Starting phenix.real_space_refine on Thu Mar 5 04:01:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oeq_20034/03_2026/6oeq_20034.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oeq_20034/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6oeq_20034/03_2026/6oeq_20034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oeq_20034/03_2026/6oeq_20034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oeq_20034/03_2026/6oeq_20034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oeq_20034/03_2026/6oeq_20034.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.03, per 1000 atoms: 0.21 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: 1.74 Conformation dependent library (CDL) restraints added in 668.7 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: 2.66 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: 5.13 Time building geometry restraints manager: 2.26 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=" 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=" 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=" N LEU A 906 " pdb=" CA LEU A 906 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.28e-02 6.10e+03 9.35e+00 bond pdb=" C TYR C 514 " pdb=" N HIS C 515 " ideal model delta sigma weight residual 1.333 1.252 0.080 2.74e-02 1.33e+03 8.55e+00 bond pdb=" N ASP C 600 " pdb=" CA ASP C 600 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.20e-02 6.94e+03 6.43e+00 ... (remaining 19968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26277 2.08 - 4.15: 1432 4.15 - 6.23: 158 6.23 - 8.30: 36 8.30 - 10.38: 7 Bond angle restraints: 27910 Sorted by residual: angle pdb=" C TYR C 725 " pdb=" N ILE C 726 " pdb=" CA ILE C 726 " ideal model delta sigma weight residual 122.66 117.66 5.00 9.70e-01 1.06e+00 2.66e+01 angle pdb=" C ARG D 73 " pdb=" N TYR D 74 " pdb=" CA TYR D 74 " ideal model delta sigma weight residual 122.85 117.53 5.32 1.10e+00 8.26e-01 2.34e+01 angle pdb=" N LEU C 655 " pdb=" CA LEU C 655 " pdb=" C LEU C 655 " ideal model delta sigma weight residual 114.62 109.15 5.47 1.14e+00 7.69e-01 2.30e+01 angle pdb=" C ASN D 268 " pdb=" N ASP D 269 " pdb=" CA ASP D 269 " ideal model delta sigma weight residual 122.46 128.93 -6.47 1.41e+00 5.03e-01 2.10e+01 angle pdb=" C THR C 400 " pdb=" N ARG C 401 " pdb=" CA ARG C 401 " ideal model delta sigma weight residual 120.28 125.96 -5.68 1.34e+00 5.57e-01 1.80e+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 - 0.054: 2115 0.054 - 0.107: 757 0.107 - 0.161: 179 0.161 - 0.215: 39 0.215 - 0.268: 5 Chirality restraints: 3095 Sorted by residual: 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=" CG LEU D 14 " pdb=" CB LEU D 14 " pdb=" CD1 LEU D 14 " pdb=" CD2 LEU D 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+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 2.35 -2.57 -0.22 2.00e-01 2.50e+01 1.26e+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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.940 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.461 19981 Z= 0.413 Angle : 1.066 22.960 27914 Z= 0.605 Chirality : 0.058 0.268 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 covalent geometry : bond 0.00853 (19973) covalent geometry : angle 1.04928 (27910) hydrogen bonds : bond 0.15293 ( 883) hydrogen bonds : angle 7.00196 ( 2354) metal coordination : bond 0.20030 ( 8) metal coordination : angle 15.63102 ( 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 : 0.611 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: 0.9090 (mt) REVERT: A 578 MET cc_start: 0.8277 (mtp) cc_final: 0.7875 (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: 0.7681 (mtt180) REVERT: A 971 PHE cc_start: 0.8673 (m-80) cc_final: 0.8421 (m-80) REVERT: A 975 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7533 (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: 0.6316 (ttt) REVERT: C 395 HIS cc_start: 0.7621 (t-170) cc_final: 0.7272 (t-90) REVERT: C 510 LEU cc_start: 0.9050 (mt) cc_final: 0.8593 (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: 0.6932 (tm-30) REVERT: C 1003 MET cc_start: 0.8710 (mmm) cc_final: 0.8488 (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: 0.8201 (t0) REVERT: D 326 THR cc_start: 0.8899 (p) cc_final: 0.8617 (p) outliers start: 10 outliers final: 4 residues processed: 211 average time/residue: 0.1436 time to fit residues: 46.1485 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 : 0.657 ------------------------------------------------------------------------------- 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: 10.0000 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 480 GLN A 495 GLN A 525 ASN A 647 ASN 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 D 47 HIS D 89 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 173 ASN D 213 ASN D 222 HIS D 268 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.079729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058947 restraints weight = 101589.