Starting phenix.real_space_refine on Thu Jul 2 22:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j62_35999/07_2026/8j62_35999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j62_35999/07_2026/8j62_35999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2026/8j62_35999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2026/8j62_35999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2026/8j62_35999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2026/8j62_35999.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2026/8j62_35999.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j62_35999/07_2026/8j62_35999.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 36 5.49 5 S 48 5.16 5 C 6578 2.51 5 N 1826 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10448 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1521 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain: "C" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1075 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 844 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 912 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 480 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "X" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 5} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 749 SG CYS A 84 32.319 53.134 49.548 1.00 41.85 S ATOM 771 SG CYS A 87 33.682 51.225 51.830 1.00 42.44 S Restraints were copied for chains: B, G, H, I, J, Y Time building chain proxies: 2.51, per 1000 atoms: 0.24 Number of scatterers: 10448 At special positions: 0 Unit cell: (86.0096, 109.933, 105.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 48 16.00 P 36 15.00 O 1958 8.00 N 1826 7.00 C 6578 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: 0.89 Conformation dependent library (CDL) restraints added in 335.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 84 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 84 " 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 35.9% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.656A pdb=" N LYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'C' and resid 14 through 31 Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.566A pdb=" N SER C 46 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'D' and resid 18 through 24 removed outlier: 3.898A pdb=" N GLU D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'E' and resid 14 through 31 Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.516A pdb=" N GLU E 45 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 111 removed outlier: 3.659A pdb=" N GLN E 105 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.556A pdb=" N LEU E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.656A pdb=" N LYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'G' and resid 14 through 31 Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.566A pdb=" N SER G 46 " --> pdb=" O HIS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 111 Processing helix chain 'G' and resid 165 through 171 Processing helix chain 'H' and resid 18 through 24 removed outlier: 3.898A pdb=" N GLU H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 50 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'I' and resid 14 through 31 Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.516A pdb=" N GLU I 45 " --> pdb=" O HIS I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 111 removed outlier: 3.659A pdb=" N GLN I 105 " --> pdb=" O ASP I 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 171 removed outlier: 3.558A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 51 Processing helix chain 'J' and resid 70 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.897A pdb=" N TRP A 81 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41 removed outlier: 4.876A pdb=" N ILE C 87 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE C 9 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 11.423A pdb=" N TRP C 89 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 14.227A pdb=" N VAL C 7 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 18.909A pdb=" N LYS C 91 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 21.500A pdb=" N TRP C 5 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 64 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 55 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP D 120 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41 removed outlier: 11.324A pdb=" N SER C 95 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE D 102 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.586A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU E 64 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG E 90 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE E 66 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU