Starting phenix.real_space_refine on Sat Sep 12 22:55:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oeq_20034/09_2026/6oeq_20034.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oeq_20034/09_2026/6oeq_20034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6oeq_20034/09_2026/6oeq_20034.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oeq_20034/09_2026/6oeq_20034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oeq_20034/09_2026/6oeq_20034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oeq_20034/09_2026/6oeq_20034.map" model { file = "/net/cci-nas-00/data/ceres_data/6oeq_20034/09_2026/6oeq_20034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oeq_20034/09_2026/6oeq_20034.cif" } resolution = 4.3 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= 0.005 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 204 5.49 5 S 104 5.16 5 C 11458 2.51 5 N 3376 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19134 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4762 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2668 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 4827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4827 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 586} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2674 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1154 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 938 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2540 SG CYS A 727 88.865 46.259 95.690 1.00176.74 S ATOM 2561 SG CYS A 730 91.881 43.361 96.831 1.00172.49 S ATOM 9974 SG CYS C 727 29.444 104.285 98.095 1.00 70.24 S ATOM 9995 SG CYS C 730 27.447 106.657 100.264 1.00 68.58 S Time building chain proxies: 3.75, per 1000 atoms: 0.20 Number of scatterers: 19134 At special positions: 0 Unit cell: (126.26, 157.29, 158.36, 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 104 16.00 P 204 15.00 O 3988 8.00 N 3376 7.00 C 11458 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: 1.71 Conformation dependent library (CDL) restraints added in 535.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 727 " Number of angles added : 4 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 20 sheets defined 36.2% alpha, 21.8% beta 98 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.876A pdb=" N GLN A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 426 through 441 Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.817A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.806A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.520A pdb=" N ALA A 562 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.675A pdb=" N LEU A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.723A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 removed outlier: 3.509A pdb=" N SER A 738 " --> pdb=" O ARG A 734 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) 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 814 removed outlier: 3.950A pdb=" N CYS A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 838 removed outlier: 4.338A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 857 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.640A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 890 Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.730A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 950 Processing helix chain 'A' and resid 962 through 974 removed outlier: 4.080A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 995 removed outlier: 3.640A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 988 " --> pdb=" O MET A 984 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 427 through 441 Processing helix chain 'C' and resid 444 through 455 removed outlier: 3.804A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 473 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 508 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 682 removed outlier: 3.556A pdb=" N LEU C 668 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 711 through 716 removed outlier: 3.682A pdb=" N GLU C 716 " --> pdb=" O VAL C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.805A pdb=" N SER C 738 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.550A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 841 Processing helix chain 'C' and resid 850 through 858 removed outlier: 3.901A pdb=" N MET C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.654A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 890 Processing helix chain 'C' and resid 890 through 895 removed outlier: 3.601A pdb=" N ARG C 894 " --> pdb=" O LYS C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 924 removed outlier: 4.021A pdb=" N CYS C 907 " --> pdb=" O PRO C 903 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.610A pdb=" N HIS C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 958 through 963 removed outlier: 3.531A pdb=" N GLN C 962 " --> pdb=" O SER C 958 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 958 through 963' Processing helix chain 'C' and resid 964 through 975 Processing helix chain 'C' and resid 981 through 996 removed outlier: 3.833A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 removed outlier: 3.638A pdb=" N GLN C1000 " --> pdb=" O SER C 996 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.824A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (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 519 removed outlier: 4.017A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 4.017A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 636 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.583A pdb=" N GLY B 330 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.189A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 116 Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 131 removed outlier: 5.926A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 182 " --> pdb=" O TYR B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 205 through 211 removed outlier: 5.139A pdb=" N HIS B 207 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 