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.060106 restraints weight = 56617.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060682 restraints weight = 34297.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060951 restraints weight = 28870.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061018 restraints weight = 25612.542| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19981 Z= 0.158 Angle : 0.666 8.368 27914 Z= 0.370 Chirality : 0.042 0.157 3095 Planarity : 0.005 0.053 2876 Dihedral : 25.941 178.295 4336 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % 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: -2.76 (0.17), residues: 1894 helix: -1.07 (0.19), residues: 631 sheet: -1.37 (0.28), residues: 323 loop : -2.56 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 915 TYR 0.021 0.001 TYR A 559 PHE 0.016 0.001 PHE C 497 TRP 0.017 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00340 (19973) covalent geometry : angle 0.66433 (27910) hydrogen bonds : bond 0.04662 ( 883) hydrogen bonds : angle 4.95261 ( 2354) metal coordination : bond 0.00907 ( 8) metal coordination : angle 4.38528 ( 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 228 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8756 (m-80) cc_final: 0.8449 (m-10) REVERT: A 503 LEU cc_start: 0.9354 (mt) cc_final: 0.9083 (mt) REVERT: A 578 MET cc_start: 0.8374 (mtp) cc_final: 0.7964 (mtp) REVERT: A 627 MET cc_start: 0.8290 (ppp) cc_final: 0.8041 (ppp) REVERT: A 708 ASP cc_start: 0.7792 (m-30) cc_final: 0.7492 (m-30) REVERT: A 714 GLU cc_start: 0.8877 (tt0) cc_final: 0.8477 (pp20) REVERT: A 761 ARG cc_start: 0.8528 (tmm-80) cc_final: 0.8046 (tmm160) REVERT: A 880 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8028 (tpp80) REVERT: A 889 MET cc_start: 0.9291 (mtp) cc_final: 0.8686 (mpp) REVERT: A 916 PHE cc_start: 0.9152 (t80) cc_final: 0.8941 (t80) REVERT: A 970 ARG cc_start: 0.8724 (mtt180) cc_final: 0.8135 (mtt180) REVERT: B 126 GLU cc_start: 0.6610 (mp0) cc_final: 0.5103 (pm20) REVERT: B 152 MET cc_start: 0.6990 (tpt) cc_final: 0.6521 (tmm) REVERT: B 162 MET cc_start: 0.9024 (mmm) cc_final: 0.8722 (mmp) REVERT: B 287 CYS cc_start: 0.7605 (m) cc_final: 0.6316 (m) REVERT: B 302 MET cc_start: 0.7064 (ptp) cc_final: 0.6419 (ttt) REVERT: C 395 HIS cc_start: 0.7522 (t70) cc_final: 0.7226 (t-90) REVERT: C 484 MET cc_start: 0.9465 (ttp) cc_final: 0.8961 (tmm) REVERT: C 510 LEU cc_start: 0.9102 (mt) cc_final: 0.8717 (mp) REVERT: C 570 MET cc_start: 0.8930 (ptp) cc_final: 0.8636 (mtm) REVERT: C 883 MET cc_start: 0.8903 (tpp) cc_final: 0.8686 (mpp) REVERT: C 985 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7966 (tm-30) REVERT: D 16 GLN cc_start: 0.7912 (pt0) cc_final: 0.7539 (pm20) REVERT: D 218 ILE cc_start: 0.9342 (mt) cc_final: 0.9051 (mp) REVERT: D 289 LEU cc_start: 0.8811 (pt) cc_final: 0.7344 (pt) REVERT: D 298 GLU cc_start: 0.8827 (tp30) cc_final: 0.8409 (tm-30) REVERT: D 326 THR cc_start: 0.8635 (p) cc_final: 0.8192 (p) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1376 time to fit residues: 49.3769 Evaluate side-chains 148 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 7.9990 chunk 99 optimal weight: 8.9990 chunk 12 optimal weight: 0.0870 chunk 41 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 HIS C 525 ASN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS D 281 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.077009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.056412 restraints weight = 104003.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.057453 restraints weight = 58786.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057883 restraints weight = 37788.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058114 restraints weight = 32254.