Starting phenix.real_space_refine on Fri Jul 3 19:23:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpx_61717/07_2026/9jpx_61717.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpx_61717/07_2026/9jpx_61717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jpx_61717/07_2026/9jpx_61717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpx_61717/07_2026/9jpx_61717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jpx_61717/07_2026/9jpx_61717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpx_61717/07_2026/9jpx_61717.map" } resolution = 2.95 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= -0.001 sd= 0.022 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 56 5.49 5 S 103 5.16 5 C 9572 2.51 5 N 2681 2.21 5 O 2983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15399 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4411 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} Conformer: "B" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} bond proxies already assigned to first conformer: 4495 Chain: "B" Number of atoms: 2708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2687 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 344, 2687 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2731 Chain: "C" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4397 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 521} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2694 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2684 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 345, 2684 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2740 Chain: "F" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "L" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "M" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 727 69.787 102.924 41.375 1.00 64.14 S ATOM 2095 SG CYS A 730 71.731 105.652 39.374 1.00 66.55 S ATOM 9193 SG CYS C 727 27.797 49.818 41.324 1.00 61.99 S ATOM 9214 SG CYS C 730 25.810 47.044 39.414 1.00 62.87 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 Time building chain proxies: 3.96, per 1000 atoms: 0.26 Number of scatterers: 15399 At special positions: 0 Unit cell: (99.64, 153.7, 103.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 103 16.00 P 56 15.00 O 2983 8.00 N 2681 7.00 C 9572 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: 1.43 Conformation dependent library (CDL) restraints added in 830.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " Number of angles added : 4 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 17 sheets defined 35.8% alpha, 23.6% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.619A pdb=" N LEU A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 682 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 792 through 812 Processing helix chain 'A' and resid 822 through 842 removed outlier: 3.529A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 828 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 867 removed outlier: 3.665A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 909 through 924 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.838A pdb=" N LYS A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 996 through 1003 removed outlier: 4.049A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 163 through 167 removed outlier: 4.089A pdb=" N ARG B 167 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.511A pdb=" N HIS B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 580 Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.655A pdb=" N CYS C 651 " --> pdb=" O SER C 648 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS C 652 " --> pdb=" O GLU C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 652' Processing helix chain 'C' and resid 664 through 684 Proline residue: C 674 - end of helix removed outlier: 4.206A pdb=" N SER C 684 " --> pdb=" O GLU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 794 through 813 removed outlier: 3.567A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 842 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 removed outlier: 3.641A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 removed outlier: 3.945A pdb=" N HIS C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 878 " --> pdb=" O GLU C 874 " (cutoff:3.500A) Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 909 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 950 removed outlier: 3.775A pdb=" N GLU C 948 " --> pdb=" O PRO C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.763A