E 88 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR E 68 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP E 70 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY E 84 " --> pdb=" O TRP E 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.586A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU E 64 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG E 90 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE E 66 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU E 88 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR E 68 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP E 70 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY E 84 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN E 83 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE E 87 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 9 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 96 through 103 Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.898A pdb=" N TRP B 81 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 removed outlier: 4.877A pdb=" N ILE G 87 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE G 9 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N TRP G 89 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 14.228A pdb=" N VAL G 7 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 18.909A pdb=" N LYS G 91 " --> pdb=" O TRP G 5 " (cutoff:3.500A) removed outlier: 21.500A pdb=" N TRP G 5 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU H 64 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE H 55 " --> pdb=" O PHE H 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP H 120 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 39 through 41 removed outlier: 11.323A pdb=" N SER G 95 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE H 102 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 39 through 41 removed outlier: 6.585A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU I 64 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG I 90 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE I 66 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU I 88 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR I 68 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER I 86 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP I 70 " --> pdb=" O GLY I 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY I 84 " --> pdb=" O TRP I 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 39 through 41 removed outlier: 6.585A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU I 64 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG I 90 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE I 66 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU I 88 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR I 68 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER I 86 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP I 70 " --> pdb=" O GLY I 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY I 84 " --> pdb=" O TRP I 70 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE I 87 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE I 9 " --> pdb=" O ILE I 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 96 through 103 582 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3012 1.34 - 1.45: 2237 1.45 - 1.57: 5425 1.57 - 1.69: 72 1.69 - 1.81: 76 Bond restraints: 10822 Sorted by residual: bond pdb=" CA TYR D 85 " pdb=" CB TYR D 85 " ideal model delta sigma weight residual 1.535 1.552 -0.017 2.09e-02 2.29e+03 6.29e-01 bond pdb=" CA TYR H 85 " pdb=" CB TYR H 85 " ideal model delta sigma weight residual 1.535 1.551 -0.016 2.09e-02 2.29e+03 5.61e-01 bond pdb=" CA GLY I 82 " pdb=" C GLY I 82 " ideal model delta sigma weight residual 1.522 1.515 0.007 1.06e-02 8.90e+03 4.67e-01 bond pdb=" CA GLY E 82 " pdb=" C GLY E 82 " ideal model delta sigma weight residual 1.522 1.515 0.007 1.06e-02 8.90e+03 4.47e-01 bond pdb=" CB GLU A 163 " pdb=" CG GLU A 163 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.15e-01 ... (remaining 10817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 14447 1.20 - 2.40: 304 2.40 - 3.60: 93 3.60 - 4.80: 8 4.80 - 6.00: 2 Bond angle restraints: 14854 Sorted by residual: angle pdb=" C VAL H 86 " pdb=" N ASP H 87 " pdb=" CA ASP H 87 " ideal model delta sigma weight residual 121.75 118.21 3.54 1.73e+00 3.34e-01 4.19e+00 angle pdb=" C3' U Y 11 " pdb=" O3' U Y 11 " pdb=" P U Y 12 " ideal model delta sigma weight residual 120.20 123.24 -3.04 1.50e+00 4.44e-01 4.11e+00 angle pdb=" C VAL D 86 " pdb=" N ASP D 87 " pdb=" CA ASP D 87 " ideal model delta sigma weight residual 121.75 118.25 3.50 1.73e+00 3.34e-01 4.08e+00 angle pdb=" C3' U X 11 " pdb=" O3' U X 11 " pdb=" P U X 12 " ideal model delta sigma