220 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER B 209 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 218 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA B 211 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL B 216 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 520 removed outlier: 6.822A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 518 through 520 removed outlier: 6.822A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 594 " --> 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) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 80 removed outlier: 3.620A pdb=" N CYS D 78 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB9, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 207 through 212 removed outlier: 3.503A pdb=" N THR D 215 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 262 through 267 removed outlier: 6.299A pdb=" N LEU D 263 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 274 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN D 265 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL D 272 " --> pdb=" O GLN D 265 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 244 hydrogen bonds 488 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 2.10 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: 5052 1.33 - 1.46: 5945 1.46 - 1.58: 8419 1.58 - 1.71: 399 1.71 - 1.83: 158 Bond restraints: 19973 Sorted by residual: bond pdb=" C1' DC I 31 " pdb=" N1 DC I 31 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.57e+01 bond pdb=" CA ALA C 502 " pdb=" C ALA C 502 " ideal model delta sigma weight residual 1.522 1.455 0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C3' DA G 44 " pdb=" O3' DA G 44 " ideal model delta sigma weight residual 1.435 1.375 0.060 1.30e-02 5.92e+03 2.16e+01 bond pdb=" CA THR C 728 " pdb=" C THR C 728 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.41e-02 5.03e+03 1.91e+01 bond pdb=" N9 DA J 29 " pdb=" C4 DA J 29 " ideal model delta sigma weight residual 1.374 1.349 0.025 6.00e-03 2.78e+04 1.80e+01 ... (remaining 19968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 25960 2.08 - 4.15: 1733 4.15 - 6.23: 172 6.23 - 8.30: 38 8.30 - 10.38: 7 Bond angle restraints: 27910 Sorted by residual: angle pdb=" O4' DA J 2 " pdb=" C4' DA J 2 " pdb=" C3' DA J 2 " ideal model delta sigma weight residual 106.00 102.03 3.97 6.00e-01 2.78e+00 4.37e+01 angle pdb=" O4' DA I 28 " pdb=" C4' DA I 28 " pdb=" C3' DA I 28 " ideal model delta sigma weight residual 106.00 102.15 3.85 6.00e-01 2.78e+00 4.12e+01 angle pdb=" O4' DG G 54 " pdb=" C1' DG G 54 " pdb=" N9 DG G 54 " ideal model delta sigma weight residual 108.00 112.45 -4.45 7.00e-01 2.04e+00 4.03e+01 angle pdb=" O5' DA I 42 " pdb=" C5' DA I 42 " pdb=" C4' DA I 42 " ideal model delta sigma weight residual 109.40 114.36 -4.96 8.00e-01 1.56e+00 3.84e+01 angle pdb=" O4' DA I 2 " pdb=" C4' DA I 2 " pdb=" C3' DA I 2 " ideal model delta sigma weight residual 106.00 102.35 3.65 6.00e-01 2.78e+00 3.70e+01 ... (remaining 27905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 10344 35.50 - 71.00: 1084 71.00 - 106.49: 17 106.49 - 141.99: 3 141.99 - 177.49: 7 Dihedral angle restraints: 11455 sinusoidal: 5908 harmonic: 5547 Sorted by residual: dihedral pdb=" CA GLU D 303 " pdb=" C GLU D 303 " pdb=" N THR D 304 " pdb=" CA THR D 304 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ASN D 101 " pdb=" C ASN D 101 " pdb=" N GLU D 102 " pdb=" CA GLU D 102 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLN A 581 " pdb=" C GLN A 581 " pdb=" N ASP A 582 " pdb=" CA ASP A 582 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 11452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2115 0.056 - 0.112: 752 0.112 - 0.168: 187 0.168 - 0.224: 37 0.224 - 0.280: 4 Chirality restraints: 3095 Sorted by residual: chirality pdb=" C3' DA F 32 " pdb=" C4' DA F 32 " pdb=" O3' DA F 32 " pdb=" C2' DA F 32 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" P DA I 42 " pdb=" OP1 DA I 42 " pdb=" OP2 DA I 42 " pdb=" O5' DA I 42 " both_signs ideal model delta sigma weight residual True 2.34 -2.57 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3092 not shown) Planarity restraints: 2876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 511 " -0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO C 512 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 512 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 512 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 91 " -0.018 2.00e-02 2.50e+03 1.92e-02 7.39e+00 pdb=" CG TYR D 91 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR D 91 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR D 91 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 91 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 91 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 91 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 91 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 673 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO C 674 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 674 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 674 " 0.037 5.00e-02 4.00e+02 ... (remaining 2873 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 54 2.37 - 3.01: 9613 3.01 - 3.64: 31301 3.64 - 4.27: 44669 4.27 - 4.90: 68375 Nonbonded interactions: 154012 Sorted by model distance: nonbonded pdb=" OE1 GLN C 962 " pdb="CA CA C1102 " model vdw 1.742 2.510 nonbonded pdb=" OD1 ASP C 600 " pdb="CA CA C1101 " model vdw 1.808 2.510 nonbonded pdb=" OD2 ASP C 708 " pdb="CA CA C1101 " model vdw 1.873 2.510 nonbonded pdb=" OD2 ASP C 600 " pdb="CA CA C1102 " model vdw 1.909 2.510 nonbonded pdb=" OG SER C 872 " pdb=" OE1 GLU C 874 " model vdw 2.234 3.040 ... (remaining 154007 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 400 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 through 43 \ 1 or (resid 432 and (name N or name CA or name C or name O or name CB )) or resi \ d 433 through 435 or (resid 436 and (name N or name CA or name C or name O or na \ me CB )) or resid 437 through 451 or (resid 452 through 453 and (name N or name \ CA or name C or name O or name CB )) or resid 454 through 455 or (resid 456 and \ (name N or name CA or name C or name O or name CB )) or resid 457 or (resid 458 \ and (name N or name CA or name C or name O or name CB )) or resid 459 through 52 \ 3 or (resid 524 and (name N or name CA or name C or name O or name CB )) or resi \ d 525 through 571 or (resid 572 and (name N or name CA or name C or name O or na \ me CB )) or resid 573 through 603 or (resid 604 and (name N or name CA or name C \ or name O or name CB )) or resid 605 through 608 or (resid 613 through 614 and \ (name N or name CA or name C or name O or name CB )) or resid 615 through 813 or \ (resid 814 and (name N or name CA or name C or name O or name CB )) or resid 81 \ 5 through 816 or (resid 817 and (name N or name CA or name C or name O or name C \ B )) or resid 818 through 823 or (resid 824 and (name N or name CA or name C or \ name O or name CB )) or resid 825 through 826 or (resid 827 through 828 and (nam \ e N or name CA or name C or name O or name CB )) or resid 829 through 879 or (re \ sid 880 and (name N or name CA or name C or name O or name CB )) or resid 881 th \ rough 979 or (resid 980 and (name N or name CA or name C or name O or name CB )) \ or resid 981 through 1008)) selection = (chain 'C' and (resid 400 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 519 or (resid 520 and (name N \ or name CA or name C or name O or name CB )) or resid 521 through 606 or (resid \ 607 through 614 and (name N or name CA or name C or name O or name CB )) or resi \ d 615 through 638 or (resid 639 and (name N or name CA or name C or name O or na \ me CB )) or resid 640 through 751 or (resid 752 and (name N or name CA or name C \ or name O or name CB )) or resid 753 through 757 or (resid 758 and (name N or n \ ame CA or name C or name O or name CB )) or resid 759 through 810 or (resid 811 \ and (name N or name CA or name C or name O or name CB )) or resid 812 through 81 \ 9 or (resid 820 through 821 and (name N or name CA or name C or name O or name C \ B )) or resid 822 through 837 or (resid 838 through 839 and (name N or name CA o \ r name C or name O or name CB )) or resid 840 through 843 or (resid 844 and (nam \ e N or name CA or name C or name O or name CB )) or resid 845 through 846 or (re \ sid 847 and (name N or name CA or name C or name O or name CB )) or resid 848 th \ rough 860 or (resid 861 and (name N or name CA or name C or name O or name CB )) \ or resid 862 through 887 or (resid 888 and (name N or name CA or name C or name \ O or name CB )) or resid 889 through 913 or (resid 914 and (name N or name CA o \ r name C or name O or name CB )) or resid 915 through 917 or (resid 918 and (nam \ e N or name CA or name C or name O or name CB )) or resid 919 through 924 or (re \ sid 925 and (name N or name CA or name C or name O or name CB )) or resid 926 or \ (resid 927 through 928 and (name N or name CA or name C or name O or name CB )) \ or resid 929 through 957 or (resid 961 and (name N or name CA or name C or name \ O or name CB )) or resid 962 through 982 or (resid 983 and (name N or name CA o \ r name C or name O or name CB )) or resid 984 through 1008)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 through 338 or (resid 339 and (name N or \ name CA or name C or name O or name CB )) or resid 340 through 351)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.770 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.010 0.461 19981 Z= 0.614 Angle : 1.123 22.960 27914 Z= 0.780 Chirality : 0.061 0.280 3095 Planarity : 0.007 0.077 2876 Dihedral : 23.244 177.489 7877 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.71 % Favored : 91.18 % Rotamer: Outliers : 0.62 % Allowed : 15.32 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.16), residues: 1894 helix: -2.70 (0.15), residues: 604 sheet: -1.61 (0.29), residues: 307 loop : -3.04 (0.16), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 558 TYR 0.047 0.003 TYR D 91 PHE 0.021 0.003 PHE C 743 TRP 0.029 0.003 TRP D 317 HIS 0.015 0.002 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00889 / 0.61 (19973) covalent geometry : angle 1.10761 / 0.78 (27910) hydrogen bonds : bond 0.15293 / 10.53 ( 883) hydrogen bonds : angle 7.00196 / 4.93 ( 2354) metal coordination : bond 0.20030 / 10.00 ( 8) metal coordination : angle 15.63102 / 9.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8673 (m-80) cc_final: 0.8468 (m-10) REVERT: A 503 LEU cc_start: 0.9372 (mt) cc_final: 0.9092 (mt) REVERT: A 578 MET cc_start: 0.8277 (mtp) cc_final: 0.7874 (mtp) REVERT: A 682 MET cc_start: 0.7926 (ptm) cc_final: 0.7450 (tmm) REVERT: A 761 ARG cc_start: 0.8360 (tmm-80) cc_final: 0.8058 (tmm160) REVERT: A 880 ARG cc_start: 0.8688 (tpp80) cc_final: 0.8189 (tpp80) REVERT: A 970 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7754 (mtt180) REVERT: A 971 PHE cc_start: 0.8673 (m-80) cc_final: 0.8424 (m-80) REVERT: A 975 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7531 (p0) REVERT: B 287 CYS cc_start: 0.6709 (m) cc_final: 0.5504 (m) REVERT: B 302 MET cc_start: 0.7038 (ptp) cc_final: 0.6315 (ttt) REVERT: C 395 HIS cc_start: 0.7621 (t-170) cc_final: 0.7271 (t-90) REVERT: C 510 LEU cc_start: 0.9050 (mt) cc_final: 0.8579 (mp) REVERT: C 883 MET cc_start: 0.8793 (tpp) cc_final: 0.8269 (tpp) REVERT: C 983 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6944 (tm-30) REVERT: C 1003 MET cc_start: 0.8710 (mmm) cc_final: 0.8489 (tpp) REVERT: D 218 ILE cc_start: 0.9441 (mt) cc_final: 0.9160 (tt) REVERT: D 281 ASN cc_start: 0.8615 (p0) cc_final: 0.8200 (t0) REVERT: D 326 THR cc_start: 0.8899 (p) cc_final: 0.8616 (p) outliers start: 10 outliers final: 4 residues processed: 211 average time/residue: 0.1447 time to fit residues: 47.1041 Evaluate side-chains 148 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 480 GLN ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN A 753 ASN A 755 GLN A 795 HIS A 860 GLN ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A 990 HIS A 991 HIS A1006 HIS B 4 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 HIS C 753 ASN C 820 ASN C 842 ASN C 876 HIS C 908 GLN C 991 HIS D 47 HIS D 89 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 173 ASN D 222 HIS D 268 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.079339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058967 restraints weight = 97452.