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.058258 restraints weight = 27864.144| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19981 Z= 0.258 Angle : 0.716 8.798 27914 Z= 0.394 Chirality : 0.043 0.163 3095 Planarity : 0.005 0.045 2876 Dihedral : 25.805 178.496 4336 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: -2.28 (0.18), residues: 1894 helix: -0.43 (0.20), residues: 629 sheet: -1.41 (0.28), residues: 328 loop : -2.34 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 458 TYR 0.031 0.002 TYR D 91 PHE 0.017 0.002 PHE C 924 TRP 0.018 0.002 TRP D 317 HIS 0.015 0.002 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00556 (19973) covalent geometry : angle 0.71187 (27910) hydrogen bonds : bond 0.05495 ( 883) hydrogen bonds : angle 4.88122 ( 2354) metal coordination : bond 0.01961 ( 8) metal coordination : angle 6.60377 ( 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 195 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.686 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: 0.8908 (m-80) cc_final: 0.8532 (m-10) REVERT: A 503 LEU cc_start: 0.9418 (mt) cc_final: 0.9167 (mt) REVERT: A 578 MET cc_start: 0.8376 (mtp) cc_final: 0.8013 (mtp) REVERT: A 627 MET cc_start: 0.8307 (ppp) cc_final: 0.8040 (ppp) REVERT: A 682 MET cc_start: 0.8817 (tmm) cc_final: 0.8589 (tmm) REVERT: A 708 ASP cc_start: 0.7608 (m-30) cc_final: 0.7319 (m-30) REVERT: A 761 ARG cc_start: 0.8668 (tmm-80) cc_final: 0.8242 (tmm160) REVERT: A 841 MET cc_start: 0.8031 (tpp) cc_final: 0.7504 (tpp) REVERT: A 880 ARG cc_start: 0.8586 (tpp80) cc_final: 0.7997 (tpp80) REVERT: A 889 MET cc_start: 0.9393 (mtp) cc_final: 0.9142 (mtt) REVERT: A 970 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8327 (mtt180) REVERT: B 126 GLU cc_start: 0.7022 (mp0) cc_final: 0.5735 (pm20) REVERT: B 152 MET cc_start: 0.7128 (tpt) cc_final: 0.6695 (mmm) REVERT: B 162 MET cc_start: 0.8995 (mmm) cc_final: 0.8653 (mmp) REVERT: B 287 CYS cc_start: 0.7650 (m) cc_final: 0.6197 (m) REVERT: B 302 MET cc_start: 0.7153 (ptp) cc_final: 0.6633 (ttt) REVERT: C 395 HIS cc_start: 0.7797 (t-90) cc_final: 0.7058 (t-90) REVERT: C 570 MET cc_start: 0.9054 (ptp) cc_final: 0.8849 (mtm) REVERT: C 578 MET cc_start: 0.9054 (mtm) cc_final: 0.8824 (mtm) REVERT: C 1004 ASN cc_start: 0.8560 (p0) cc_final: 0.8040 (p0) REVERT: D 218 ILE cc_start: 0.9396 (mt) cc_final: 0.9126 (mp) REVERT: D 326 THR cc_start: 0.8727 (p) cc_final: 0.8049 (p) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1424 time to fit residues: 43.4166 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 : 0.651 ------------------------------------------------------------------------------- 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: 0.0270 chunk 20 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.079981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.058629 restraints weight = 102127.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059959 restraints weight = 55905.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060810 restraints weight = 37085.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.061348 restraints weight = 28334.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.061688 restraints weight = 23949.438| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19981 Z= 0.138 Angle : 0.604 7.844 27914 Z= 0.335 Chirality : 0.041 0.161 3095 Planarity : 0.004 0.039 2876 Dihedral : 25.573 178.044 4336 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % 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: -1.86 (0.19), residues: 1894 helix: -0.08 (0.20), residues: 637 sheet: -1.08 (0.29), residues: 321 loop : -2.14 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.016 0.001 TYR C 805 PHE 0.018 0.001 PHE C 497 TRP 0.012 0.001 TRP B 317 HIS 0.006 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00299 (19973) covalent geometry : angle 0.60261 (27910) hydrogen bonds : bond 0.03961 ( 883) hydrogen bonds : angle 4.44919 ( 2354) metal coordination : bond 0.01638 ( 8) metal coordination : angle 3.30705 ( 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 213 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8926 (m-80) cc_final: 0.8567 (m-80) REVERT: A 503 LEU cc_start: 0.9333 (mt) cc_final: 0.9111 (mt) REVERT: A 569 ASP cc_start: 0.8696 (p0) cc_final: 0.8161 (t0) REVERT: A 578 MET cc_start: 0.8168 (mtp) cc_final: 0.7854 (mtp) REVERT: A 627 MET cc_start: 0.8353 (ppp) cc_final: 0.8032 (ppp) REVERT: A 682 MET cc_start: 0.8807 (tmm) cc_final: 0.8458 (tmm) REVERT: A 687 LEU cc_start: 0.9268 (tp) cc_final: 0.8654 (tp) REVERT: A 708 ASP cc_start: 0.7593 (m-30) cc_final: 0.7360 (m-30) REVERT: A 713 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7955 (ttm170) REVERT: A 841 MET cc_start: 0.8080 (tpp) cc_final: 0.7597 (tpp) REVERT: A 880 ARG cc_start: 0.8536 (tpp80) cc_final: 0.7977 (tpp80) REVERT: A 889 MET cc_start: 0.9342 (mtp) cc_final: 0.8908 (mtt) REVERT: A 970 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8189 (mtt180) REVERT: A 984 MET cc_start: 0.8975 (mmp) cc_final: 0.8229 (mmm) REVERT: B 126 GLU cc_start: 0.7132 (mp0) cc_final: 0.5680 (pm20) REVERT: B 152 MET cc_start: 0.7245 (tpt) cc_final: 0.6899 (mmm) REVERT: B 287 CYS cc_start: 0.7496 (m) cc_final: 0.6074 (m) REVERT: B 302 MET cc_start: 0.6894 (ptp) cc_final: 0.6251 (ttt) REVERT: C 395 HIS cc_start: 0.7669 (t-90) cc_final: 0.7068 (t-90) REVERT: C 480 GLN cc_start: 0.9472 (mp10) cc_final: 0.9202 (mp10) REVERT: C 484 MET cc_start: 0.9120 (tmm) cc_final: 0.8824 (tmm) REVERT: C 510 LEU cc_start: 0.9163 (mt) cc_final: 0.8484 (mp) REVERT: C 790 SER cc_start: 0.9183 (t) cc_final: 0.8735 (m) REVERT: C 1004 ASN cc_start: 0.8135 (p0) cc_final: 0.7722 (p0) REVERT: D 214 ASP cc_start: 0.7303 (m-30) cc_final: 0.7043 (p0) REVERT: D 218 ILE cc_start: 0.9326 (mt) cc_final: 0.9084 (mp) REVERT: D 289 LEU cc_start: 0.8597 (pt) cc_final: 0.6956 (pt) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1356 time to fit residues: 45.5337 Evaluate side-chains 158 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 4.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.078543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.057782 restraints weight = 103281.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058966 restraints weight = 58217.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059602 restraints weight = 35547.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059819 restraints weight = 28264.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059873 restraints weight = 25515.214| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19981 Z= 0.186 Angle : 0.634 7.375 27914 Z= 0.349 Chirality : 0.041 0.165 3095 Planarity : 0.004 0.044 2876 Dihedral : 25.532 178.575 4336 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: -1.73 (0.19), residues: 1894 helix: 0.07 (0.20), residues: 646 sheet: -1.04 (0.29), residues: 327 loop : -2.10 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 212 TYR 0.023 0.001 TYR D 91 PHE 0.015 0.002 PHE C 936 TRP 0.016 0.001 TRP B 317 HIS 0.008 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00403 (19973) covalent geometry : angle 0.63033 (27910) hydrogen bonds : bond 0.04559 ( 883) hydrogen bonds : angle 4.50459 ( 2354) metal coordination : bond 0.01460 ( 8) metal coordination : angle 5.36415 ( 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 206 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8896 (m-80) cc_final: 0.8475 (m-10) REVERT: A 503 LEU cc_start: 0.9362 (mt) cc_final: 0.9118 (mt) REVERT: A 505 ASN cc_start: 0.9213 (m-40) cc_final: 0.8979 (m-40) REVERT: A 578 MET cc_start: 0.8294 (mtp) cc_final: 0.7950 (mtp) REVERT: A 627 MET cc_start: 0.8268 (ppp) cc_final: 0.7939 (ppp) REVERT: A 682 MET cc_start: 0.8830 (tmm) cc_final: 0.8584 (tmm) REVERT: A 687 LEU cc_start: 0.9360 (tp) cc_final: 0.8714 (tp) REVERT: A 708 ASP cc_start: 0.7665 (m-30) cc_final: 0.7403 (m-30) REVERT: A 761 ARG cc_start: 0.8284 (tmm160) cc_final: 0.8032 (tmm160) REVERT: A 841 MET cc_start: 0.8122 (tpp) cc_final: 0.7558 (tpp) REVERT: A 880 ARG cc_start: 0.8480 (tpp80) cc_final: 0.7922 (tpp80) REVERT: A 889 MET cc_start: 0.9324 (mtp) cc_final: 0.9105 (mtt) REVERT: A 970 ARG cc_start: 0.8609 (mtt180) cc_final: 0.8284 (mtt180) REVERT: A 1003 MET cc_start: 0.9088 (mmt) cc_final: 0.8826 (tpp) REVERT: B 126 GLU cc_start: 0.7069 (mp0) cc_final: 0.5790 (pm20) REVERT: B 152 MET cc_start: 0.7283 (tpt) cc_final: 0.6876 (mmm) REVERT: B 287 CYS cc_start: 0.7623 (m) cc_final: 0.6319 (m) REVERT: B 302 MET cc_start: 0.6892 (ptp) cc_final: 0.6409 (ttt) REVERT: C 395 HIS cc_start: 0.7712 (t-90) cc_final: 0.7100 (t-90) REVERT: C 480 GLN cc_start: 0.9488 (mp10) cc_final: 0.9237 (mp10) REVERT: C 484 MET cc_start: 0.9168 (tmm) cc_final: 0.8811 (tmm) REVERT: C 510 LEU cc_start: 0.9058 (mt) cc_final: 0.8810 (mt) REVERT: C 578 MET cc_start: 0.8961 (mtp) cc_final: 0.8678 (mtm) REVERT: C 790 SER cc_start: 0.9116 (t) cc_final: 0.8747 (m) REVERT: C 883 MET cc_start: 0.9019 (mmm) cc_final: 0.8754 (mmm) REVERT: D 102 GLU cc_start: 0.8253 (mp0) cc_final: 0.8046 (mp0) REVERT: D 218 ILE cc_start: 0.9359 (mt) cc_final: 0.9092 (mp) REVERT: D 289 LEU cc_start: 0.8911 (pt) cc_final: 0.7903 (pt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1288 time to fit residues: 42.9388 Evaluate side-chains 155 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 10.0000 chunk 168 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 161 optimal weight: 0.1980 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.079591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057777 restraints weight = 101821.