pdb=" N LYS C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 Processing helix chain 'C' and resid 996 through 1004 removed outlier: 4.052A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C1004 " --> pdb=" O GLN C1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.576A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.354A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.354A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.678A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.529A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.083A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N CYS B 124 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B 114 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG B 123 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL B 112 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR B 125 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N MET B 110 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS B 127 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR B 108 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.250A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.890A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 518 through 519 removed outlier: 6.526A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 6.526A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.870A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 10.109A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.131A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.520A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.916A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 262 through 267 removed outlier: 7.047A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4534 1.33 - 1.45: 2829 1.45 - 1.57: 8240 1.57 - 1.69: 110 1.69 - 1.81: 157 Bond restraints: 15870 Sorted by residual: bond pdb=" C4' DA M 18 " pdb=" C3' DA M 18 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.00e-02 1.00e+04 8.37e+00 bond pdb=" C3' DG G 41 " pdb=" C2' DG G 41 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.87e+00 bond pdb=" C3' DT M 22 " pdb=" C2' DT M 22 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.89e+00 bond pdb=" O4' DG G 41 " pdb=" C1' DG G 41 " ideal model delta sigma weight residual 1.420 1.392 0.028 1.10e-02 8.26e+03 6.35e+00 bond pdb=" C3' DT L 22 " pdb=" C2' DT L 22 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.29e+00 ... (remaining 15865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 20920 1.36 - 2.72: 652 2.72 - 4.08: 105 4.08 - 5.44: 17 5.44 - 6.80: 5 Bond angle restraints: 21699 Sorted by residual: angle pdb=" O4' DA M 18 " pdb=" C4' DA M 18 " pdb=" C3' DA M 18 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" O4' DT F 29 " pdb=" C4' DT F 29 " pdb=" C3' DT F 29 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O4' DT G 40 " pdb=" C4' DT G 40 " pdb=" C3' DT G 40 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT G 38 " pdb=" C4 DT G 38 " pdb=" O4 DT G 38 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT F 27 " pdb=" C4 DT F 27 " pdb=" O4 DT F 27 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 ... (remaining 21694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 8602 17.73 - 35.46: 522 35.46 - 53.19: 252 53.19 - 70.93: 36 70.93 - 88.66: 2 Dihedral angle restraints: 9414 sinusoidal: 4212 harmonic: 5202 Sorted by residual: dihedral pdb=" CA ALA C 941 " pdb=" C ALA C 941 " pdb=" N HIS C 942 " pdb=" CA HIS C 942 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ALA A 941 " pdb=" C ALA A 941 " pdb=" N HIS A 942 " pdb=" CA HIS A 942 " ideal model delta harmonic sigma weight residual 180.00 -161.53 -18.47 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA VAL A 776 " pdb=" C VAL A 776 " pdb=" N LYS A 777 " pdb=" CA LYS A 777 " ideal model delta harmonic sigma weight residual -180.00 -163.81 -16.19 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 9411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1370 0.032 - 0.064: 601 0.064 - 0.096: 266 0.096 - 0.128: 113 0.128 - 0.160: 10 Chirality restraints: 2360 Sorted by residual: chirality pdb=" C3' DT G 38 " pdb=" C4' DT G 38 " pdb=" O3' DT G 38 " pdb=" C2' DT G 38 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" C3' DT F 27 " pdb=" C4' DT F 27 " pdb=" O3' DT F 27 " pdb=" C2' DT F 27 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA PHE C 784 " pdb=" N PHE C 784 " pdb=" C PHE C 784 " pdb=" CB PHE C 784 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 