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060153 restraints weight = 54269.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060981 restraints weight = 31673.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061138 restraints weight = 24974.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061195 restraints weight = 22565.860| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19981 Z= 0.159 Angle : 0.734 11.733 27914 Z= 0.406 Chirality : 0.049 0.360 3095 Planarity : 0.005 0.045 2876 Dihedral : 26.354 177.116 4336 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.17), residues: 1894 helix: -1.26 (0.18), residues: 631 sheet: -1.48 (0.28), residues: 316 loop : -2.61 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 915 TYR 0.025 0.002 TYR A 559 PHE 0.015 0.002 PHE A 622 TRP 0.015 0.002 TRP C 956 HIS 0.009 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (19973) covalent geometry : angle 0.73186 / 0.41 (27910) hydrogen bonds : bond 0.05382 / 3.58 ( 883) hydrogen bonds : angle 5.18164 / 3.64 ( 2354) metal coordination : bond 0.02860 / 1.10 ( 8) metal coordination : angle 5.00545 / 2.52 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8773 (m-80) cc_final: 0.8479 (m-10) REVERT: A 503 LEU cc_start: 0.9387 (mt) cc_final: 0.9118 (mt) REVERT: A 578 MET cc_start: 0.8411 (mtp) cc_final: 0.7984 (mtp) REVERT: A 627 MET cc_start: 0.8305 (ppp) cc_final: 0.8100 (ppp) REVERT: A 708 ASP cc_start: 0.7617 (m-30) cc_final: 0.7350 (m-30) REVERT: A 761 ARG cc_start: 0.8583 (tmm-80) cc_final: 0.8309 (tmm160) REVERT: A 880 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8008 (tpp80) REVERT: A 889 MET cc_start: 0.9305 (mtp) cc_final: 0.8711 (mpp) REVERT: A 916 PHE cc_start: 0.9174 (t80) cc_final: 0.8946 (t80) REVERT: A 970 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8174 (mtt180) REVERT: B 152 MET cc_start: 0.7094 (tpt) cc_final: 0.6697 (tmm) REVERT: B 162 MET cc_start: 0.9040 (mmm) cc_final: 0.8774 (mmp) REVERT: B 287 CYS cc_start: 0.7455 (m) cc_final: 0.6231 (m) REVERT: B 302 MET cc_start: 0.7092 (ptp) cc_final: 0.6459 (ttt) REVERT: C 395 HIS cc_start: 0.7550 (t70) cc_final: 0.7280 (t-90) REVERT: C 480 GLN cc_start: 0.9488 (mp10) cc_final: 0.9166 (mp10) REVERT: C 484 MET cc_start: 0.9440 (ttp) cc_final: 0.8988 (tmm) REVERT: C 510 LEU cc_start: 0.9084 (mt) cc_final: 0.8718 (mp) REVERT: C 570 MET cc_start: 0.8935 (ptp) cc_final: 0.8573 (mtm) REVERT: D 218 ILE cc_start: 0.9353 (mt) cc_final: 0.9058 (mp) REVERT: D 289 LEU cc_start: 0.8822 (pt) cc_final: 0.7276 (pt) REVERT: D 298 GLU cc_start: 0.8787 (tp30) cc_final: 0.8394 (tm-30) REVERT: D 326 THR cc_start: 0.8653 (p) cc_final: 0.8342 (p) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1396 time to fit residues: 47.8160 Evaluate side-chains 154 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 179 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 190 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 144 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 836 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 282 GLN C 395 HIS C 965 ASN C 991 HIS D 47 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.078654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058031 restraints weight = 101739.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059032 restraints weight = 57553.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.059656 restraints weight = 36202.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.059827 restraints weight = 30040.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059908 restraints weight = 27579.644| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19981 Z= 0.188 Angle : 0.698 9.180 27914 Z= 0.390 Chirality : 0.047 0.374 3095 Planarity : 0.005 0.054 2876 Dihedral : 26.104 179.598 4336 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.18), residues: 1894 helix: -0.58 (0.19), residues: 633 sheet: -1.35 (0.28), residues: 328 loop : -2.41 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 494 TYR 0.019 0.002 TYR A 559 PHE 0.013 0.002 PHE A 853 TRP 0.013 0.001 TRP D 317 HIS 0.008 0.001 HIS C1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (19973) covalent geometry : angle 0.69572 / 0.39 (27910) hydrogen bonds : bond 0.05322 / 3.52 ( 883) hydrogen bonds : angle 4.92656 / 3.46 ( 2354) metal coordination : bond 0.01520 / 1.02 ( 8) metal coordination : angle 5.16945 / 2.91 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8825 (m-80) cc_final: 0.8520 (m-10) REVERT: A 503 LEU cc_start: 0.9404 (mt) cc_final: 0.9132 (mt) REVERT: A 578 MET cc_start: 0.8398 (mtp) cc_final: 0.7995 (mtp) REVERT: A 582 ASP cc_start: 0.8529 (m-30) cc_final: 0.8224 (p0) REVERT: A 627 MET cc_start: 0.8340 (ppp) cc_final: 0.8060 (ppp) REVERT: A 682 MET cc_start: 0.8695 (tmm) cc_final: 0.8473 (tmm) REVERT: A 708 ASP cc_start: 0.7609 (m-30) cc_final: 0.7342 (m-30) REVERT: A 761 ARG cc_start: 0.8415 (tmm-80) cc_final: 0.8202 (tmm160) REVERT: A 841 MET cc_start: 0.8057 (tpp) cc_final: 0.7568 (tpp) REVERT: A 880 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8102 (tpp80) REVERT: A 889 MET cc_start: 0.9341 (mtp) cc_final: 0.8654 (mpp) REVERT: A 970 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8376 (mtt180) REVERT: A 971 PHE cc_start: 0.8888 (m-80) cc_final: 0.8572 (m-10) REVERT: B 126 GLU cc_start: 0.7428 (pm20) cc_final: 0.7045 (pm20) REVERT: B 152 MET cc_start: 0.7177 (tpt) cc_final: 0.6678 (tmm) REVERT: B 162 MET cc_start: 0.9029 (mmm) cc_final: 0.8732 (mmp) REVERT: B 287 CYS cc_start: 0.7664 (m) cc_final: 0.6304 (m) REVERT: B 302 MET cc_start: 0.7123 (ptp) cc_final: 0.6561 (ttt) REVERT: C 395 HIS cc_start: 0.7722 (t-90) cc_final: 0.7149 (t-90) REVERT: C 480 GLN cc_start: 0.9449 (mp10) cc_final: 0.9121 (mp10) REVERT: C 484 MET cc_start: 0.9455 (ttp) cc_final: 0.8840 (tmm) REVERT: C 510 LEU cc_start: 0.9035 (mt) cc_final: 0.8768 (mp) REVERT: C 570 MET cc_start: 0.8994 (ptp) cc_final: 0.8704 (mtm) REVERT: C 1004 ASN cc_start: 0.8417 (p0) cc_final: 0.7817 (p0) REVERT: D 218 ILE cc_start: 0.9373 (mt) cc_final: 0.9071 (mp) REVERT: D 289 LEU cc_start: 0.8870 (pt) cc_final: 0.7805 (pt) REVERT: D 326 THR cc_start: 0.8707 (p) cc_final: 0.8190 (p) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.1416 time to fit residues: 45.2784 Evaluate side-chains 153 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 93 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 107 optimal weight: 0.0010 chunk 95 optimal weight: 4.