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059262 restraints weight = 52868.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060192 restraints weight = 33840.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.060783 restraints weight = 25361.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061140 restraints weight = 21158.223| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19981 Z= 0.143 Angle : 0.599 7.576 27914 Z= 0.331 Chirality : 0.041 0.155 3095 Planarity : 0.004 0.038 2876 Dihedral : 25.442 177.724 4336 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -1.53 (0.19), residues: 1894 helix: 0.19 (0.20), residues: 650 sheet: -0.85 (0.29), residues: 327 loop : -1.99 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 894 TYR 0.015 0.001 TYR D 91 PHE 0.021 0.001 PHE C 641 TRP 0.015 0.001 TRP D 317 HIS 0.007 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00312 (19973) covalent geometry : angle 0.59690 (27910) hydrogen bonds : bond 0.03915 ( 883) hydrogen bonds : angle 4.32998 ( 2354) metal coordination : bond 0.01314 ( 8) metal coordination : angle 4.49626 ( 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 200 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.8996 (m-80) cc_final: 0.8587 (m-80) REVERT: A 476 LEU cc_start: 0.8880 (tp) cc_final: 0.8626 (tp) REVERT: A 578 MET cc_start: 0.8125 (mtp) cc_final: 0.7827 (mtp) REVERT: A 627 MET cc_start: 0.8347 (ppp) cc_final: 0.8002 (ppp) REVERT: A 682 MET cc_start: 0.8812 (tmm) cc_final: 0.8524 (tmm) REVERT: A 687 LEU cc_start: 0.9305 (tp) cc_final: 0.8627 (tp) REVERT: A 708 ASP cc_start: 0.7639 (m-30) cc_final: 0.7425 (m-30) REVERT: A 761 ARG cc_start: 0.8169 (tmm160) cc_final: 0.7921 (tmm160) REVERT: A 841 MET cc_start: 0.8041 (tpp) cc_final: 0.7473 (tpp) REVERT: A 849 MET cc_start: 0.4208 (tpt) cc_final: 0.3259 (ppp) REVERT: A 880 ARG cc_start: 0.8487 (tpp80) cc_final: 0.7911 (tpp80) REVERT: A 889 MET cc_start: 0.9306 (mtp) cc_final: 0.9103 (mtt) REVERT: A 970 ARG cc_start: 0.8628 (mtt180) cc_final: 0.8230 (mtt180) REVERT: B 126 GLU cc_start: 0.7002 (mp0) cc_final: 0.5955 (pm20) REVERT: B 152 MET cc_start: 0.7230 (tpt) cc_final: 0.6888 (mmm) REVERT: B 287 CYS cc_start: 0.7436 (m) cc_final: 0.6140 (m) REVERT: B 302 MET cc_start: 0.6708 (ptp) cc_final: 0.6190 (ttt) REVERT: C 395 HIS cc_start: 0.7579 (t-90) cc_final: 0.6979 (t-90) REVERT: C 480 GLN cc_start: 0.9478 (mp10) cc_final: 0.9240 (mp10) REVERT: C 484 MET cc_start: 0.9121 (tmm) cc_final: 0.8697 (tmm) REVERT: C 510 LEU cc_start: 0.8923 (mt) cc_final: 0.8706 (mt) REVERT: C 578 MET cc_start: 0.8937 (mtp) cc_final: 0.8656 (mtm) REVERT: C 790 SER cc_start: 0.9100 (t) cc_final: 0.8718 (m) REVERT: C 971 PHE cc_start: 0.9401 (m-10) cc_final: 0.8970 (m-80) REVERT: D 102 GLU cc_start: 0.8296 (mp0) cc_final: 0.8066 (mp0) REVERT: D 197 LEU cc_start: 0.8433 (tp) cc_final: 0.8220 (tp) REVERT: D 214 ASP cc_start: 0.7129 (m-30) cc_final: 0.6866 (p0) REVERT: D 218 ILE cc_start: 0.9326 (mt) cc_final: 0.9112 (mp) REVERT: D 289 LEU cc_start: 0.8811 (pt) cc_final: 0.8296 (pt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1375 time to fit residues: 43.8098 Evaluate side-chains 160 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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: 3.9990 chunk 182 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.079587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057850 restraints weight = 101673.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059310 restraints weight = 52739.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060235 restraints weight = 33912.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.060814 restraints weight = 25425.