Starting phenix.real_space_refine on Thu Sep 18 09:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpx_61717/09_2025/9jpx_61717.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpx_61717/09_2025/9jpx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jpx_61717/09_2025/9jpx_61717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpx_61717/09_2025/9jpx_61717.map" model { file = "/net/cci-nas-00/data/ceres_data/9jpx_61717/09_2025/9jpx_61717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpx_61717/09_2025/9jpx_61717.cif" } 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-2.0-5805/lib/python3.9/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, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 6.03, per 1000 atoms: 0.39 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: 1.47 Conformation dependent library (CDL) restraints added in 917.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.10 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: 3.51 Time building geometry restraints manager: 1.91 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=" C ASP B 294 " pdb=" N ASN B 295 " ideal model delta sigma weight residual 1.332 1.314 0.018 1.40e-02 5.10e+03 1.72e+00 bond pdb=" CG PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 1.512 1.480 0.032 2.70e-02 1.37e+03 1.42e+00 bond pdb=" C4' DG G 41 " pdb=" O4' DG G 41 " ideal model delta sigma weight residual 1.450 1.426 0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C4' DA M 18 " pdb=" C3' DA M 18 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C4' DT M 22 " pdb=" O4' DT M 22 " ideal model delta sigma weight residual 1.450 1.427 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 15865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 21102 1.36 - 2.72: 479 2.72 - 4.08: 96 4.08 - 5.44: 17 5.44 - 6.80: 5 Bond angle restraints: 21699 Sorted by residual: angle pdb=" C HIS C 942 " pdb=" N VAL C 943 " pdb=" CA VAL C 943 " ideal model delta sigma weight residual 120.24 122.37 -2.13 6.30e-01 2.52e+00 1.14e+01 angle pdb=" N GLY D 221 " pdb=" CA GLY D 221 " pdb=" C GLY D 221 " ideal model delta sigma weight residual 110.56 114.84 -4.28 1.36e+00 5.41e-01 9.89e+00 angle pdb=" C VAL C 943 " pdb=" CA VAL C 943 " pdb=" CB VAL C 943 " ideal model delta sigma weight residual 114.35 111.66 2.69 1.06e+00 8.90e-01 6.44e+00 angle pdb=" C ASN C 740 " pdb=" N LEU C 741 " pdb=" CA LEU C 741 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.75e+00 angle pdb=" N LEU C 741 " pdb=" CA LEU C 741 " pdb=" C LEU C 741 " ideal model delta sigma weight residual 110.80 115.90 -5.10 2.13e+00 2.20e-01 5.73e+00 ... (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 - 0.029: 1329 0.029 - 0.058: 633 0.058 - 0.087: 240 0.087 - 0.116: 125 0.116 - 0.146: 33 Chirality restraints: 2360 Sorted by residual: 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 chirality pdb=" CA ILE A 953 " pdb=" N ILE A 953 " pdb=" C ILE A 953 " pdb=" CB ILE A 953 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE D 93 " pdb=" N ILE D 93 " pdb=" C ILE D 93 " pdb=" CB ILE D 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.220 Find NCS groups from input model: 0.270 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:8.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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= 0.243 Angle : 0.539 6.803 21703 Z= 0.291 Chirality : 0.043 0.146 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 aren 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 covalent geometry : bond 0.00562 (15870) covalent geometry : angle 0.53668 (21699) hydrogen bonds : bond 0.07681 ( 699) hydrogen bonds : angle 5.04121 ( 2007) metal coordination : bond 0.00916 ( 8) metal coordination : angle 3.32257 ( 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 : 0.614 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: 0.7496 time to fit residues: 198.3685 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 : 0.629 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.072787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.053911 restraints weight = 72852.513| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 4.41 r_work: 0.2438 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 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 = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15878 Z= 0.126 Angle : 0.567 7.513 21703 Z= 0.300 Chirality : 0.040 0.251 2360 Planarity : 0.004 0.054 2602 Dihedral : 15.811 98.066 2589 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.98 % Allowed : 11.09 % Favored : 86.93 % 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 aren not