) cc_final: 0.7102 (p0) REVERT: A 555 SER cc_start: 0.7721 (m) cc_final: 0.6690 (p) REVERT: A 602 ASP cc_start: 0.8614 (p0) cc_final: 0.8230 (p0) REVERT: A 689 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: A 859 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7982 (mppt) REVERT: A 883 SER cc_start: 0.8734 (p) cc_final: 0.8456 (m) REVERT: A 1060 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: A 1088 PRO cc_start: 0.8414 (Cg_endo) cc_final: 0.8160 (Cg_exo) REVERT: B 466 LEU cc_start: 0.8274 (mt) cc_final: 0.8038 (mm) REVERT: B 471 ASP cc_start: 0.8472 (m-30) cc_final: 0.8037 (m-30) REVERT: B 516 LEU cc_start: 0.8232 (mm) cc_final: 0.8008 (mm) REVERT: B 553 GLU cc_start: 0.7868 (pt0) cc_final: 0.7382 (pp20) REVERT: B 1067 TYR cc_start: 0.8576 (t80) cc_final: 0.8346 (t80) outliers start: 34 outliers final: 16 residues processed: 140 average time/residue: 0.3404 time to fit residues: 52.4676 Evaluate side-chains 136 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 24 optimal weight: 0.0980 chunk 71 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 892 GLN A 965 HIS B 540 HIS B 706 HIS B 934 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115645 restraints weight = 12662.856| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.00 r_work: 0.3242 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10624 Z= 0.136 Angle : 0.457 6.122 14488 Z= 0.246 Chirality : 0.039 0.166 1698 Planarity : 0.003 0.049 1798 Dihedral : 4.889 38.005 1562 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.48 % Allowed : 13.72 % Favored : 82.80 % 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: 1.15 (0.23), residues: 1346 helix: 1.99 (0.19), residues: 778 sheet: -0.22 (0.41), residues: 142 loop : -1.23 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 464 TYR 0.019 0.001 TYR B 827 PHE 0.030 0.001 PHE A 881 TRP 0.008 0.001 TRP A 779 HIS 0.006 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00307 (10624) covalent geometry : angle 0.45684 (14488) hydrogen bonds : bond 0.03865 ( 604) hydrogen bonds : angle 4.15096 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7599 (ttt) REVERT: A 440 TYR cc_start: 0.7796 (m-80) cc_final: 0.7480 (m-10) REVERT: A 466 LEU cc_start: 0.8774 (mt) cc_final: 0.8538 (mm) REVERT: A 514 SER cc_start: 0.8940 (t) cc_final: 0.8688 (p) REVERT: A 548 ASN cc_start: 0.8505 (t0) cc_final: 0.7285 (p0) REVERT: A 555 SER cc_start: 0.7898 (m) cc_final: 0.6927 (p) REVERT: A 689 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: A 735 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8564 (mmmt) REVERT: A 859 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8283 (mttp) REVERT: A 892 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6479 (mt0) REVERT: A 1030 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6468 (tp30) REVERT: A 1088 PRO cc_start: 0.8368 (Cg_endo) cc_final: 0.8087 (Cg_exo) REVERT: B 466 LEU cc_start: 0.8545 (mt) cc_final: 0.8337 (mm) REVERT: B 471 ASP cc_start: 0.8466 (m-30) cc_final: 0.8067 (m-30) REVERT: B 516 LEU cc_start: 0.8351 (mm) cc_final: 0.8109 (mm) REVERT: B 553 GLU cc_start: 0.7947 (pt0) cc_final: 0.7537 (pp20) REVERT: B 934 GLN cc_start: 0.8810 (mt0) cc_final: 0.8303 (mt0) REVERT: B 1067 TYR cc_start: 0.8774 (t80) cc_final: 0.8485 (t80) outliers start: 35 outliers final: 18 residues processed: 142 average time/residue: 0.3895 time to fit residues: 61.1515 Evaluate side-chains 141 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 892 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116059 restraints weight = 12750.756| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.99 r_work: 0.3267 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10624 Z= 0.125 Angle : 0.446 5.859 14488 Z= 0.241 Chirality : 0.039 0.164 1698 Planarity : 0.003 0.046 1798 Dihedral : 4.795 36.743 1562 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.08 % Allowed : 14.91 % Favored : 82.01 % 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: 1.28 (0.23), residues: 1346 helix: 2.07 (0.18), residues: 778 sheet: -0.05 (0.42), residues: 142 loop : -1.18 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 759 TYR 0.019 0.001 TYR B 827 PHE 0.018 0.001 PHE B 766 TRP 0.008 0.001 TRP A 779 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00281 (10624) covalent geometry : angle 0.44638 (14488) hydrogen bonds : bond 0.03715 ( 604) hydrogen bonds : angle 4.09256 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.427 Fit side-chains REVERT: A 440 TYR cc_start: 0.7808 (m-80) cc_final: 0.7469 (m-10) REVERT: A 466 LEU cc_start: 0.8802 (mt) cc_final: 0.8564 (mm) REVERT: A 514 SER cc_start: 0.8981 (t) cc_final: 0.8736 (p) REVERT: A 548 ASN cc_start: 0.8546 (t0) cc_final: 0.7345 (p0) REVERT: A 555 SER cc_start: 0.7815 (m) cc_final: 0.6964 (p) REVERT: A 689 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: A 735 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8558 (mmmt) REVERT: A 859 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8314 (mttp) REVERT: A 883 SER cc_start: 0.8948 (p) cc_final: 0.8675 (m) REVERT: A 1030 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6548 (tp30) REVERT: A 1060 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8708 (mt-10) REVERT: A 1088 PRO cc_start: 0.8397 (Cg_endo) cc_final: 0.8103 (Cg_exo) REVERT: B 458 ASP cc_start: 0.8423 (p0) cc_final: 0.8086 (p0) REVERT: B 466 LEU cc_start: 0.8556 (mt) cc_final: 0.8352 (mm) REVERT: B 471 ASP cc_start: 0.8479 (m-30) cc_final: 0.8086 (m-30) REVERT: B 516 LEU cc_start: 0.8390 (mm) cc_final: 0.8133 (mm) REVERT: B 553 GLU cc_start: 0.7963 (pt0) cc_final: 0.7568 (pp20) REVERT: B 934 GLN cc_start: 0.8783 (mt0) cc_final: 0.8248 (mt0) REVERT: B 1067 TYR cc_start: 0.8774 (t80) cc_final: 0.8475 (t80) outliers start: 31 outliers final: 19 residues processed: 144 average time/residue: 0.4406 time to fit residues: 69.8091 Evaluate side-chains 145 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 122 optimal weight: 0.0010 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117134 restraints weight = 12664.837| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.99 r_work: 0.3283 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10624 Z= 0.103 Angle : 0.445 8.193 14488 Z= 0.236 Chirality : 0.039 0.162 1698 Planarity : 0.003 0.048 1798 Dihedral : 4.632 33.826 1562 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.49 % Allowed : 15.81 % Favored : 81.71 % 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: 1.45 (0.23), residues: 1346 helix: 2.18 (0.19), residues: 778 sheet: 0.11 (0.43), residues: 142 loop : -1.08 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 759 TYR 0.018 0.001 TYR B 827 PHE 0.018 0.001 PHE B 881 TRP 0.007 0.001 TRP A 779 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00226 (10624) covalent geometry : angle 0.44491 (14488) hydrogen bonds : bond 0.03466 ( 604) hydrogen bonds : angle 4.01928 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.439 Fit side-chains REVERT: A 440 TYR cc_start: 0.7727 (m-80) cc_final: 0.7382 (m-10) REVERT: A 466 LEU cc_start: 0.8779 (mt) cc_final: 0.8535 (mm) REVERT: A 514 SER cc_start: 0.9002 (t) cc_final: 0.8759 (p) REVERT: A 548 ASN cc_start: 0.8545 (t0) cc_final: 0.7400 (p0) REVERT: A 555 SER cc_start: 0.7805 (m) cc_final: 0.6958 (p) REVERT: A 689 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: A 700 MET cc_start: 0.3620 (tmt) cc_final: 0.2443 (tpt) REVERT: A 735 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8572 (mmmt) REVERT: A 859 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8319 (mttp) REVERT: A 892 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6551 (mt0) REVERT: A 1030 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6554 (tp30) REVERT: A 1060 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8718 (mt-10) REVERT: A 1088 PRO cc_start: 0.8362 (Cg_endo) cc_final: 0.8074 (Cg_exo) REVERT: B 458 ASP cc_start: 0.8382 (p0) cc_final: 0.8027 (p0) REVERT: B 466 LEU cc_start: 0.8490 (mt) cc_final: 0.8287 (mm) REVERT: B 471 ASP cc_start: 0.8457 (m-30) cc_final: 0.8066 (m-30) REVERT: B 516 LEU cc_start: 0.8384 (mm) cc_final: 0.8103 (mm) REVERT: B 553 GLU cc_start: 0.7945 (pt0) cc_final: 0.7582 (pp20) REVERT: B 1067 TYR cc_start: 0.8751 (t80) cc_final: 0.8453 (t80) outliers start: 25 outliers final: 20 residues processed: 145 average time/residue: 0.4258 time to fit residues: 68.5417 Evaluate side-chains 144 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 64 optimal weight: 0.0270 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN B 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119101 restraints weight = 12691.253| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.05 r_work: 0.3264 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10624 Z= 0.097 Angle : 0.428 6.287 14488 Z= 0.229 Chirality : 0.038 0.161 1698 Planarity : 0.003 0.045 1798 Dihedral : 4.489 31.955 1562 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.78 % Allowed : 15.90 % Favored : 81.31 % 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: 1.60 (0.23), residues: 1346 helix: 2.27 (0.18), residues: 778 sheet: 0.26 (0.43), residues: 142 loop : -0.98 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 759 TYR 0.017 0.001 TYR B 827 PHE 0.020 0.001 PHE A 881 TRP 0.007 0.001 TRP A 779 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00211 (10624) covalent geometry : angle 0.42784 (14488) hydrogen bonds : bond 0.03298 ( 604) hydrogen bonds : angle 3.95091 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.435 Fit side-chains REVERT: A 440 TYR cc_start: 0.7740 (m-80) cc_final: 0.7430 (m-10) REVERT: A 466 LEU cc_start: 0.8868 (mt) cc_final: 0.8622 (mm) REVERT: A 508 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7447 (ttm-80) REVERT: A 514 SER cc_start: 0.9013 (t) cc_final: 0.8781 (p) REVERT: A 548 ASN cc_start: 0.8533 (t0) cc_final: 0.7430 (p0) REVERT: A 555 SER cc_start: 0.7834 (m) cc_final: 0.7036 (p) REVERT: A 700 MET cc_start: 0.3634 (tmt) cc_final: 0.2461 (tpt) REVERT: A 735 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8643 (mmmt) REVERT: A 1030 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6598 (tp30) REVERT: A 1088 PRO cc_start: 0.8390 (Cg_endo) cc_final: 0.8114 (Cg_exo) REVERT: B 458 ASP cc_start: 0.8445 (p0) cc_final: 0.8064 (p0) REVERT: B 471 ASP cc_start: 0.8485 (m-30) cc_final: 0.8017 (m-30) REVERT: B 516 LEU cc_start: 0.8406 (mm) cc_final: 0.8140 (mm) REVERT: B 553 GLU cc_start: 0.7840 (pt0) cc_final: 0.7534 (pp20) REVERT: B 1067 TYR cc_start: 0.8790 (t80) cc_final: 0.8482 (t80) outliers start: 28 outliers final: 18 residues processed: 141 average time/residue: 0.4156 time to fit residues: 64.9086 Evaluate side-chains 146 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 892 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121513 restraints weight = 12943.396| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.97 r_work: 0.3270 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10624 Z= 0.114 Angle : 0.439 5.806 14488 Z= 0.236 Chirality : 0.039 0.156 1698 Planarity : 0.003 0.044 1798 Dihedral : 4.585 34.448 1562 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.39 % Allowed : 16.50 % Favored : 81.11 % 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: 1.74 (0.23), residues: 1346 helix: 2.41 (0.18), residues: 766 sheet: 0.32 (0.43), residues: 142 loop : -0.89 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 759 TYR 0.017 0.001 TYR B 827 PHE 0.023 0.001 PHE B 881 TRP 0.007 0.001 TRP A 779 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00255 (10624) covalent geometry : angle 0.43927 (14488) hydrogen bonds : bond 0.03518 ( 604) hydrogen bonds : angle 4.00648 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.358 Fit side-chains REVERT: A 440 TYR cc_start: 0.7780 (m-80) cc_final: 0.7382 (m-10) REVERT: A 466 LEU cc_start: 0.8709 (mt) cc_final: 0.8471 (mm) REVERT: A 514 SER cc_start: 0.9032 (t) cc_final: 0.8793 (p) REVERT: A 521 ASP cc_start: 0.6246 (p0) cc_final: 0.6000 (p0) REVERT: A 543 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6956 (mtp) REVERT: A 