weight residual 120.20 123.22 -3.02 1.50e+00 4.44e-01 4.06e+00 angle pdb=" C HIS I 28 " pdb=" N MET I 29 " pdb=" CA MET I 29 " ideal model delta sigma weight residual 121.66 118.60 3.06 1.76e+00 3.23e-01 3.03e+00 ... (remaining 14849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 5864 32.69 - 65.37: 302 65.37 - 98.06: 22 98.06 - 130.74: 0 130.74 - 163.43: 2 Dihedral angle restraints: 6190 sinusoidal: 2738 harmonic: 3452 Sorted by residual: dihedral pdb=" O4' C Y 1 " pdb=" C1' C Y 1 " pdb=" N1 C Y 1 " pdb=" C2 C Y 1 " ideal model delta sinusoidal sigma weight residual 200.00 36.57 163.43 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' C X 1 " pdb=" C1' C X 1 " pdb=" N1 C X 1 " pdb=" C2 C X 1 " ideal model delta sinusoidal sigma weight residual 200.00 36.64 163.36 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" CB GLU I 54 " pdb=" CG GLU I 54 " pdb=" CD GLU I 54 " pdb=" OE1 GLU I 54 " ideal model delta sinusoidal sigma weight residual 0.00 -90.15 90.15 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 6187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 961 0.027 - 0.053: 372 0.053 - 0.080: 126 0.080 - 0.106: 95 0.106 - 0.133: 40 Chirality restraints: 1594 Sorted by residual: chirality pdb=" CA ILE I 57 " pdb=" N ILE I 57 " pdb=" C ILE I 57 " pdb=" CB ILE I 57 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE I 66 " pdb=" N ILE I 66 " pdb=" C ILE I 66 " pdb=" CB ILE I 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE E 57 " pdb=" N ILE E 57 " pdb=" C ILE E 57 " pdb=" CB ILE E 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1591 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 113 " -0.011 2.00e-02 2.50e+03 1.21e-02 3.66e+00 pdb=" CG TRP F 113 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP F 113 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP F 113 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 113 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 113 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 113 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 113 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 113 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 113 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 113 " 0.011 2.00e-02 2.50e+03 1.18e-02 3.50e+00 pdb=" CG TRP J 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP J 113 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP J 113 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 113 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 113 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 113 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 86 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00 pdb=" C VAL H 86 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL H 86 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP H 87 " 0.006 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1205 2.75 - 3.29: 9360 3.29 - 3.83: 18363 3.83 - 4.36: 22026 4.36 - 4.90: 37780 Nonbonded interactions: 88734 Sorted by model distance: nonbonded pdb=" OG SER H 53 " pdb=" O6 G Y 10 " model vdw 2.216 3.040 nonbonded pdb=" OG SER D 53 " pdb=" O6 G X 10 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 112 " pdb=" OP1 U X 8 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 112 " pdb=" OP1 U Y 8 " model vdw 2.227 3.040 nonbonded pdb=" NH2 ARG G 23 " pdb=" OP2 C Y 17 " model vdw 2.239 3.120 ... (remaining 88729 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 : 0.002 0.020 10828 Z= 0.092 Angle : 0.464 6.001 14854 Z= 0.252 Chirality : 0.041 0.133 1594 Planarity : 0.003 0.027 1728 Dihedral : 17.898 163.427 3950 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.91 % Allowed : 24.35 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1130 helix: 1.85 (0.28), residues: 352 sheet: 0.51 (0.27), residues: 326 loop : 0.93 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 118 TYR 0.014 0.001 TYR D 85 PHE 0.007 0.001 PHE A 58 TRP 0.033 0.001 TRP F 113 HIS 0.002 0.000 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.09 (10822) covalent geometry : angle 0.46417 / 0.25 (14854) hydrogen bonds : bond 0.13887 / 9.22 ( 512) hydrogen bonds : angle 6.21967 / 4.52 ( 1566) metal coordination : bond 0.00103 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.402 Fit side-chains REVERT: C 99 ASP cc_start: 0.7721 (p0) cc_final: 0.7166 (p0) REVERT: E 88 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7088 (tm-30) REVERT: H 21 LEU cc_start: 0.8074 (mp) cc_final: 0.7857 (mp) outliers start: 29 outliers final: 16 residues processed: 341 average time/residue: 0.6387 time to fit residues: 231.7039 Evaluate side-chains 276 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 114 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.0050 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN C 43 HIS D 45 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN G 43 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.125418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097835 restraints weight = 18125.447| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.63 r_work: 0.3463 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10828 Z= 0.114 Angle : 0.533 5.904 14854 Z= 0.281 Chirality : 0.042 0.143 1594 Planarity : 0.004 0.027 1728 Dihedral : 11.745 160.330 1748 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.41 % Allowed : 27.96 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1130 helix: 1.77 (0.27), residues: 374 sheet: 0.74 (0.27), residues: 328 loop : 1.08 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 49 TYR 0.017 0.001 TYR J 29 PHE 0.008 0.001 PHE F 44 TRP 0.024 0.001 TRP J 113 HIS 0.004 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10822) covalent geometry : angle 0.53270 / 0.28 (14854) hydrogen bonds : bond 0.03111 / 2.04 ( 512) hydrogen bonds : angle 4.96738 / 3.56 ( 1566) metal coordination : bond 0.00135 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.7884 (m110) cc_final: 0.7601 (m110) REVERT: C 167 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8169 (ttm-80) REVERT: D 122 MET cc_start: 0.8824 (mmp) cc_final: 0.8604 (mmp) REVERT: E 17 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8312 (ttp80) REVERT: E 88 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6373 (tm-30) REVERT: G 99 ASP cc_start: 0.7717 (p0) cc_final: 0.7384 (p0) REVERT: G 101 ASP cc_start: 0.8592 (m-30) cc_final: 0.8205 (p0) REVERT: G 108 HIS cc_start: 0.8454 (m-70) cc_final: 0.8111 (t-90) REVERT: H 122 MET cc_start: 0.8790 (mmp) cc_final: 0.8533 (mmp) REVERT: I 17 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8348 (ttp-170) outliers start: 34 outliers final: 18 residues processed: 289 average time/residue: 0.6178 time to fit residues: 190.0293 Evaluate side-chains 281 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN D 45 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 HIS ** 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 = 0.4015 r_free = 0.4015 target = 0.121015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093163 restraints weight = 18052.417| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.56 r_work: 0.3380 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10828 Z= 0.170 Angle : 0.561 6.106 14854 Z= 0.296 Chirality : 0.044 0.164 1594 Planarity : 0.004 0.027 1728 Dihedral : 11.709 164.653 1734 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 6.91 % Allowed : 27.25 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.25), residues: 1130 helix: 1.75 (0.26), residues: 378 sheet: 0.65 (0.27), residues: 330 loop : 1.11 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 49 TYR 0.012 0.001 TYR G 69 PHE 0.009 0.001 PHE B 58 TRP 0.024 0.001 TRP I 89 HIS 0.004 0.001 HIS B 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (10822) covalent geometry : angle 0.56089 / 0.30 (14854) hydrogen bonds : bond 0.03238 / 2.11 ( 512) hydrogen bonds : angle 4.90455 / 3.48 ( 1566) metal coordination : bond 0.00373 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 254 time to evaluate : 0.397 Fit side-chains REVERT: A 57 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7892 (ttm110) REVERT: A 97 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: A 166 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8280 (mp10) REVERT: C 167 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8180 (ttm-80) REVERT: D 21 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8458 (mp) REVERT: E 12 GLN cc_start: 0.8355 (mp10) cc_final: 0.8133 (mp10) REVERT: E 17 ARG cc_start: 0.8701 (mtt-85) cc_final: 0.8439 (mtm180) REVERT: E 88 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: B 166 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8281 (mp10) REVERT: G 91 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8275 (tppt) REVERT: G 108 HIS cc_start: 0.8467 (m-70) cc_final: 0.8238 (t-90) REVERT: H 21 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8402 (mp) REVERT: I 12 GLN cc_start: 0.8344 (mp10) cc_final: 0.8075 (mp10) REVERT: I 17 ARG cc_start: 0.8687 (mtt-85) cc_final: 0.8334 (mtm180) outliers start: 69 outliers final: 32 residues processed: 288 average time/residue: 0.6277 time to fit residues: 192.2858 Evaluate side-chains 276 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN H 45 GLN ** I 28 HIS ** 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 = 0.3993 r_free = 0.3993 target = 0.119539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091573 restraints weight = 18201.948| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.61 r_work: 0.3348 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10828 