2357 not shown) Planarity restraints: 2602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 179 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO D 180 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 180 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 180 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 179 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO B 180 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO B 99 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.023 5.00e-02 4.00e+02 ... (remaining 2599 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1798 2.74 - 3.28: 13913 3.28 - 3.82: 25387 3.82 - 4.36: 30517 4.36 - 4.90: 52759 Nonbonded interactions: 124374 Sorted by model distance: nonbonded pdb=" OH TYR A 805 " pdb=" OD1 ASP A 834 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR A 559 " pdb=" OE2 GLU A 597 " model vdw 2.207 3.040 nonbonded pdb=" O MET A 691 " pdb=" NH1 ARG A 696 " model vdw 2.236 3.120 nonbonded pdb=" OH TYR C 559 " pdb=" OE2 GLU C 597 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 308 " pdb=" OD1 ASP B 310 " model vdw 2.247 3.040 ... (remaining 124369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 461 through 906 or resid 908 through 1006 or (resid 1007 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1101 through 11 \ 02)) selection = (chain 'C' and (resid 461 through 906 or resid 908 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 80 or (resid 81 through 8 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 89 through 1 \ 17 or (resid 118 and (name N or name CA or name C or name O or name CB )) or res \ id 119 through 236 or resid 238 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 350)) } 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=0.50 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.090 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.006 0.036 15878 Z= 0.340 Angle : 0.571 6.803 21703 Z= 0.378 Chirality : 0.045 0.160 2360 Planarity : 0.004 0.044 2602 Dihedral : 13.842 88.658 6066 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.29 % Allowed : 4.84 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1784 helix: 2.10 (0.23), residues: 550 sheet: 0.98 (0.28), residues: 348 loop : -0.46 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 137 TYR 0.018 0.002 TYR A 805 PHE 0.019 0.002 PHE C 916 TRP 0.015 0.002 TRP C 893 HIS 0.005 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.34 (15870) covalent geometry : angle 0.56969 / 0.38 (21699) hydrogen bonds : bond 0.07681 / 4.87 ( 699) hydrogen bonds : angle 5.04121 / 3.58 ( 2007) metal coordination : bond 0.00916 / 0.60 ( 8) metal coordination : angle 3.32257 / 1.72 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 8 residues processed: 243 average time/residue: 0.6760 time to fit residues: 179.8656 Evaluate side-chains 106 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 731 ASP Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 GLN A 637 ASN A 961 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 961 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.072925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.054479 restraints weight = 72926.048| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 4.26 r_work: 0.2446 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15878 Z= 0.137 Angle : 0.587 7.257 21703 Z= 0.316 Chirality : 0.041 0.232 2360 Planarity : 0.004 0.059 2602 Dihedral : 16.022 110.244 2589 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.98 % Allowed : 11.28 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1784 helix: 2.16 (0.23), residues: 552 sheet: 0.99 (0.28), residues: 341 loop : -0.40 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 828 TYR 0.017 0.001 TYR A 805 PHE 0.023 0.001 PHE A 911 TRP 0.019 0.001 TRP C 893 HIS 0.006 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (15870) covalent geometry : angle 0.58640 / 0.32 (21699) hydrogen bonds : bond 0.03655 / 2.49 ( 699) hydrogen bonds : angle 4.52308 / 3.16 ( 2007) metal coordination : bond 0.00584 / 0.44 ( 8) metal coordination : angle 2.24605 / 1.