related in a simple way. whole: 1.00 (0.20), residues: 1784 helix: 2.08 (0.23), residues: 559 sheet: 1.06 (0.28), residues: 339 loop : -0.41 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 848 TYR 0.017 0.001 TYR A 805 PHE 0.027 0.001 PHE A 911 TRP 0.021 0.001 TRP C 893 HIS 0.006 0.001 HIS D 10 Details of bonding type rmsd covalent geometry : bond 0.00288 (15870) covalent geometry : angle 0.56577 (21699) hydrogen bonds : bond 0.03200 ( 699) hydrogen bonds : angle 4.42040 ( 2007) metal coordination : bond 0.00423 ( 8) metal coordination : angle 2.46782 ( 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 138 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 302 MET cc_start: 0.8321 (ptp) cc_final: 0.7957 (ptp) REVERT: B 339 MET cc_start: 0.8231 (mmm) cc_final: 0.7879 (mmm) REVERT: C 595 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8802 (p) REVERT: C 806 LYS cc_start: 0.8529 (mtpm) cc_final: 0.8263 (ttmm) REVERT: C 824 GLU cc_start: 0.8785 (pm20) cc_final: 0.8556 (pm20) REVERT: D 302 MET cc_start: 0.8165 (ptp) cc_final: 0.7810 (ptp) REVERT: D 339 MET cc_start: 0.8030 (mmm) cc_final: 0.7584 (mmm) outliers start: 31 outliers final: 10 residues processed: 130 average time/residue: 0.7144 time to fit residues: 101.8790 Evaluate side-chains 104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER 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 133 VAL 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: 0.9980 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 HIS ** 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 = 0.3036 r_free = 0.3036 target = 0.071464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.050170 restraints weight = 86148.833| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 4.59 r_work: 0.2389 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15878 Z= 0.275 Angle : 0.610 8.698 21703 Z= 0.320 Chirality : 0.043 0.174 2360 Planarity : 0.004 0.041 2602 Dihedral : 16.037 59.899 2584 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.04 % Allowed : 11.92 % Favored : 86.04 % 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 aren not related in a simple way. whole: 1.10 (0.21), residues: 1784 helix: 2.19 (0.23), residues: 553 sheet: 1.19 (0.29), residues: 338 loop : -0.39 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 848 TYR 0.015 0.001 TYR A 805 PHE 0.019 0.001 PHE A 911 TRP 0.014 0.001 TRP C 893 HIS 0.005 0.001 HIS D 10 Details of bonding type rmsd covalent geometry : bond 0.00634 (15870) covalent geometry : angle 0.60895 (21699) hydrogen bonds : bond 0.03908 ( 699) hydrogen bonds : angle 4.48632 ( 2007) metal coordination : bond 0.01643 ( 8) metal coordination : angle 3.23106 ( 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 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: B 302 MET cc_start: 0.8521 (ptp) cc_final: 0.8021 (ptp) REVERT: B 339 MET cc_start: 0.8607 (mmm) cc_final: 0.8269 (mmm) REVERT: C 595 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.9063 (p) REVERT: C 709 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: C 806 LYS cc_start: 0.8751 (mtpm) cc_final: 0.8454 (ttmm) REVERT: C 824 GLU cc_start: 0.8809 (pm20) cc_final: 0.8529 (pm20) REVERT: C 828 ARG cc_start: 0.9290 (tpp-160) cc_final: 0.8945 (mmm160) REVERT: C 925 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9168 (ttmm) REVERT: D 302 MET cc_start: 0.8436 (ptp) cc_final: 0.7976 (ptp) REVERT: D 339 MET cc_start: 0.8165 (mmm) cc_final: 0.7655 (mmm) outliers start: 32 outliers final: 15 residues processed: 116 average time/residue: 0.7105 time to fit residues: 90.2868 Evaluate side-chains 103 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 320 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 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 866 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 173 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3004 r_free = 0.3004 target = 0.070081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.050816 restraints weight = 96500.064| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 4.81 r_work: 0.2359 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2365 r_free = 0.2365 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2365 r_free = 0.2365 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15878 Z= 0.129 Angle : 0.522 9.293 21703 Z= 0.275 Chirality : 0.040 0.166 2360 Planarity : 0.004 0.040 2602 Dihedral : 15.792 59.963 2584 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.66 % Allowed : 12.62 % 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 aren not related in a simple way. whole: 1.18 (0.21), residues: 1784 helix: 2.26 (0.23), residues: 553 sheet: 1.18 (0.29), residues: 340 loop : -0.32 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 848 TYR 0.014 0.001 TYR A 805 PHE 0.019 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 covalent geometry : bond 0.00294 (15870) covalent geometry : angle 0.52068 (21699) hydrogen bonds : bond 0.03125 ( 699) hydrogen bonds : angle 4.31182 ( 2007) metal coordination : bond 0.00659 ( 8) metal coordination : angle 2.99135 ( 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: 26 poor density : 90 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8641 (mtpp) REVERT: B 302 MET cc_start: 0.8462 (ptp) cc_final: 0.8174 (ptp) REVERT: B 339 MET cc_start: 0.8626 (mmm) cc_final: 0.8211 (mmm) REVERT: C 595 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8869 (p) REVERT: C 709 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: C 806 LYS cc_start: 0.8648 (mtpm) cc_final: 0.8357 (ttmm) REVERT: C 824 GLU cc_start: 0.8813 (pm20) cc_final: 0.8500 (pm20) REVERT: C 828 ARG cc_start: 0.9247 (tpp-160) cc_final: 0.8928 (mmm160) REVERT: C 925 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9037 (ttmm) REVERT: C 974 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: D 302 MET cc_start: 0.8384 (ptp) cc_final: 0.7870 (ptp) REVERT: D 339 MET cc_start: 0.8112 (mmm) cc_final: 0.7616 (mmm) outliers start: 26 outliers final: 11 residues processed: 112 average time/residue: 0.7157 time to fit residues: 88.1781 Evaluate side-chains 98 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 69 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3049 r_free = 0.3049 target = 0.072034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.050859 restraints weight = 83821.601| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 4.55 r_work: 0.2404 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15878 Z= 0.200 Angle : 0.550 9.141 21703 Z= 0.289 Chirality : 0.041 0.178 2360 Planarity : 0.003 0.041 2602 Dihedral : 15.922 59.987 2584 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.78 % Allowed : 12.68 % Favored : 85.53 % 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 aren not related in a simple way. whole: 1.22 (0.21), residues: 1784 helix: 2.28 (0.23), residues: 552 sheet: 1.24 (0.29), residues: 341 loop : -0.29 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 848 TYR 0.014 0.001 TYR A 805 PHE 0.016 0.001 PHE A 911 TRP 0.014 0.001 TRP C 893 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd covalent geometry : bond 0.00459 (15870) covalent geometry : angle 0.54903 (21699) hydrogen bonds : bond 0.03381 ( 699) hydrogen bonds : angle 4.35096 ( 2007) metal coordination : bond 0.01214 ( 8) metal coordination : angle 2.99448 ( 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 115 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8749 (mtpp) REVERT: B 302 MET cc_start: 0.8575 (ptp) cc_final: 0.8007 (ptp) REVERT: B 339 MET cc_start: 0.8658 (mmm) cc_final: 0.8167 (mmm) REVERT: C 595 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9064 (p) REVERT: C 709 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: C 824 GLU cc_start: 0.8798 (pm20) cc_final: 0.8552 (pm20) REVERT: C 828 ARG cc_start: 0.9293 (tpp-160) cc_final: 0.8972 (mmm160) REVERT: C 925 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9182 (ttmm) REVERT: C 974 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8220 (mpp) REVERT: D 143 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8830 (m-30) REVERT: D 152 MET cc_start: 0.8896 (ttm) cc_final: 0.8530 (mmm) REVERT: D 302 MET cc_start: 0.8524 (ptp) cc_final: 0.8034 (ptp) REVERT: D 339 MET cc_start: 0.8427 (mmm) cc_final: 0.7953 (mmm) outliers start: 28 outliers final: 13 residues processed: 111 average time/residue: 0.6966 time to fit residues: 84.9829 Evaluate side-chains 104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 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 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 264 THR 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: 1.9990 chunk 86 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 HIS C 961 ASN D 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.068322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.050027 restraints weight = 57400.623| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 3.84 r_work: 0.2364 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2372 r_free = 0.2372 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2372 r_free = 0.2372 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15878 Z= 0.193 Angle : 0.545 8.746 21703 Z= 0.286 Chirality : 0.041 0.166 2360 Planarity : 0.003 0.043 2602 Dihedral : 