Z= 0.193 Angle : 0.580 7.261 14854 Z= 0.304 Chirality : 0.044 0.168 1594 Planarity : 0.004 0.028 1728 Dihedral : 11.842 166.585 1734 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.91 % Allowed : 27.15 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1130 helix: 1.77 (0.26), residues: 378 sheet: 0.65 (0.27), residues: 330 loop : 1.12 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 49 TYR 0.021 0.001 TYR F 29 PHE 0.008 0.001 PHE A 140 TRP 0.015 0.001 TRP J 113 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (10822) covalent geometry : angle 0.57979 / 0.30 (14854) hydrogen bonds : bond 0.03167 / 2.07 ( 512) hydrogen bonds : angle 4.93595 / 3.47 ( 1566) metal coordination : bond 0.00378 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 0.406 Fit side-chains REVERT: A 50 LEU cc_start: 0.9066 (mt) cc_final: 0.8808 (mm) REVERT: A 57 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7918 (ttm110) REVERT: A 166 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: C 91 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8378 (tppt) REVERT: C 167 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8197 (ttm-80) REVERT: D 20 LYS cc_start: 0.9366 (ttpp) cc_final: 0.9138 (tmmt) REVERT: D 30 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8027 (m) REVERT: E 12 GLN cc_start: 0.8268 (mp10) cc_final: 0.8005 (mp10) REVERT: E 97 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: F 41 GLN cc_start: 0.8867 (mt0) cc_final: 0.8555 (mp10) REVERT: B 50 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8749 (mm) REVERT: B 136 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8037 (m110) REVERT: B 166 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8271 (mp10) REVERT: G 88 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: G 91 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8285 (tppt) REVERT: I 12 GLN cc_start: 0.8311 (mp10) cc_final: 0.7996 (mp10) REVERT: I 17 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8417 (ttp-170) REVERT: I 97 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7143 (mp10) outliers start: 59 outliers final: 28 residues processed: 275 average time/residue: 0.6414 time to fit residues: 187.4904 Evaluate side-chains 274 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 0.0040 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN C 110 HIS ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN H 45 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.119654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091948 restraints weight = 17980.898| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.56 r_work: 0.3357 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10828 Z= 0.170 Angle : 0.589 10.048 14854 Z= 0.304 Chirality : 0.044 0.162 1594 Planarity : 0.004 0.035 1728 Dihedral : 11.842 167.152 1734 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.41 % Allowed : 27.86 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1130 helix: 1.84 (0.26), residues: 378 sheet: 0.62 (0.27), residues: 330 loop : 1.07 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 49 TYR 0.010 0.001 TYR C 69 PHE 0.007 0.001 PHE A 58 TRP 0.013 0.001 TRP I 89 HIS 0.003 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (10822) covalent geometry : angle 0.58860 / 0.30 (14854) hydrogen bonds : bond 0.03137 / 2.05 ( 512) hydrogen bonds : angle 4.90420 / 3.45 ( 1566) metal coordination : bond 0.00310 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.399 Fit side-chains REVERT: A 50 LEU cc_start: 0.9075 (mt) cc_final: 0.8828 (mm) REVERT: A 57 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7867 (ttm110) REVERT: A 97 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: A 136 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7985 (m110) REVERT: A 166 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: C 167 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8198 (ttm-80) REVERT: D 20 LYS cc_start: 0.9391 (ttpp) cc_final: 0.9115 (tmmt) REVERT: D 30 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.8015 (m) REVERT: E 12 GLN cc_start: 0.8264 (mp10) cc_final: 0.7872 (mp10) REVERT: E 17 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8388 (ttp-170) REVERT: F 41 GLN cc_start: 0.8888 (mt0) cc_final: 0.8638 (mp10) REVERT: F 69 PHE cc_start: 0.8493 (m-10) cc_final: 0.8169 (m-10) REVERT: B 50 LEU cc_start: 0.9043 (mt) cc_final: 0.8773 (mm) REVERT: B 89 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8261 (mtm110) REVERT: B 136 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7983 (m110) REVERT: B 166 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: G 88 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: I 12 GLN cc_start: 0.8295 (mp10) cc_final: 0.7851 (mp10) REVERT: J 68 PHE cc_start: 0.8123 (m-80) cc_final: 0.6059 (t80) outliers