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ASP cc_start: 0.9170 (m-30) cc_final: 0.8964 (p0) REVERT: B 302 MET cc_start: 0.8362 (ptp) cc_final: 0.8040 (ptp) REVERT: B 339 MET cc_start: 0.8089 (mmm) cc_final: 0.7750 (mmm) REVERT: C 595 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8810 (p) REVERT: C 849 MET cc_start: 0.9034 (tpp) cc_final: 0.8830 (tpp) REVERT: D 302 MET cc_start: 0.8127 (ptp) cc_final: 0.7730 (ptp) REVERT: D 339 MET cc_start: 0.7972 (mmm) cc_final: 0.7530 (mmm) outliers start: 31 outliers final: 8 residues processed: 132 average time/residue: 0.6753 time to fit residues: 97.8905 Evaluate side-chains 99 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 159 optimal weight: 7.9990 chunk 171 optimal weight: 0.0670 chunk 172 optimal weight: 0.0060 chunk 113 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.057167 restraints weight = 82102.377| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 4.50 r_work: 0.2519 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15878 Z= 0.108 Angle : 0.527 7.357 21703 Z= 0.283 Chirality : 0.040 0.229 2360 Planarity : 0.004 0.042 2602 Dihedral : 15.775 59.743 2584 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.78 % Allowed : 11.60 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1784 helix: 2.06 (0.23), residues: 561 sheet: 1.10 (0.28), residues: 339 loop : -0.39 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 848 TYR 0.017 0.001 TYR A 805 PHE 0.024 0.001 PHE A 911 TRP 0.014 0.001 TRP C 893 HIS 0.004 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (15870) covalent geometry : angle 0.52625 / 0.28 (21699) hydrogen bonds : bond 0.03201 / 2.23 ( 699) hydrogen bonds : angle 4.37664 / 3.06 ( 2007) metal coordination : bond 0.00451 / 0.33 ( 8) metal coordination : angle 2.35307 / 0.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 ASP cc_start: 0.9185 (m-30) cc_final: 0.8970 (p0) REVERT: A 679 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8686 (ttp80) REVERT: B 302 MET cc_start: 0.8340 (ptp) cc_final: 0.7814 (ptp) REVERT: B 339 MET cc_start: 0.8325 (mmm) cc_final: 0.7899 (mmm) REVERT: C 582 ASP cc_start: 0.9445 (m-30) cc_final: 0.8959 (p0) REVERT: C 595 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8954 (p) REVERT: C 709 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: C 849 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8830 (tpp) REVERT: D 302 MET cc_start: 0.8209 (ptp) cc_final: 0.7740 (ptp) REVERT: D 339 MET cc_start: 0.8002 (mmm) cc_final: 0.7532 (mmm) outliers start: 28 outliers final: 10 residues processed: 123 average time/residue: 0.6117 time to fit residues: 82.8183 Evaluate side-chains 100 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 961 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS C 961 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.071187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.052235 restraints weight = 96658.135| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 4.79 r_work: 0.2374 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2381 r_free = 0.2381 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2381 r_free = 0.2381 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15878 Z= 0.176 Angle : 0.549 7.828 21703 Z= 0.291 Chirality : 0.041 0.158 2360 Planarity : 0.004 0.041 2602 Dihedral : 15.981 59.904 2584 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.78 % Allowed : 12.36 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1784 helix: 2.32 (0.23), residues: 552 sheet: 1.16 (0.28), residues: 341 loop : -0.32 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 848 TYR 0.015 0.001 TYR A 805 PHE 0.019 0.001 PHE A 911 TRP 0.012 0.001 TRP C 893 HIS 0.004 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (15870) covalent geometry : angle 0.54771 / 0.29 (21699) hydrogen bonds : bond 0.03486 / 2.40 ( 699) hydrogen bonds : angle 4.36588 / 3.04 ( 2007) metal coordination : bond 0.00923 / 0.60 ( 8) metal coordination : angle 3.05892 / 1.49 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 582 ASP cc_start: 0.9218 (m-30) cc_final: 0.9013 (p0) REVERT: B 38 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8629 (mtpp) REVERT: B 302 MET cc_start: 0.8439 (ptp) cc_final: 0.7988 (ptp) REVERT: B 339 MET cc_start: 0.8453 (mmm) cc_final: 0.8009 (mmm) REVERT: C 595 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8838 (p) REVERT: C 709 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 828 ARG cc_start: 0.9217 (tpp-160) cc_final: 0.8620 (mmp80) REVERT: C 849 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8772 (tpp) REVERT: C 974 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8199 (mpp) REVERT: D 302 MET cc_start: 0.8220 (ptp) cc_final: 0.7688 (ptp) REVERT: D 339 MET cc_start: 0.8289 (mmm) cc_final: 0.7751 (mmm) outliers start: 28 outliers final: 12 residues processed: 109 average time/residue: 0.6636 time to fit residues: 79.6899 Evaluate side-chains 100 