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 836 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.078341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057704 restraints weight = 101042.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058605 restraints weight = 58184.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059338 restraints weight = 36644.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.059738 restraints weight = 28051.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059716 restraints weight = 25532.059| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19981 Z= 0.188 Angle : 0.678 8.910 27914 Z= 0.378 Chirality : 0.047 0.361 3095 Planarity : 0.004 0.041 2876 Dihedral : 25.949 179.580 4336 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.19), residues: 1894 helix: -0.23 (0.20), residues: 635 sheet: -1.23 (0.28), residues: 328 loop : -2.30 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 458 TYR 0.017 0.002 TYR D 91 PHE 0.020 0.002 PHE C 475 TRP 0.017 0.002 TRP D 317 HIS 0.005 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (19973) covalent geometry : angle 0.67564 / 0.38 (27910) hydrogen bonds : bond 0.05057 / 3.31 ( 883) hydrogen bonds : angle 4.77858 / 3.37 ( 2354) metal coordination : bond 0.01238 / 0.75 ( 8) metal coordination : angle 5.21874 / 2.94 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8893 (m-80) cc_final: 0.8523 (m-10) REVERT: A 503 LEU cc_start: 0.9403 (mt) cc_final: 0.9176 (mt) REVERT: A 578 MET cc_start: 0.8368 (mtp) cc_final: 0.7989 (mtp) REVERT: A 582 ASP cc_start: 0.8481 (m-30) cc_final: 0.8142 (p0) REVERT: A 627 MET cc_start: 0.8362 (ppp) cc_final: 0.8066 (ppp) REVERT: A 682 MET cc_start: 0.8767 (tmm) cc_final: 0.8474 (tmm) REVERT: A 708 ASP cc_start: 0.7742 (m-30) cc_final: 0.7441 (m-30) REVERT: A 841 MET cc_start: 0.8001 (tpp) cc_final: 0.7429 (tpp) REVERT: A 880 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8095 (tpp80) REVERT: A 889 MET cc_start: 0.9347 (mtp) cc_final: 0.8827 (mtt) REVERT: A 970 ARG cc_start: 0.8656 (mtt180) cc_final: 0.8307 (mtt180) REVERT: A 984 MET cc_start: 0.9122 (mmp) cc_final: 0.8532 (tpp) REVERT: B 126 GLU cc_start: 0.7417 (pm20) cc_final: 0.7044 (pm20) REVERT: B 152 MET cc_start: 0.7197 (tpt) cc_final: 0.6946 (mmm) REVERT: B 162 MET cc_start: 0.9014 (mmm) cc_final: 0.8688 (mmp) REVERT: B 287 CYS cc_start: 0.7653 (m) cc_final: 0.6235 (m) REVERT: B 302 MET cc_start: 0.7139 (ptp) cc_final: 0.6568 (ttt) REVERT: C 395 HIS cc_start: 0.7714 (t-90) cc_final: 0.7132 (t-90) REVERT: C 480 GLN cc_start: 0.9464 (mp10) cc_final: 0.9098 (mp10) REVERT: C 484 MET cc_start: 0.9507 (ttp) cc_final: 0.8977 (tmm) REVERT: C 510 LEU cc_start: 0.9168 (mt) cc_final: 0.8258 (mp) REVERT: D 218 ILE cc_start: 0.9368 (mt) cc_final: 0.9096 (mp) REVERT: D 289 LEU cc_start: 0.8971 (pt) cc_final: 0.8154 (pt) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1374 time to fit residues: 43.2644 Evaluate side-chains 152 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 7 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.0670 chunk 69 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 185 optimal weight: 0.2980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 647 ASN A 795 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.079870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059412 restraints weight = 97627.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.060554 restraints weight = 54280.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.061501 restraints weight = 31793.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061633 restraints weight = 23758.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061627 restraints weight = 22227.768| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19981 Z= 0.130 Angle : 0.636 7.660 27914 Z= 0.356 Chirality : 0.046 0.378 3095 Planarity : 0.004 0.051 2876 Dihedral : 25.782 179.630 4336 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.19), residues: 1894 helix: -0.13 (0.20), residues: 638 sheet: -1.01 (0.29), residues: 331 loop : -2.15 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 970 TYR 0.016 0.001 TYR C 805 PHE 0.032 0.001 PHE A 924 TRP 0.031 0.002 TRP A 829 HIS 0.004 0.001 HIS C1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (19973) covalent geometry : angle 0.63418 / 0.36 (27910) hydrogen bonds : bond 0.04468 / 2.93 ( 883) hydrogen bonds : angle 4.59928 / 3.25 ( 2354) metal coordination : bond 0.00956 / 0.56 ( 8) metal coordination : angle 3.66617 / 2.