start: 54 outliers final: 32 residues processed: 274 average time/residue: 0.6625 time to fit residues: 192.3580 Evaluate side-chains 276 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 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 = 0.3993 r_free = 0.3993 target = 0.119663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.091965 restraints weight = 18203.904| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.58 r_work: 0.3356 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10828 Z= 0.159 Angle : 0.583 8.144 14854 Z= 0.302 Chirality : 0.044 0.168 1594 Planarity : 0.004 0.040 1728 Dihedral : 11.792 167.111 1734 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.61 % Allowed : 28.76 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1130 helix: 1.89 (0.27), residues: 378 sheet: 0.71 (0.28), residues: 324 loop : 0.98 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 23 TYR 0.022 0.001 TYR J 29 PHE 0.007 0.001 PHE A 58 TRP 0.012 0.001 TRP C 89 HIS 0.008 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10822) covalent geometry : angle 0.58331 / 0.30 (14854) hydrogen bonds : bond 0.03044 / 1.99 ( 512) hydrogen bonds : angle 4.87622 / 3.42 ( 1566) metal coordination : bond 0.00276 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.372 Fit side-chains REVERT: A 50 LEU cc_start: 0.9035 (mt) cc_final: 0.8814 (mm) REVERT: A 57 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7863 (ttm110) REVERT: A 86 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8308 (pttm) REVERT: A 89 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8281 (mtm110) REVERT: A 97 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: A 136 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7990 (m110) REVERT: A 166 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: C 33 ARG cc_start: 0.8245 (mtp85) cc_final: 0.8000 (mtp85) REVERT: C 88 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7458 (pt0) REVERT: C 167 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8217 (ttm-80) REVERT: D 30 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (m) REVERT: E 12 GLN cc_start: 0.8272 (mp10) cc_final: 0.7889 (mp10) REVERT: E 17 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8415 (ttp-170) REVERT: E 97 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: F 41 GLN cc_start: 0.8877 (mt0) cc_final: 0.8606 (mp10) REVERT: B 50 LEU cc_start: 0.9036 (mt) cc_final: 0.8796 (mm) REVERT: B 89 ARG cc_start: 0.8687 (ttp-110) cc_final: 0.8299 (mtm110) REVERT: B 136 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7966 (m110) REVERT: B 166 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: G 88 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: G 99 ASP cc_start: 0.8126 (p0) cc_final: 0.7705 (p0) REVERT: G 101 ASP cc_start: 0.8446 (m-30) cc_final: 0.8136 (p0) REVERT: H 20 LYS cc_start: 0.9372 (ttpp) cc_final: 0.9131 (tmmt) REVERT: I 12 GLN cc_start: 0.8251 (mp10) cc_final: 0.7796 (mp10) REVERT: I 17 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8387 (ttp-170) REVERT: I 97 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7209 (mp10) outliers start: 56 outliers final: 35 residues processed: 271 average time/residue: 0.6622 time to fit residues: 190.6506 Evaluate side-chains 282 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 79 optimal weight: 0.0470 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN D 41 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN G 110 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.117691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.090004 restraints weight = 18018.666| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.59 r_work: 0.3322 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10828 Z= 0.226 Angle : 0.631 8.795 14854 Z= 0.326 Chirality : 0.045 0.157 1594 Planarity : 0.004 0.044 1728 Dihedral : 11.961 169.026 1734 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.61 % Allowed : 28.66 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.25), residues: 1130 helix: 1.86 (0.27), residues: 376 sheet: 0.64 (0.28), residues: 326 loop : 0.93 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 90 TYR 0.011 0.001 TYR H 96 PHE 0.009 0.001 PHE A 140 TRP 0.011 0.001 TRP C 89 HIS 0.007 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (10822) covalent geometry : angle 0.63139 / 0.33 (14854) hydrogen bonds : bond 0.03278 / 2.15 ( 512) hydrogen bonds : angle 4.98865 / 3.49 ( 1566) metal coordination : bond 0.00439 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.407 Fit side-chains REVERT: A 50 LEU cc_start: 0.9100 (mt) cc_final: 0.8871 (mm) REVERT: A 57 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7884 (ttm110) REVERT: A 89 ARG cc_start: 0.8685 (ttp-110) cc_final: 0.8288 (mtm110) REVERT: A 97 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8201 (mt-10) REVERT: A 136 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7955 (m110) REVERT: A 166 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: C 88 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: C 167 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8193 (ttm-80) REVERT: D 30 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8074 (m) REVERT: E 12 GLN cc_start: 0.8231 (mp10) cc_final: 0.7792 (mp10) REVERT: E 17 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8377 (ttp-170) REVERT: E 97 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: F 41 GLN cc_start: 0.8898 (mt0) cc_final: 0.8603 (mp10) REVERT: B 50 LEU cc_start: 0.9093 (mt) cc_final: 0.8847 (mm) REVERT: B 89 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8315 (mtm110) REVERT: B 136 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7937 (m110) REVERT: B 166 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: G 88 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: H 30 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8031 (m) REVERT: I 12 GLN cc_start: 0.8222 (mp10) cc_final: 0.7721 (mp10) REVERT: I 17 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8393 (ttp-170) REVERT: I 97 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7150 (mp10) outliers start: 56 outliers final: 36 residues processed: 271 average time/residue: 0.6426 time to fit residues: 184.9597 Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 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 = 0.4005 r_free = 0.4005 target = 0.120769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093512 restraints weight = 17965.033| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.61 r_work: 0.3387 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10828 Z= 0.120 Angle : 0.602 10.161 14854 Z= 0.307 Chirality : 0.043 0.143 1594 Planarity : 0.004 0.034 1728 Dihedral : 11.686 167.123 1734 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.71 % Allowed : 30.16 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.26), residues: 1130 helix: 1.98 (0.27), residues: 376 sheet: 0.75 (0.28), residues: 324 loop : 0.98 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 90 TYR 0.020 0.001 TYR F 29 PHE 0.008 0.001 PHE J 44 TRP 0.016 0.001 TRP C 89 HIS 0.007 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10822) covalent geometry : angle 0.60240 / 0.31 (14854) hydrogen bonds : bond 0.02898 / 1.91 ( 512) hydrogen bonds : angle 4.80494 / 3.37 ( 1566) metal coordination : bond 0.00116 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.260 Fit side-chains REVERT: A 50 LEU cc_start: 0.8988 (mt) cc_final: 0.8787 (mm) REVERT: A 57 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7816 (ttm110) REVERT: A 66 LYS cc_start: 0.9056 (mmtp) cc_final: 0.8745 (mptp) REVERT: A 86 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8315 (pttm) REVERT: A 89 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8260 (mtm110) REVERT: A 136 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7918 (m110) REVERT: A 166 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: C 33 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7937 (mtp85) REVERT: C 88 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: C 167 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8211 (ttm-80) REVERT: E 12 GLN cc_start: 0.8222 (mp10) cc_final: 0.7840 (mp10) REVERT: E 17 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8342 (ttp-170) REVERT: F 41 GLN cc_start: 0.8882 (mt0) cc_final: 0.8622 (mp10) REVERT: B 50 LEU cc_start: 0.8991 (mt) cc_final: 0.8775 (mm) REVERT: B 86 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8294 (pttm) REVERT: B 89 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8285 (mtm110) REVERT: B 136 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7882 (m110) REVERT: G 88 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: G 99 ASP cc_start: 0.8096 (p0) cc_final: 0.7726 (p0) REVERT: G 101 ASP cc_start: 0.8443 (m-30) cc_final: 0.8125 (p0) REVERT: I 12 GLN cc_start: 0.8236 (mp10) cc_final: 0.7758 (mp10) REVERT: I 17 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8446 (ttp-170) outliers start: 47 outliers final: 27 residues processed: 280 average time/residue: 0.6042 time to fit residues: 180.0384 Evaluate side-chains 275 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 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 = 0.3978 r_free = 0.3978 target = 0.118727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091126 restraints weight = 18082.468| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.61 r_work: 0.3342 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10828 Z= 0.186 Angle : 0.644 10.305 14854 Z= 0.329 Chirality : 0.044 0.186 1594 Planarity : 0.004 0.058 1728 Dihedral : 11.786 