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061183 restraints weight = 21250.117| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19981 Z= 0.148 Angle : 0.602 7.238 27914 Z= 0.330 Chirality : 0.040 0.158 3095 Planarity : 0.004 0.067 2876 Dihedral : 25.333 177.960 4336 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -1.35 (0.19), residues: 1894 helix: 0.40 (0.21), residues: 634 sheet: -0.84 (0.28), residues: 334 loop : -1.87 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 756 TYR 0.012 0.001 TYR C 805 PHE 0.017 0.001 PHE C 641 TRP 0.014 0.001 TRP B 317 HIS 0.005 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00325 (19973) covalent geometry : angle 0.60020 (27910) hydrogen bonds : bond 0.03984 ( 883) hydrogen bonds : angle 4.30802 ( 2354) metal coordination : bond 0.01034 ( 8) metal coordination : angle 4.41937 ( 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 191 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.9023 (m-80) cc_final: 0.8509 (m-10) REVERT: A 468 LEU cc_start: 0.9450 (mm) cc_final: 0.9222 (mp) REVERT: A 503 LEU cc_start: 0.9292 (mt) cc_final: 0.9064 (mt) REVERT: A 578 MET cc_start: 0.8105 (mtp) cc_final: 0.7799 (mtp) REVERT: A 627 MET cc_start: 0.8156 (ppp) cc_final: 0.7826 (ppp) REVERT: A 682 MET cc_start: 0.8842 (tmm) cc_final: 0.8576 (tmm) REVERT: A 687 LEU cc_start: 0.9343 (tp) cc_final: 0.8652 (tp) REVERT: A 761 ARG cc_start: 0.8186 (tmm160) cc_final: 0.7911 (tmm160) REVERT: A 841 MET cc_start: 0.7927 (tpp) cc_final: 0.7340 (tpp) REVERT: A 849 MET cc_start: 0.4626 (tpt) cc_final: 0.3446 (ppp) REVERT: A 880 ARG cc_start: 0.8441 (tpp80) cc_final: 0.7889 (tpp80) REVERT: A 889 MET cc_start: 0.9345 (mtp) cc_final: 0.9119 (mtt) REVERT: A 916 PHE cc_start: 0.9157 (t80) cc_final: 0.8940 (t80) REVERT: A 984 MET cc_start: 0.8972 (mmp) cc_final: 0.8256 (mmm) REVERT: B 110 MET cc_start: 0.7114 (tmm) cc_final: 0.6734 (tmm) REVERT: B 126 GLU cc_start: 0.6950 (mp0) cc_final: 0.5947 (pm20) REVERT: B 152 MET cc_start: 0.7227 (tpt) cc_final: 0.6926 (mmm) REVERT: B 287 CYS cc_start: 0.7469 (m) cc_final: 0.6179 (m) REVERT: B 302 MET cc_start: 0.6737 (ptp) cc_final: 0.6248 (ttt) REVERT: C 395 HIS cc_start: 0.7625 (t-90) cc_final: 0.7049 (t-90) REVERT: C 480 GLN cc_start: 0.9470 (mp10) cc_final: 0.9236 (mp10) REVERT: C 484 MET cc_start: 0.9164 (tmm) cc_final: 0.8804 (tmm) REVERT: C 578 MET cc_start: 0.8925 (mtp) cc_final: 0.8720 (mtm) REVERT: C 790 SER cc_start: 0.9096 (t) cc_final: 0.8648 (m) REVERT: D 102 GLU cc_start: 0.8294 (mp0) cc_final: 0.7980 (mp0) REVERT: D 197 LEU cc_start: 0.8449 (tp) cc_final: 0.8225 (tp) REVERT: D 214 ASP cc_start: 0.7266 (m-30) cc_final: 0.6967 (p0) REVERT: D 218 ILE cc_start: 0.9318 (mt) cc_final: 0.9105 (mp) REVERT: D 289 LEU cc_start: 0.8880 (pt) cc_final: 0.8435 (pt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1356 time to fit residues: 41.7209 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 : 0.685 ------------------------------------------------------------------------------- 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: 5.9990 chunk 149 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS C 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.077461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056136 restraints weight = 103611.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057395 restraints weight = 57845.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.058209 restraints weight = 38857.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058731 restraints weight = 30014.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059035 restraints weight = 25490.466| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19981 Z= 0.244 Angle : 0.691 10.064 27914 Z= 0.375 Chirality : 0.043 0.159 3095 Planarity : 0.004 0.057 2876 Dihedral : 25.359 179.963 4336 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.44 % 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: -1.61 (0.19), residues: 1894 helix: 0.12 (0.20), residues: 647 sheet: -0.91 (0.29), residues: 323 loop : -2.02 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 756 TYR 0.021 0.002 TYR D 91 PHE 0.020 0.002 PHE C 924 TRP 0.023 0.002 TRP B 317 HIS 0.007 0.002 HIS C 744 Details of bonding type rmsd covalent geometry : bond 0.00529 (19973) covalent geometry : angle 0.68541 (27910) hydrogen bonds : bond 0.04980 ( 883) hydrogen bonds : angle 4.58386 ( 2354) metal coordination : bond 0.02060 ( 8) metal coordination : angle 7.24933 ( 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 181 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.9057 (m-80) cc_final: 0.8556 (m-10) REVERT: A 503 LEU cc_start: 0.9323 (mt) cc_final: 0.8999 (mt) REVERT: A 578 MET cc_start: 0.8253 (mtp) cc_final: 0.7940 (mtp) REVERT: A 627 MET cc_start: 0.8186 (ppp) cc_final: 0.7901 (ppp) REVERT: A 682 MET cc_start: 0.8905 (tmm) cc_final: 0.8606 (tmm) REVERT: A 708 ASP cc_start: 0.7602 (m-30) cc_final: 0.7369 (m-30) REVERT: A 849 MET cc_start: 0.4795 (tpt) cc_final: 0.3405 (ppp) REVERT: A 880 ARG cc_start: 0.8458 (tpp80) cc_final: 0.7922 (tpp80) REVERT: A 889 MET cc_start: 0.9319 (mtp) cc_final: 