15.960 59.727 2584 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.23 % Allowed : 12.43 % 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 aren not related in a simple way. whole: 1.22 (0.21), residues: 1784 helix: 2.31 (0.23), residues: 552 sheet: 1.20 (0.29), residues: 336 loop : -0.30 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 848 TYR 0.014 0.001 TYR A 805 PHE 0.018 0.001 PHE B 189 TRP 0.014 0.001 TRP C 893 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd covalent geometry : bond 0.00445 (15870) covalent geometry : angle 0.54373 (21699) hydrogen bonds : bond 0.03376 ( 699) hydrogen bonds : angle 4.34250 ( 2007) metal coordination : bond 0.01127 ( 8) metal coordination : angle 3.18020 ( 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 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8336 (ttp80) REVERT: B 38 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8668 (mtpp) REVERT: B 302 MET cc_start: 0.8514 (ptp) cc_final: 0.7996 (ptp) REVERT: B 339 MET cc_start: 0.8536 (mmm) cc_final: 0.8156 (mmm) REVERT: C 595 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8875 (p) REVERT: C 709 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: C 824 GLU cc_start: 0.8790 (pm20) cc_final: 0.8573 (pm20) REVERT: C 828 ARG cc_start: 0.9270 (tpp-160) cc_final: 0.8931 (mmm160) REVERT: C 925 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9056 (ttmm) REVERT: C 974 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8063 (mpp) REVERT: D 143 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8824 (m-30) REVERT: D 152 MET cc_start: 0.8855 (ttm) cc_final: 0.8640 (mmm) REVERT: D 162 MET cc_start: 0.9426 (mmm) cc_final: 0.9196 (mmm) REVERT: D 302 MET cc_start: 0.8488 (ptp) cc_final: 0.7906 (ptp) REVERT: D 339 MET cc_start: 0.8483 (mmm) cc_final: 0.7976 (mmm) outliers start: 35 outliers final: 16 residues processed: 117 average time/residue: 0.6495 time to fit residues: 84.0462 Evaluate side-chains 107 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 679 ARG 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 B residue 320 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 705 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 866 VAL 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 143 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 264 THR 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: 1.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 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 = 0.3044 r_free = 0.3044 target = 0.069175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.050203 restraints weight = 79338.835| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 4.43 r_work: 0.2403 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2478 r_free = 0.2478 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2478 r_free = 0.2478 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15878 Z= 0.185 Angle : 0.550 9.748 21703 Z= 0.286 Chirality : 0.041 0.156 2360 Planarity : 0.003 0.040 2602 Dihedral : 15.972 59.911 2584 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.85 % Allowed : 13.19 % 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 aren not related in a simple way. whole: 1.23 (0.21), residues: 1784 helix: 2.33 (0.23), residues: 552 sheet: 1.17 (0.29), residues: 341 loop : -0.29 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 848 TYR 0.013 0.001 TYR A 805 PHE 0.015 0.001 PHE A 911 TRP 0.014 0.001 TRP C 893 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00428 (15870) covalent geometry : angle 0.54819 (21699) hydrogen bonds : bond 0.03348 ( 699) hydrogen bonds : angle 4.32045 ( 2007) metal coordination : bond 0.01103 ( 8) metal coordination : angle 3.09995 ( 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 114 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 679 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8463 (ttp80) REVERT: B 38 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8733 (mtpp) REVERT: B 152 MET cc_start: 0.8957 (tpp) cc_final: 0.8724 (mmm) REVERT: B 339 MET cc_start: 0.8593 (mmm) cc_final: 0.8297 (mmm) REVERT: C 595 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9034 (p) REVERT: C 709 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: C 824 GLU cc_start: 0.8799 (pm20) cc_final: 0.8591 (pm20) REVERT: C 828 ARG cc_start: 0.9289 (tpp-160) cc_final: 0.8955 (mmm160) REVERT: C 925 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9130 (ttmm) REVERT: C 974 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8180 (mpp) REVERT: D 143 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8872 (m-30) REVERT: D 152 MET cc_start: 0.8881 (ttm) cc_final: 0.8296 (mmm) REVERT: D 302 MET cc_start: 0.8623 (ptp) cc_final: 0.8119 (ptp) REVERT: D 339 MET cc_start: 0.8566 (mmm) cc_final: 0.8063 (mmm) outliers start: 29 outliers final: 17 residues processed: 109 average time/residue: 0.6872 time to fit residues: 82.4001 Evaluate side-chains 107 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 679 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 320 SER 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 C residue 974 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 264 THR 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: 0.9990 chunk 21 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3010 r_free = 0.3010 target = 0.070053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.051194 restraints weight = 77413.026| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 4.41 r_work: 0.2381 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15878 Z= 0.118 Angle : 0.521 14.142 21703 Z= 0.270 Chirality : 0.040 0.170 2360 Planarity : 0.003 0.038 2602 Dihedral : 15.823 59.765 2584 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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 aren not related in a simple way. whole: 1.26 (0.21), residues: 1784 helix: 2.36 (0.23), residues: 553 sheet: 1.11 (0.28), residues: 352 loop : -0.25 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 848 TYR 0.015 0.001 TYR A 805 PHE 0.017 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 covalent geometry : bond 0.00270 (15870) covalent geometry : angle 0.51933 (21699) hydrogen bonds : bond 0.02976 ( 699) hydrogen bonds : angle 4.22503 ( 2007) metal coordination : bond 0.00553 ( 8) metal coordination : angle 2.90773 ( 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 110 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8265 (ttp80) REVERT: B 38 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8623 (mtpp) REVERT: B 339 MET cc_start: 0.8592 (mmm) cc_final: 0.8311 (mmm) REVERT: C 595 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8864 (p) REVERT: C 709 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: C 824 GLU cc_start: 0.8813 (pm20) cc_final: 0.8510 (pm20) REVERT: C 828 ARG cc_start: 0.9251 (tpp-160) cc_final: 0.8903 (mmm160) REVERT: D 143 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8816 (m-30) REVERT: D 152 MET cc_start: 0.8831 (ttm) cc_final: 0.8231 (mmm) REVERT: D 302 MET cc_start: 0.8485 (ptp) cc_final: 0.7939 (ptp) REVERT: D 339 MET cc_start: 0.8569 (mmm) cc_final: 0.8081 (mmm) outliers start: 23 outliers final: 15 residues processed: 106 average time/residue: 0.6797 time to fit residues: 79.6603 Evaluate side-chains 105 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 679 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 114 CYS 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 D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 264 THR 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: 0.9980 chunk 179 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3093 r_free = 0.3093 target = 0.073624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.052620 restraints weight = 94298.109| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.74 r_work: 0.2411 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15878 Z= 0.154 Angle : 0.529 9.836 21703 Z= 0.275 Chirality : 0.040 0.153 2360 Planarity : 0.003 0.042 2602 Dihedral : 15.869 59.977 2584 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.27 % Allowed : 14.40 % Favored : 84.32 % 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 aren not related in a simple way. whole: 1.31 (0.21), residues: 1784 helix: 2.39 (0.23), residues: 553 sheet: 1.20 (0.29), residues: 341 loop : -0.23 (0.21), residues: 890 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 0.014 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 covalent geometry : bond 0.00355 (15870) covalent geometry : angle 0.52739 (21699) hydrogen bonds : bond 0.03102 ( 699) hydrogen bonds : angle 4.23394 ( 2007) metal coordination : bond 0.00895 ( 8) metal coordination : angle 2.87251 ( 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 104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 679 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8409 (ttp80) REVERT: A 849 MET cc_start: 0.8949 (tpp) cc_final: 0.8600 (ttp) REVERT: B 38 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8692 (mtpp) REVERT: B 339 MET cc_start: 0.8608 (mmm) cc_final: 0.8340 (mmm) REVERT: C 595 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9053 (p) REVERT: C 709 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: C 824 GLU cc_start: 0.8820 (pm20) cc_final: 0.8557 (pm20) REVERT: C 828 ARG cc_start: 0.9288 (tpp-160) cc_final: 0.8947 (mmm160) REVERT: D 152 MET cc_start: 0.8909 (ttm) cc_final: 0.8460 (mmm) REVERT: D 302 MET cc_start: 0.8635 (ptp) cc_final: 0.8089 (ptp) REVERT: D 339 MET cc_start: 0.8556 (mmm) cc_final: 0.8057 (mmm) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.7061 time to fit residues: 79.5151 Evaluate side-chains 103 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 679 ARG Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 114 CYS 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 866 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 264 THR 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: 3.9990 chunk 104 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 157 optimal weight: 0.0970 chunk 103 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3122 r_free = 0.3122 target = 0.075126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.054276 restraints weight = 84567.221| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 4.59 r_work: 0.2457 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15878 Z= 0.112 Angle : 0.518 13.845 21703 Z= 0.268 Chirality : 0.039 0.152 2360 Planarity : 0.003 0.038 2602 Dihedral : 15.745 59.690 2584 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.15 % Allowed : 14.53 % Favored : 84.32 % 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 aren not related in a simple way. whole: 1.32 (0.21), residues: 1784 helix: 2.39 (0.23), residues: 554 sheet: 1.26 (0.28), residues: 343 loop : -0.26 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 848 TYR 0.014 0.001 TYR A 805 PHE 0.016 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 covalent geometry : bond 0.00254 (15870) covalent geometry : angle 0.51694 (21699) hydrogen bonds : bond 0.02859 ( 699) hydrogen bonds : angle 4.18413 ( 2007) metal coordination : bond 0.00478 ( 8) metal coordination : angle 2.82438 ( 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 105 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 849 MET cc_start: 0.8901 (tpp) cc_final: 0.8539 (ttp) REVERT: B 38 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8666 (mtpp) REVERT: B 339 MET cc_start: 0.8505 (mmm) cc_final: 0.8272 (mmm) REVERT: C 595 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.9031 (p) REVERT: C 709 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: C 828 ARG cc_start: 0.9242 (tpp-160) cc_final: 0.8655 (mmp80) REVERT: C 859 THR cc_start: 0.9233 (p) cc_final: 0.9015 (t) REVERT: C 861 GLU cc_start: 0.8936 (mp0) cc_final: 0.8722 (mp0) REVERT: D 152 MET cc_start: 0.8834 (ttm) cc_final: 0.8221 (mmm) REVERT: D 302 MET cc_start: 0.8618 (ptp) cc_final: 0.8112 (ptp) REVERT: D 339 MET cc_start: 0.8537 (mmm) cc_final: 0.8027 (mmm) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.6748 time to fit residues: 76.8775 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 : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER 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 866 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 264 THR 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: 0.0050 chunk 131 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 158 optimal weight: 0.0570 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 overall best weight: 0.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.055052 restraints weight = 94275.009| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 4.75 r_work: 0.2473 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- 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 = 0.42 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15878 Z= 0.101 Angle : 0.503 8.861 21703 Z= 0.264 Chirality : 0.039 0.156 2360 Planarity : 0.003 0.038 2602 Dihedral : 15.674 59.975 2583 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.15 % Allowed : 14.72 % Favored : 84.13 % 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 aren not related in a simple way. whole: 1.33 (0.21), residues: 1784 helix: 2.35 (0.23), residues: 555 sheet: 1.31 (0.28), residues: 343 loop : -0.23 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 848 TYR 0.014 0.001 TYR A 805 PHE 0.015 0.001 PHE A 911 TRP 0.012 0.001 TRP C 893 HIS 0.003 0.000 HIS D 10 Details of bonding type rmsd covalent geometry : bond 0.00224 (15870) covalent geometry : angle 0.50208 (21699) hydrogen bonds : bond 0.02763 ( 699) hydrogen bonds : angle 4.14648 ( 2007) metal coordination : bond 0.00399 ( 8) metal coordination : angle 2.58273 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4505.49 seconds wall clock time: 77 minutes 44.92 seconds (4664.92 seconds total)