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 925 LYS Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 162 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 15 optimal weight: 0.0270 chunk 64 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.074294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.053128 restraints weight = 83373.500| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 4.56 r_work: 0.2462 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15878 Z= 0.135 Angle : 0.526 8.396 21703 Z= 0.281 Chirality : 0.040 0.151 2360 Planarity : 0.003 0.040 2602 Dihedral : 15.941 59.990 2584 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.59 % Allowed : 12.68 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1784 helix: 2.33 (0.23), residues: 551 sheet: 1.20 (0.28), residues: 341 loop : -0.30 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 848 TYR 0.014 0.001 TYR A 805 PHE 0.018 0.001 PHE A 911 TRP 0.013 0.001 TRP C 893 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15870) covalent geometry : angle 0.52448 / 0.28 (21699) hydrogen bonds : bond 0.03274 / 2.27 ( 699) hydrogen bonds : angle 4.29422 / 2.98 ( 2007) metal coordination : bond 0.00727 / 0.48 ( 8) metal coordination : angle 2.78458 / 1.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 ASP cc_start: 0.9200 (m-30) cc_final: 0.8994 (p0) REVERT: B 38 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8704 (mtpp) REVERT: B 302 MET cc_start: 0.8522 (ptp) cc_final: 0.7975 (ptp) REVERT: C 595 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9001 (p) REVERT: C 709 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: C 828 ARG cc_start: 0.9227 (tpp-160) cc_final: 0.8676 (mmp80) REVERT: C 974 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8288 (mpp) REVERT: D 152 MET cc_start: 0.8867 (ttm) cc_final: 0.8574 (ttm) REVERT: D 302 MET cc_start: 0.8405 (ptp) cc_final: 0.7901 (ptp) REVERT: D 339 MET cc_start: 0.8199 (mmm) cc_final: 0.7669 (mmm) outliers start: 25 outliers final: 11 residues processed: 104 average time/residue: 0.6082 time to fit residues: 69.8236 Evaluate side-chains 95 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 925 LYS Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 118 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 175 optimal weight: 0.0030 chunk 154 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS A 961 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.053664 restraints weight = 57789.692| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.95 r_work: 0.2451 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15878 Z= 0.103 Angle : 0.511 9.381 21703 Z= 0.271 Chirality : 0.040 0.163 2360 Planarity : 0.003 0.043 2602 Dihedral : 15.840 59.953 2584 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.53 % Allowed : 13.13 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1784 helix: 2.26 (0.23), residues: 557 sheet: 1.22 (0.28), residues: 339 loop : -0.31 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 848 TYR 0.016 0.001 TYR A 586 PHE 0.018 0.001 PHE A 911 TRP 0.013 0.001 TRP C 893 HIS 0.003 0.000 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (15870) covalent geometry : angle 0.50997 / 0.27 (21699) hydrogen bonds : bond 0.03102 / 2.17 ( 699) hydrogen bonds : angle 4.23715 / 2.95 ( 2007) metal coordination : bond 0.00503 / 0.32 ( 8) metal coordination : angle 2.59272 / 1.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8612 (ttp80) REVERT: B 38 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8540 (mtpp) REVERT: B 302 MET cc_start: 0.8429 (ptp) cc_final: 0.7793 (ptp) REVERT: B 339 MET cc_start: 0.8369 (mmm) cc_final: 0.7916 (mmm) REVERT: C 595 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8720 (p) REVERT: C 709 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: C 828 ARG cc_start: 0.9173 (tpp-160) cc_final: 0.8586 (mmp80) REVERT: C 925 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9069 (ttmm) REVERT: D 152 MET cc_start: 0.8852 (ttm) cc_final: 0.8623 (ttm) REVERT: D 302 MET cc_start: 0.8159 (ptp) cc_final: 0.7563 (ptp) REVERT: D 339 MET cc_start: 0.8191 (mmm) cc_final: 0.7651 (mmm) outliers start: 24 outliers final: 10 residues processed: 109 average time/residue: 0.5426 time to fit residues: 65.3465 Evaluate side-chains 97 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 925 LYS Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.075602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.054735 restraints weight = 