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8809 (m-80) cc_final: 0.8513 (m-80) REVERT: A 476 LEU cc_start: 0.8789 (tp) cc_final: 0.8562 (tp) REVERT: A 503 LEU cc_start: 0.9427 (mt) cc_final: 0.9145 (mt) REVERT: A 578 MET cc_start: 0.8281 (mtp) cc_final: 0.7921 (mtp) REVERT: A 582 ASP cc_start: 0.8247 (m-30) cc_final: 0.8001 (p0) REVERT: A 627 MET cc_start: 0.8368 (ppp) cc_final: 0.8052 (ppp) REVERT: A 682 MET cc_start: 0.8796 (tmm) cc_final: 0.8438 (tmm) REVERT: A 687 LEU cc_start: 0.9342 (tp) cc_final: 0.8679 (tp) REVERT: A 708 ASP cc_start: 0.7732 (m-30) cc_final: 0.7430 (m-30) REVERT: A 841 MET cc_start: 0.7953 (tpp) cc_final: 0.7404 (tpp) REVERT: A 880 ARG cc_start: 0.8557 (tpp80) cc_final: 0.7961 (tpp80) REVERT: A 970 ARG cc_start: 0.8649 (mtt180) cc_final: 0.8212 (mtt180) REVERT: A 984 MET cc_start: 0.9036 (mmp) cc_final: 0.8758 (tpp) REVERT: B 152 MET cc_start: 0.7320 (tpt) cc_final: 0.7002 (mmm) REVERT: B 162 MET cc_start: 0.8978 (mmm) cc_final: 0.8536 (mmp) REVERT: B 287 CYS cc_start: 0.7553 (m) cc_final: 0.6191 (m) REVERT: B 302 MET cc_start: 0.6956 (ptp) cc_final: 0.6355 (ttt) REVERT: C 395 HIS cc_start: 0.7682 (t-90) cc_final: 0.7075 (t-90) REVERT: C 480 GLN cc_start: 0.9485 (mp10) cc_final: 0.9185 (mp10) REVERT: C 484 MET cc_start: 0.9497 (ttp) cc_final: 0.9002 (tmm) REVERT: C 510 LEU cc_start: 0.8915 (mt) cc_final: 0.8470 (mp) REVERT: C 970 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8652 (ttp-170) REVERT: C 1004 ASN cc_start: 0.8410 (p0) cc_final: 0.7825 (p0) REVERT: D 16 GLN cc_start: 0.8004 (pt0) cc_final: 0.7502 (pm20) REVERT: D 214 ASP cc_start: 0.7312 (m-30) cc_final: 0.7025 (p0) REVERT: D 218 ILE cc_start: 0.9325 (mt) cc_final: 0.9086 (mp) REVERT: D 289 LEU cc_start: 0.8833 (pt) cc_final: 0.8177 (pt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1351 time to fit residues: 43.7696 Evaluate side-chains 161 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 192 optimal weight: 30.0000 chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 795 HIS A 818 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.078912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058170 restraints weight = 101495.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059396 restraints weight = 56721.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059891 restraints weight = 34717.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060305 restraints weight = 28096.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060257 restraints weight = 25480.148| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19981 Z= 0.171 Angle : 0.655 7.993 27914 Z= 0.364 Chirality : 0.045 0.355 3095 Planarity : 0.004 0.041 2876 Dihedral : 25.740 179.725 4336 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.19), residues: 1894 helix: -0.08 (0.20), residues: 652 sheet: -1.02 (0.28), residues: 331 loop : -2.17 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 970 TYR 0.017 0.001 TYR D 91 PHE 0.031 0.002 PHE C 641 TRP 0.015 0.002 TRP A 829 HIS 0.005 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (19973) covalent geometry : angle 0.65327 / 0.36 (27910) hydrogen bonds : bond 0.04773 / 3.13 ( 883) hydrogen bonds : angle 4.59649 / 3.24 ( 2354) metal coordination : bond 0.00885 / 0.50 ( 8) metal coordination : angle 4.55074 / 2.58 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8908 (m-80) cc_final: 0.8513 (m-10) REVERT: A 503 LEU cc_start: 0.9484 (mt) cc_final: 0.9234 (mt) REVERT: A 578 MET cc_start: 0.8251 (mtp) cc_final: 0.7909 (mtp) REVERT: A 582 ASP cc_start: 0.8321 (m-30) cc_final: 0.8068 (p0) REVERT: A 627 MET cc_start: 0.8364 (ppp) cc_final: 0.8048 (ppp) REVERT: A 682 MET cc_start: 0.8793 (tmm) cc_final: 0.8504 (tmm) REVERT: A 687 LEU cc_start: 0.9391 (tp) cc_final: 0.8738 (tp) REVERT: A 708 ASP cc_start: 0.7817 (m-30) cc_final: 0.7533 (m-30) REVERT: A 713 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7946 (ttm170) REVERT: A 841 MET cc_start: 0.7998 (tpp) cc_final: 0.7498 (tpp) REVERT: A 880 ARG cc_start: 0.8533 (tpp80) cc_final: 0.7962 (tpp80) REVERT: A 889 MET cc_start: 0.9357 (mtp) cc_final: 0.9106 (mtt) REVERT: A 970 ARG cc_start: 0.8708 (mtt180) cc_final: 0.8439 (mtt180) REVERT: A 971 PHE cc_start: 0.8829 (m-80) cc_final: 0.8537 (m-10) REVERT: A 984 MET cc_start: 0.9109 (mmp) cc_final: 0.8471 (tpp) REVERT: B 126 GLU cc_start: 0.6981 (mp0) cc_final: 0.6139 (pm20) REVERT: B 152 MET cc_start: 0.7294 (tpt) cc_final: 0.6865 (mmm) REVERT: C 395 HIS cc_start: 0.7717 (t-90) cc_final: 0.7119 (t-90) REVERT: C 480 GLN cc_start: 0.9492 (mp10) cc_final: 0.9224 (mp10) REVERT: D 218 ILE cc_start: 0.9345 (mt) cc_final: 0.9091 (mp) REVERT: D 289 LEU cc_start: 0.8902 (pt) cc_final: 0.8319 (pt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1345 time to fit residues: 41.3992 Evaluate side-chains 146 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 144 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 203 optimal weight: 40.0000 chunk 98 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 795 HIS A 818 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 ASN ** C 740 ASN ** 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 = 0.3651 r_free = 0.3651 target = 0.078909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.057834 restraints weight = 100991.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059143 restraints weight = 56187.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059760 restraints weight = 33439.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059994 restraints weight = 27694.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.060060 restraints weight = 25276.971| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19981 Z= 0.163 Angle : 0.646 8.147 27914 Z= 0.358 Chirality : 0.046 0.358 3095 Planarity : 0.004 0.042 2876 Dihedral : 25.678 179.818 4336 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.19), residues: 1894 helix: 0.01 (0.20), residues: 651 sheet: -0.95 (0.29), residues: 327 loop : -2.09 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.014 0.001 TYR C 805 PHE 0.022 0.002 PHE C 641 TRP 0.015 0.001 TRP B 317 HIS 0.005 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (19973) covalent geometry : angle 0.64379 / 0.36 (27910) hydrogen bonds : bond 0.04639 / 3.03 ( 883) hydrogen bonds : angle 4.52006 / 3.19 ( 2354) metal coordination : bond 0.01863 / 1.05 ( 8) metal coordination : angle 4.66573 / 2.70 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8891 (m-80) cc_final: 0.8486 (m-10) REVERT: A 503 LEU cc_start: 0.9471 (mt) cc_final: 0.9208 (mt) REVERT: A 578 MET cc_start: 0.8311 (mtp) cc_final: 0.7962 (mtp) REVERT: A 582 ASP cc_start: 0.8309 (m-30) cc_final: 0.8067 (p0) REVERT: A 627 MET cc_start: 0.8399 (ppp) cc_final: 0.8045 (ppp) REVERT: A 682 MET cc_start: 0.8800 (tmm) cc_final: 0.8494 (tmm) REVERT: A 687 LEU