0.8856 (mtt) REVERT: A 916 PHE cc_start: 0.9189 (t80) cc_final: 0.8978 (t80) REVERT: A 970 ARG cc_start: 0.8726 (mtt180) cc_final: 0.8283 (mtt180) REVERT: B 110 MET cc_start: 0.7182 (tmm) cc_final: 0.6795 (tmm) REVERT: B 126 GLU cc_start: 0.6937 (mp0) cc_final: 0.6516 (pm20) REVERT: B 152 MET cc_start: 0.7363 (tpt) cc_final: 0.6835 (mmm) REVERT: B 274 VAL cc_start: 0.8352 (p) cc_final: 0.8114 (p) REVERT: B 287 CYS cc_start: 0.7067 (m) cc_final: 0.5847 (m) REVERT: C 395 HIS cc_start: 0.7707 (t-90) cc_final: 0.7151 (t-90) REVERT: C 480 GLN cc_start: 0.9518 (mp10) cc_final: 0.9274 (mp10) REVERT: C 484 MET cc_start: 0.9170 (tmm) cc_final: 0.8775 (tmm) REVERT: D 102 GLU cc_start: 0.8299 (mp0) cc_final: 0.8068 (mp0) REVERT: D 197 LEU cc_start: 0.8531 (tp) cc_final: 0.8310 (tp) REVERT: D 218 ILE cc_start: 0.9361 (mt) cc_final: 0.9109 (mp) REVERT: D 289 LEU cc_start: 0.9022 (pt) cc_final: 0.8450 (pt) outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.1372 time to fit residues: 39.8740 Evaluate side-chains 146 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 5.9990 chunk 159 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 181 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.079359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057661 restraints weight = 101990.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059075 restraints weight = 53836.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.059976 restraints weight = 34967.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060558 restraints weight = 26363.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.060887 restraints weight = 22069.674| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19981 Z= 0.145 Angle : 0.624 8.005 27914 Z= 0.340 Chirality : 0.041 0.154 3095 Planarity : 0.004 0.053 2876 Dihedral : 25.261 177.703 4336 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: 0.27 (0.21), residues: 650 sheet: -0.93 (0.29), residues: 315 loop : -1.84 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 756 TYR 0.024 0.001 TYR D 91 PHE 0.015 0.001 PHE C 641 TRP 0.015 0.001 TRP B 317 HIS 0.008 0.001 HIS C 766 Details of bonding type rmsd covalent geometry : bond 0.00320 (19973) covalent geometry : angle 0.62151 (27910) hydrogen bonds : bond 0.04016 ( 883) hydrogen bonds : angle 4.39549 ( 2354) metal coordination : bond 0.00731 ( 8) metal coordination : angle 4.31653 ( 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 184 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.9048 (m-80) cc_final: 0.8529 (m-10) REVERT: A 627 MET cc_start: 0.8139 (ppp) cc_final: 0.7845 (ppp) REVERT: A 682 MET cc_start: 0.8857 (tmm) cc_final: 0.8554 (tmm) REVERT: A 761 ARG cc_start: 0.7937 (tmm160) cc_final: 0.7652 (tmm160) REVERT: A 841 MET cc_start: 0.7584 (tpp) cc_final: 0.6754 (tpp) REVERT: A 849 MET cc_start: 0.4772 (tpt) cc_final: 0.3399 (ppp) REVERT: A 880 ARG cc_start: 0.8420 (tpp80) cc_final: 0.7931 (tpp80) REVERT: A 916 PHE cc_start: 0.9171 (t80) cc_final: 0.8939 (t80) REVERT: A 970 ARG cc_start: 0.8720 (mtt180) cc_final: 0.8228 (mtt180) REVERT: B 126 GLU cc_start: 0.6738 (mp0) cc_final: 0.5716 (pm20) REVERT: B 152 MET cc_start: 0.7299 (tpt) cc_final: 0.6925 (mmm) REVERT: C 395 HIS cc_start: 0.7584 (t-90) cc_final: 0.7027 (t-90) REVERT: C 480 GLN cc_start: 0.9501 (mp10) cc_final: 0.9217 (mp10) REVERT: C 484 MET cc_start: 0.9158 (tmm) cc_final: 0.8764 (tmm) REVERT: C 790 SER cc_start: 0.8902 (t) cc_final: 0.8574 (m) REVERT: D 197 LEU cc_start: 0.8508 (tp) cc_final: 0.8268 (tp) REVERT: D 218 ILE cc_start: 0.9313 (mt) cc_final: 0.9104 (mp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1384 time to fit residues: 40.5962 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 : 0.631 ------------------------------------------------------------------------------- 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: 9.9990 chunk 179 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 156 optimal weight: 0.0020 chunk 165 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 195 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 HIS ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN ** C 495 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 = 0.3675 r_free = 0.3675 target = 0.079991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058728 restraints weight = 102820.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060055 restraints weight = 56821.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.060907 restraints weight = 37798.