548 ASN cc_start: 0.8556 (t0) cc_final: 0.7576 (p0) REVERT: A 555 SER cc_start: 0.7699 (m) cc_final: 0.7034 (p) REVERT: A 700 MET cc_start: 0.3597 (tmt) cc_final: 0.2433 (tpt) REVERT: A 735 LYS cc_start: 0.8851 (ttmm) cc_final: 0.8527 (mmmt) REVERT: A 1030 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6497 (tp30) REVERT: A 1088 PRO cc_start: 0.8368 (Cg_endo) cc_final: 0.8094 (Cg_exo) REVERT: B 458 ASP cc_start: 0.8373 (p0) cc_final: 0.7980 (p0) REVERT: B 466 LEU cc_start: 0.8498 (mm) cc_final: 0.8126 (mm) REVERT: B 471 ASP cc_start: 0.8415 (m-30) cc_final: 0.8013 (m-30) REVERT: B 516 LEU cc_start: 0.8346 (mm) cc_final: 0.8078 (mm) REVERT: B 553 GLU cc_start: 0.7795 (pt0) cc_final: 0.7455 (pp20) REVERT: B 1067 TYR cc_start: 0.8764 (t80) cc_final: 0.8448 (t80) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 0.3738 time to fit residues: 59.4324 Evaluate side-chains 137 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117310 restraints weight = 12616.970| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.01 r_work: 0.3292 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10624 Z= 0.111 Angle : 0.453 9.316 14488 Z= 0.239 Chirality : 0.039 0.156 1698 Planarity : 0.003 0.044 1798 Dihedral : 4.512 32.984 1562 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.19 % Allowed : 17.00 % Favored : 80.82 % 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: 1.69 (0.23), residues: 1346 helix: 2.34 (0.18), residues: 778 sheet: 0.40 (0.43), residues: 142 loop : -0.98 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 759 TYR 0.017 0.001 TYR B 827 PHE 0.020 0.001 PHE A 881 TRP 0.007 0.001 TRP A 779 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00248 (10624) covalent geometry : angle 0.45331 (14488) hydrogen bonds : bond 0.03438 ( 604) hydrogen bonds : angle 4.01191 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.402 Fit side-chains REVERT: A 440 TYR cc_start: 0.7785 (m-80) cc_final: 0.7440 (m-10) REVERT: A 466 LEU cc_start: 0.8845 (mt) cc_final: 0.8608 (mm) REVERT: A 514 SER cc_start: 0.9071 (t) cc_final: 0.8840 (p) REVERT: A 543 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7090 (mtp) REVERT: A 548 ASN cc_start: 0.8595 (t0) cc_final: 0.8064 (p0) REVERT: A 700 MET cc_start: 0.3716 (tmt) cc_final: 0.2442 (tpt) REVERT: A 735 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8619 (mmmt) REVERT: A 1030 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6582 (tp30) REVERT: A 1088 PRO cc_start: 0.8406 (Cg_endo) cc_final: 0.8138 (Cg_exo) REVERT: B 458 ASP cc_start: 0.8454 (p0) cc_final: 0.8059 (p0) REVERT: B 471 ASP cc_start: 0.8480 (m-30) cc_final: 0.8101 (m-30) REVERT: B 516 LEU cc_start: 0.8399 (mm) cc_final: 0.8155 (mm) REVERT: B 1067 TYR cc_start: 0.8838 (t80) cc_final: 0.8529 (t80) outliers start: 22 outliers final: 19 residues processed: 135 average time/residue: 0.3657 time to fit residues: 54.7966 Evaluate side-chains 137 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 93 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122942 restraints weight = 12886.393| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.92 r_work: 0.3314 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10624 Z= 0.101 Angle : 0.439 8.360 14488 Z= 0.234 Chirality : 0.038 0.153 1698 Planarity : 0.003 0.044 1798 Dihedral : 4.378 31.114 1562 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.19 % Allowed : 17.10 % Favored : 80.72 % 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: 1.79 (0.23), residues: 1346 helix: 2.41 (0.18), residues: 778 sheet: 0.47 (0.43), residues: 142 loop : -0.93 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 759 TYR 0.017 0.001 TYR B 827 PHE 0.027 0.001 PHE B 881 TRP 0.007 0.001 TRP B 806 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00222 (10624) covalent geometry : angle 0.43946 (14488) hydrogen bonds : bond 0.03297 ( 604) hydrogen bonds : angle 3.97214 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3125.82 seconds wall clock time: 54 minutes 10.14 seconds (3250.14 seconds total)