cc_start: 0.9386 (tp) cc_final: 0.8717 (tp) REVERT: A 708 ASP cc_start: 0.7859 (m-30) cc_final: 0.7609 (m-30) REVERT: A 713 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7950 (ttm170) REVERT: A 841 MET cc_start: 0.8023 (tpp) cc_final: 0.7468 (tpp) REVERT: A 880 ARG cc_start: 0.8512 (tpp80) cc_final: 0.7934 (tpp80) REVERT: A 889 MET cc_start: 0.9328 (mtp) cc_final: 0.9060 (mtt) REVERT: A 970 ARG cc_start: 0.8647 (mtt180) cc_final: 0.8320 (mtt180) REVERT: A 984 MET cc_start: 0.9035 (mmp) cc_final: 0.8761 (tpp) REVERT: B 126 GLU cc_start: 0.7248 (mp0) cc_final: 0.6508 (pm20) REVERT: B 152 MET cc_start: 0.7324 (tpt) cc_final: 0.6851 (mmm) REVERT: C 395 HIS cc_start: 0.7742 (t-90) cc_final: 0.7148 (t-90) REVERT: C 480 GLN cc_start: 0.9499 (mp10) cc_final: 0.9233 (mp10) REVERT: C 790 SER cc_start: 0.9050 (t) cc_final: 0.8622 (m) REVERT: C 1004 ASN cc_start: 0.8521 (p0) cc_final: 0.7944 (p0) REVERT: D 218 ILE cc_start: 0.9336 (mt) cc_final: 0.9076 (mp) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1326 time to fit residues: 41.8462 Evaluate side-chains 146 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 34 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 159 optimal weight: 0.0770 chunk 101 optimal weight: 0.0370 chunk 131 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 795 HIS A 818 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.079919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058758 restraints weight = 97701.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060143 restraints weight = 53041.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.061025 restraints weight = 34857.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.061601 restraints weight = 26431.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.061938 restraints weight = 22123.525| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19981 Z= 0.129 Angle : 0.632 7.840 27914 Z= 0.349 Chirality : 0.045 0.371 3095 Planarity : 0.004 0.040 2876 Dihedral : 25.588 179.965 4336 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.06 % Allowed : 0.87 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.19), residues: 1894 helix: 0.16 (0.21), residues: 641 sheet: -0.80 (0.29), residues: 331 loop : -1.90 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 761 TYR 0.019 0.001 TYR C 725 PHE 0.020 0.001 PHE C 641 TRP 0.041 0.002 TRP A 829 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (19973) covalent geometry : angle 0.62986 / 0.35 (27910) hydrogen bonds : bond 0.04251 / 2.79 ( 883) hydrogen bonds : angle 4.43506 / 3.13 ( 2354) metal coordination : bond 0.00850 / 0.54 ( 8) metal coordination : angle 4.22464 / 2.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8890 (m-80) cc_final: 0.8547 (m-80) REVERT: A 434 LEU cc_start: 0.9338 (mt) cc_final: 0.9098 (pp) REVERT: A 503 LEU cc_start: 0.9456 (mt) cc_final: 0.9208 (mt) REVERT: A 578 MET cc_start: 0.8150 (mtp) cc_final: 0.7838 (mtp) REVERT: A 582 ASP cc_start: 0.8102 (m-30) cc_final: 0.7869 (p0) REVERT: A 627 MET cc_start: 0.8307 (ppp) cc_final: 0.7963 (ppp) REVERT: A 682 MET cc_start: 0.8769 (tmm) cc_final: 0.8366 (tmm) REVERT: A 687 LEU cc_start: 0.9383 (tp) cc_final: 0.8735 (tp) REVERT: A 708 ASP cc_start: 0.7654 (m-30) cc_final: 0.7429 (m-30) REVERT: A 841 MET cc_start: 0.7888 (tpp) cc_final: 0.7323 (tpp) REVERT: A 858 MET cc_start: 0.7154 (ppp) cc_final: 0.6867 (ppp) REVERT: A 880 ARG cc_start: 0.8465 (tpp80) cc_final: 0.7883 (tpp80) REVERT: A 916 PHE cc_start: 0.9153 (t80) cc_final: 0.8947 (t80) REVERT: A 984 MET cc_start: 0.9049 (mmp) cc_final: 0.8361 (tpp) REVERT: B 126 GLU cc_start: 0.7222 (mp0) cc_final: 0.6502 (mp0) REVERT: B 152 MET cc_start: 0.7244 (tpt) cc_final: 0.6972 (mmm) REVERT: C 395 HIS cc_start: 0.7602 (t-90) cc_final: 0.7003 (t-90) REVERT: C 480 GLN cc_start: 0.9489 (mp10) cc_final: 0.9197 (mp10) REVERT: C 790 SER cc_start: 0.8972 (t) cc_final: 0.8569 (m) REVERT: C 1004 ASN cc_start: 0.8266 (p0) cc_final: 0.7784 (p0) REVERT: D 16 GLN cc_start: 0.8148 (pt0) cc_final: 0.7551 (pm20) REVERT: D 214 ASP cc_start: 0.7193 (m-30) cc_final: 0.6904 (p0) REVERT: D 218 ILE cc_start: 0.9285 (mt) cc_final: 0.9056 (mp) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1310 time to fit residues: 42.9836 Evaluate side-chains 152 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 181 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 818 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** 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 = 0.3643 r_free = 0.3643 target = 0.078445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057624 restraints weight = 101594.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058780 restraints weight = 58692.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059387 restraints weight = 36254.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059729 restraints weight = 28711.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059774 restraints weight = 26322.801| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 19981 Z= 0.198 Angle : 0.686 8.594 27914 Z= 0.375 Chirality : 0.046 0.353 3095 Planarity : 0.004 0.055 2876 Dihedral : 25.609 179.350 4336 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.19), residues: 1894 helix: 0.16 (0.21), residues: 638 sheet: -0.86 (0.29), residues: 315 loop : -1.96 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 486 TYR 0.019 0.002 TYR D 91 PHE 0.018 0.002 PHE C 497 TRP 0.026 0.002 TRP A 829 HIS 0.006 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (19973) covalent geometry : angle 0.68287 / 0.38 (27910) hydrogen bonds : bond 0.04938 / 3.23 ( 883) hydrogen bonds : angle 4.58982 / 3.23 ( 2354) metal coordination : bond 0.01702 / 1.00 ( 8) metal coordination : angle 5.92013 / 3.