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061461 restraints weight = 28916.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061787 restraints weight = 24374.434| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19981 Z= 0.140 Angle : 0.619 8.337 27914 Z= 0.337 Chirality : 0.041 0.170 3095 Planarity : 0.004 0.054 2876 Dihedral : 25.176 177.246 4336 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.28 (0.20), residues: 653 sheet: -0.72 (0.29), residues: 316 loop : -1.80 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 756 TYR 0.021 0.001 TYR D 91 PHE 0.018 0.001 PHE A 911 TRP 0.029 0.001 TRP D 317 HIS 0.004 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00309 (19973) covalent geometry : angle 0.61758 (27910) hydrogen bonds : bond 0.03886 ( 883) hydrogen bonds : angle 4.34968 ( 2354) metal coordination : bond 0.00692 ( 8) metal coordination : angle 3.85043 ( 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 188 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 PHE cc_start: 0.9072 (m-80) cc_final: 0.8540 (m-10) REVERT: A 503 LEU cc_start: 0.9310 (mt) cc_final: 0.9029 (mt) REVERT: A 627 MET cc_start: 0.8093 (ppp) cc_final: 0.7776 (ppp) REVERT: A 682 MET cc_start: 0.8900 (tmm) cc_final: 0.8578 (tmm) REVERT: A 687 LEU cc_start: 0.9406 (tp) cc_final: 0.8739 (tp) REVERT: A 761 ARG cc_start: 0.8079 (tmm160) cc_final: 0.7730 (tmm160) REVERT: A 841 MET cc_start: 0.7564 (tpp) cc_final: 0.6737 (tpp) REVERT: A 849 MET cc_start: 0.5023 (tpt) cc_final: 0.3669 (ppp) REVERT: A 880 ARG cc_start: 0.8411 (tpp80) cc_final: 0.7879 (tpp80) REVERT: A 916 PHE cc_start: 0.9187 (t80) cc_final: 0.8962 (t80) REVERT: A 970 ARG cc_start: 0.8779 (mtt180) cc_final: 0.8247 (mtt180) REVERT: A 984 MET cc_start: 0.8948 (mmp) cc_final: 0.8295 (mmp) REVERT: B 110 MET cc_start: 0.6793 (tmm) cc_final: 0.6143 (tmm) REVERT: B 126 GLU cc_start: 0.6732 (mp0) cc_final: 0.5657 (pm20) REVERT: B 152 MET cc_start: 0.7266 (tpt) cc_final: 0.6879 (mmm) REVERT: C 395 HIS cc_start: 0.7510 (t-90) cc_final: 0.6963 (t-90) REVERT: C 480 GLN cc_start: 0.9545 (mp10) cc_final: 0.9185 (mp10) REVERT: C 484 MET cc_start: 0.9157 (tmm) cc_final: 0.8825 (tmm) REVERT: C 578 MET cc_start: 0.8966 (mtm) cc_final: 0.8701 (mtm) REVERT: C 790 SER cc_start: 0.8859 (t) cc_final: 0.8544 (m) REVERT: C 847 MET cc_start: 0.7088 (mpp) cc_final: 0.6861 (mpp) REVERT: D 197 LEU cc_start: 0.8523 (tp) cc_final: 0.8268 (tp) REVERT: D 218 ILE cc_start: 0.9305 (mt) cc_final: 0.9066 (mp) REVERT: D 326 THR cc_start: 0.8400 (p) cc_final: 0.8129 (p) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1287 time to fit residues: 38.7664 Evaluate side-chains 158 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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: 0.8980 chunk 194 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 177 optimal weight: 0.0470 chunk 154 optimal weight: 0.4980 chunk 204 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 overall best weight: 2.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 473 ASN ** C 495 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 = 0.3642 r_free = 0.3642 target = 0.078514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057178 restraints weight = 103987.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058461 restraints weight = 58102.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059277 restraints weight = 39043.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059827 restraints weight = 30133.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060101 restraints weight = 25475.208| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19981 Z= 0.198 Angle : 0.652 8.100 27914 Z= 0.355 Chirality : 0.042 0.149 3095 Planarity : 0.004 0.053 2876 Dihedral : 25.203 178.339 4336 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % 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: -1.27 (0.19), residues: 1894 helix: 0.38 (0.21), residues: 643 sheet: -0.71 (0.29), residues: 334 loop : -1.79 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 756 TYR 0.024 0.002 TYR D 91 PHE 0.023 0.002 PHE A 743 TRP 0.034 0.002 TRP D 317 HIS 0.006 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00433 (19973) covalent geometry : angle 0.64876 (27910) hydrogen bonds : bond 0.04448 ( 883) hydrogen bonds : angle 4.43520 ( 2354) metal coordination : bond 0.01541 ( 8) metal coordination : angle 5.71607 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3280.32 seconds wall clock time: 57 minutes 48.92 seconds (3468.92 seconds total)