82930.557| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 4.55 r_work: 0.2468 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15878 Z= 0.137 Angle : 0.522 9.484 21703 Z= 0.275 Chirality : 0.040 0.173 2360 Planarity : 0.003 0.039 2602 Dihedral : 15.940 59.808 2584 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.34 % Allowed : 13.70 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.21), residues: 1784 helix: 2.33 (0.23), residues: 552 sheet: 1.27 (0.28), residues: 339 loop : -0.23 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 848 TYR 0.013 0.001 TYR A 805 PHE 0.016 0.001 PHE A 911 TRP 0.012 0.001 TRP C 893 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (15870) covalent geometry : angle 0.52099 / 0.28 (21699) hydrogen bonds : bond 0.03208 / 2.22 ( 699) hydrogen bonds : angle 4.24954 / 2.95 ( 2007) metal coordination : bond 0.00806 / 0.54 ( 8) metal coordination : angle 2.64383 / 1.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8660 (mtpp) REVERT: B 302 MET cc_start: 0.8517 (ptp) cc_final: 0.7903 (ptp) REVERT: B 339 MET cc_start: 0.8419 (mmm) cc_final: 0.7967 (mmm) REVERT: C 595 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.8977 (p) REVERT: C 709 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: C 828 ARG cc_start: 0.9232 (tpp-160) cc_final: 0.8869 (mmm160) REVERT: C 974 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8117 (mpp) REVERT: D 152 MET cc_start: 0.8922 (ttm) cc_final: 0.8716 (ttm) REVERT: D 302 MET cc_start: 0.8385 (ptp) cc_final: 0.7836 (ptp) REVERT: D 339 MET cc_start: 0.8224 (mmm) cc_final: 0.7683 (mmm) outliers start: 21 outliers final: 13 residues processed: 105 average time/residue: 0.6170 time to fit residues: 71.4329 Evaluate side-chains 101 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 925 LYS Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.074772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.053909 restraints weight = 79901.746| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 4.47 r_work: 0.2450 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15878 Z= 0.153 Angle : 0.530 8.889 21703 Z= 0.279 Chirality : 0.041 0.163 2360 Planarity : 0.003 0.045 2602 Dihedral : 16.013 59.989 2584 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.47 % Allowed : 13.58 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1784 helix: 2.35 (0.23), residues: 552 sheet: 1.22 (0.28), residues: 346 loop : -0.20 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 848 TYR 0.016 0.001 TYR A 586 PHE 0.017 0.001 PHE B 189 TRP 0.012 0.001 TRP C 893 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15870) covalent geometry : angle 0.52854 / 0.28 (21699) hydrogen bonds : bond 0.03298 / 2.27 ( 699) hydrogen bonds : angle 4.25091 / 2.95 ( 2007) metal coordination : bond 0.00950 / 0.62 ( 8) metal coordination : angle 2.76660 / 1.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 694 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9155 (pp) REVERT: B 38 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8696 (mtpp) REVERT: B 302 MET cc_start: 0.8571 (ptp) cc_final: 0.7919 (ptp) REVERT: B 339 MET cc_start: 0.8508 (mmm) cc_final: 0.8165 (mmm) REVERT: C 595 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.8999 (p) REVERT: C 709 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: C 828 ARG cc_start: 0.9249 (tpp-160) cc_final: 0.8909 (mmm160) REVERT: C 974 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8119 (mpp) REVERT: D 302 MET cc_start: 0.8507 (ptp) cc_final: 0.7970 (ptp) REVERT: D 339 MET cc_start: 0.8421 (mmm) cc_final: 0.7901 (mmm) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 0.6066 time to fit residues: 71.8409 Evaluate side-chains 105 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 925 LYS Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 750 HIS ** C 473 ASN ** 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 = 0.3073 r_free = 0.3073 target = 0.073121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.051813 restraints weight = 94591.959| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 4.77 r_work: 0.2425 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15878 Z= 0.165 Angle : 0.531 9.754 21703 Z= 0.280 Chirality : 0.041 0.159 2360 Planarity : 0.003 0.042 2602 Dihedral : 16.035 59.402 2584 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.40 % Allowed : 13.64 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.21), residues: 1784 helix: 2.36 (0.23), residues: 552 sheet: 1.24 (0.29), residues: 341 loop : -0.23 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 848 TYR 0.013 0.001 TYR A 805 PHE 0.014 0.001 PHE A 911 TRP 0.013 0.001 TRP C 893 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (15870) covalent geometry : angle 0.52982 / 0.28 (21699) hydrogen bonds : bond 0.03354 / 2.30 ( 699) hydrogen bonds : angle 4.28026 / 2.96 ( 2007) metal coordination : bond 0.01039 / 0.69 ( 8) metal coordination : angle 2.89511 / 1.