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8908 (m-80) cc_final: 0.8483 (m-10) REVERT: A 503 LEU cc_start: 0.9455 (mt) cc_final: 0.9249 (mt) REVERT: A 578 MET cc_start: 0.8244 (mtp) cc_final: 0.7903 (mtp) REVERT: A 582 ASP cc_start: 0.8315 (m-30) cc_final: 0.8077 (p0) REVERT: A 627 MET cc_start: 0.8237 (ppp) cc_final: 0.7897 (ppp) REVERT: A 682 MET cc_start: 0.8846 (tmm) cc_final: 0.8516 (tmm) REVERT: A 687 LEU cc_start: 0.9358 (tp) cc_final: 0.8746 (tp) REVERT: A 841 MET cc_start: 0.8007 (tpp) cc_final: 0.7547 (tpp) REVERT: A 880 ARG cc_start: 0.8493 (tpp80) cc_final: 0.7913 (tpp80) REVERT: A 889 MET cc_start: 0.9295 (mtp) cc_final: 0.9034 (mtt) REVERT: A 984 MET cc_start: 0.9092 (mmp) cc_final: 0.8870 (tpp) REVERT: A 1003 MET cc_start: 0.9042 (mmt) cc_final: 0.8669 (mmt) REVERT: B 110 MET cc_start: 0.7148 (tmm) cc_final: 0.6629 (tmm) REVERT: B 126 GLU cc_start: 0.7194 (mp0) cc_final: 0.6557 (mp0) REVERT: B 152 MET cc_start: 0.7315 (tpt) cc_final: 0.6837 (mmm) REVERT: C 395 HIS cc_start: 0.7647 (t-90) cc_final: 0.7025 (t-90) REVERT: C 480 GLN cc_start: 0.9467 (mp10) cc_final: 0.9159 (mp10) REVERT: C 790 SER cc_start: 0.9046 (t) cc_final: 0.8645 (m) REVERT: C 924 PHE cc_start: 0.8985 (m-80) cc_final: 0.8777 (m-80) REVERT: D 218 ILE cc_start: 0.9319 (mt) cc_final: 0.9050 (mp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1319 time to fit residues: 39.6669 Evaluate side-chains 139 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 94 optimal weight: 8.9990 chunk 179 optimal weight: 0.0980 chunk 122 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 156 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 195 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 818 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.080506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058592 restraints weight = 99991.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.060090 restraints weight = 51727.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061029 restraints weight = 33111.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061616 restraints weight = 24900.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.061912 restraints weight = 20890.909| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 19981 Z= 0.130 Angle : 0.641 8.598 27914 Z= 0.352 Chirality : 0.046 0.373 3095 Planarity : 0.004 0.039 2876 Dihedral : 25.519 179.964 4336 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 1894 helix: 0.26 (0.21), residues: 636 sheet: -0.67 (0.29), residues: 322 loop : -1.91 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 212 TYR 0.020 0.001 TYR D 91 PHE 0.015 0.001 PHE C 641 TRP 0.025 0.001 TRP A 829 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (19973) covalent geometry : angle 0.63994 / 0.35 (27910) hydrogen bonds : bond 0.04218 / 2.79 ( 883) hydrogen bonds : angle 4.42165 / 3.11 ( 2354) metal coordination : bond 0.00718 / 0.43 ( 8) metal coordination : angle 3.49991 / 2.05 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8940 (m-80) cc_final: 0.8568 (m-80) REVERT: A 434 LEU cc_start: 0.9354 (mt) cc_final: 0.9089 (pp) REVERT: A 503 LEU cc_start: 0.9433 (mt) cc_final: 0.9137 (mt) REVERT: A 578 MET cc_start: 0.8092 (mtp) cc_final: 0.7776 (mtp) REVERT: A 582 ASP cc_start: 0.8052 (m-30) cc_final: 0.7847 (p0) REVERT: A 627 MET cc_start: 0.8282 (ppp) cc_final: 0.7948 (ppp) REVERT: A 682 MET cc_start: 0.8738 (tmm) cc_final: 0.8349 (tmm) REVERT: A 687 LEU cc_start: 0.9298 (tp) cc_final: 0.8666 (tp) REVERT: A 841 MET cc_start: 0.7936 (tpp) cc_final: 0.7416 (tpp) REVERT: A 880 ARG cc_start: 0.8451 (tpp80) cc_final: 0.7878 (tpp80) REVERT: A 916 PHE cc_start: 0.9164 (t80) cc_final: 0.8963 (t80) REVERT: A 984 MET cc_start: 0.9031 (mmp) cc_final: 0.8767 (tpp) REVERT: A 1003 MET cc_start: 0.9054 (mmt) cc_final: 0.8665 (mmt) REVERT: B 110 MET cc_start: 0.7176 (tmm) cc_final: 0.6655 (tmm) REVERT: B 126 GLU cc_start: 0.7102 (mp0) cc_final: 0.6482 (mp0) REVERT: B 152 MET cc_start: 0.7212 (tpt) cc_final: 0.6953 (mmm) REVERT: C 395 HIS cc_start: 0.7615 (t-90) cc_final: 0.7034 (t-90) REVERT: C 480 GLN cc_start: 0.9430 (mp10) cc_final: 0.9187 (mp10) REVERT: C 790 SER cc_start: 0.8794 (t) cc_final: 0.8469 (m) REVERT: D 16 GLN cc_start: 0.8167 (pt0) cc_final: 0.7571 (pm20) REVERT: D 197 LEU cc_start: 0.8427 (tp) cc_final: 0.8219 (tp) REVERT: D 214 ASP cc_start: 0.7346 (m-30) cc_final: 0.6898 (p0) REVERT: D 218 ILE cc_start: 0.9277 (mt) cc_final: 0.9063 (mp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1348 time to fit residues: 42.1970 Evaluate side-chains 154 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 169 optimal weight: 2.9990 chunk 194 optimal weight: 30.0000 chunk 157 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 204 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 818 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 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 = 0.3673 r_free = 0.3673 target = 0.079876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058843 restraints weight = 100094.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.060136 restraints weight = 55406.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060807 restraints weight = 33484.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061102 restraints weight = 26592.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061056 restraints weight = 23840.236| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 19981 Z= 0.137 Angle : 0.629 8.379 27914 Z= 0.347 Chirality : 0.045 0.370 3095 Planarity : 0.004 0.039 2876 Dihedral : 25.502 179.366 4336 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.06 % Allowed : 0.12 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.19), residues: 1894 helix: 0.30 (0.21), residues: 637 sheet: -0.54 (0.29), residues: 322 loop : -1.87 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 212 TYR 0.012 0.001 TYR C 559 PHE 0.016 0.001 PHE C 641 TRP 0.022 0.001 TRP D 317 HIS 0.003 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (19973) covalent geometry : angle 0.62707 / 0.35 (27910) hydrogen bonds : bond 0.04280 / 2.82 ( 883) hydrogen bonds : angle 4.39437 / 3.09 ( 2354) metal coordination : bond 0.00635 / 0.36 ( 8) metal coordination : angle 3.60762 / 2.10 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.08 seconds wall clock time: 51 minutes 5.88 seconds (3065.88 seconds total)