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 694 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9137 (pp) REVERT: B 38 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8741 (mtpp) REVERT: B 302 MET cc_start: 0.8600 (ptp) cc_final: 0.7936 (ptp) REVERT: B 339 MET cc_start: 0.8562 (mmm) cc_final: 0.8218 (mmm) REVERT: C 595 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9031 (p) REVERT: C 709 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: C 828 ARG cc_start: 0.9277 (tpp-160) cc_final: 0.8937 (mmm160) REVERT: C 974 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: D 302 MET cc_start: 0.8571 (ptp) cc_final: 0.8005 (ptp) REVERT: D 339 MET cc_start: 0.8473 (mmm) cc_final: 0.7958 (mmm) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.6389 time to fit residues: 74.7629 Evaluate side-chains 101 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 925 LYS Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 961 ASN ** C 473 ASN ** 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 = 0.3092 r_free = 0.3092 target = 0.074139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.053000 restraints weight = 84785.028| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 4.59 r_work: 0.2457 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15878 Z= 0.115 Angle : 0.523 10.370 21703 Z= 0.275 Chirality : 0.040 0.168 2360 Planarity : 0.003 0.041 2602 Dihedral : 15.959 59.828 2584 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.15 % Allowed : 13.77 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1784 helix: 2.36 (0.23), residues: 552 sheet: 1.20 (0.28), residues: 355 loop : -0.21 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 848 TYR 0.013 0.001 TYR A 805 PHE 0.016 0.001 PHE B 189 TRP 0.013 0.001 TRP C 893 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (15870) covalent geometry : angle 0.52202 / 0.28 (21699) hydrogen bonds : bond 0.03151 / 2.18 ( 699) hydrogen bonds : angle 4.24063 / 2.93 ( 2007) metal coordination : bond 0.00678 / 0.44 ( 8) metal coordination : angle 2.84856 / 1.19 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8697 (mtpp) REVERT: B 339 MET cc_start: 0.8523 (mmm) cc_final: 0.8187 (mmm) REVERT: C 595 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.8976 (p) REVERT: C 709 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: C 828 ARG cc_start: 0.9251 (tpp-160) cc_final: 0.8699 (mmp80) REVERT: C 925 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9206 (ttmm) REVERT: D 302 MET cc_start: 0.8536 (ptp) cc_final: 0.7993 (ptp) REVERT: D 339 MET cc_start: 0.8441 (mmm) cc_final: 0.7936 (mmm) outliers start: 18 outliers final: 11 residues processed: 101 average time/residue: 0.5779 time to fit residues: 64.4819 Evaluate side-chains 97 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 925 LYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 66 optimal weight: 0.0020 chunk 131 optimal weight: 0.6980 chunk 114 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 158 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.055379 restraints weight = 93654.150| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 4.78 r_work: 0.2482 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15878 Z= 0.100 Angle : 0.523 11.997 21703 Z= 0.273 Chirality : 0.040 0.165 2360 Planarity : 0.003 0.056 2602 Dihedral : 15.862 59.666 2584 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.83 % Allowed : 14.53 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1784 helix: 2.36 (0.23), residues: 552 sheet: 1.27 (0.28), residues: 340 loop : -0.22 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 848 TYR 0.013 0.001 TYR A 805 PHE 0.016 0.001 PHE A 911 TRP 0.013 0.001 TRP C 893 HIS 0.003 0.000 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (15870) covalent geometry : angle 0.52217 / 0.27 (21699) hydrogen bonds : bond 0.03038 / 2.12 ( 699) hydrogen bonds : angle 4.21080 / 2.92 ( 2007) metal coordination : bond 0.00430 / 0.28 ( 8) metal coordination : angle 2.55809 / 1.04 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.62 seconds wall clock time: 69 minutes 55.71 seconds (4195.71 seconds total)