168.153 1734 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.61 % Allowed : 30.66 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.25), residues: 1130 helix: 1.91 (0.27), residues: 376 sheet: 0.73 (0.28), residues: 320 loop : 0.92 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 23 TYR 0.011 0.001 TYR H 96 PHE 0.010 0.001 PHE F 69 TRP 0.011 0.001 TRP C 89 HIS 0.006 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (10822) covalent geometry : angle 0.64441 / 0.33 (14854) hydrogen bonds : bond 0.03144 / 2.08 ( 512) hydrogen bonds : angle 4.88238 / 3.41 ( 1566) metal coordination : bond 0.00341 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.407 Fit side-chains REVERT: A 57 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7855 (ttm110) REVERT: A 66 LYS cc_start: 0.9050 (mmtp) cc_final: 0.8748 (mptp) REVERT: A 86 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8311 (pttm) REVERT: A 89 ARG cc_start: 0.8681 (ttp-110) cc_final: 0.8298 (mtm110) REVERT: A 136 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7893 (m110) REVERT: A 166 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: C 88 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: C 167 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.8215 (ttm-80) REVERT: D 52 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7883 (mtp-110) REVERT: D 88 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8167 (mm) REVERT: E 12 GLN cc_start: 0.8190 (mp10) cc_final: 0.7763 (mp10) REVERT: E 17 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8386 (ttp-170) REVERT: F 41 GLN cc_start: 0.8898 (mt0) cc_final: 0.8657 (mp10) REVERT: B 50 LEU cc_start: 0.9064 (mt) cc_final: 0.8845 (mm) REVERT: B 86 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8283 (pttm) REVERT: B 89 ARG cc_start: 0.8673 (ttp-110) cc_final: 0.8302 (mtm110) REVERT: B 136 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7880 (m110) REVERT: G 88 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: H 52 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7876 (mtp-110) REVERT: I 12 GLN cc_start: 0.8203 (mp10) cc_final: 0.7701 (mp10) REVERT: I 17 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8321 (mtp85) REVERT: I 171 GLU cc_start: 0.8303 (pp20) cc_final: 0.8092 (pm20) outliers start: 46 outliers final: 31 residues processed: 266 average time/residue: 0.6479 time to fit residues: 183.0366 Evaluate side-chains 272 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 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 = 0.4018 r_free = 0.4018 target = 0.121447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.094318 restraints weight = 18019.931| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.61 r_work: 0.3402 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10828 Z= 0.119 Angle : 0.629 10.456 14854 Z= 0.317 Chirality : 0.043 0.168 1594 Planarity : 0.004 0.054 1728 Dihedral : 11.553 166.031 1734 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.41 % Allowed : 31.96 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.26), residues: 1130 helix: 2.03 (0.27), residues: 376 sheet: 0.81 (0.28), residues: 320 loop : 1.08 (0.33), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 23 TYR 0.019 0.001 TYR J 29 PHE 0.009 0.001 PHE F 69 TRP 0.017 0.001 TRP G 89 HIS 0.006 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10822) covalent geometry : angle 0.62935 / 0.32 (14854) hydrogen bonds : bond 0.02807 / 1.86 ( 512) hydrogen bonds : angle 4.71908 / 3.31 ( 1566) metal coordination : bond 0.00115 / 0.07 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.399 Fit side-chains REVERT: A 57 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7778 (ttm110) REVERT: A 66 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8744 (mptp) REVERT: A 86 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8339 (pttm) REVERT: A 89 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8277 (mtm110) REVERT: A 136 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7771 (m110) REVERT: C 23 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7806 (mtt-85) REVERT: C 167 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8195 (ttm-80) REVERT: D 52 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.7787 (mtp-110) REVERT: E 12 GLN cc_start: 0.8178 (mp10) cc_final: 0.7795 (mp10) REVERT: E 17 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8411 (ttp-170) REVERT: B 86 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8301 (pttm) REVERT: B 89 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8282 (mtm110) REVERT: B 136 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7726 (m110) REVERT: B 166 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: G 23 ARG cc_start: 0.8192 (mtm110) cc_final: 0.7811 (mtt-85) REVERT: G 91 LYS cc_start: 0.8434 (tppp) cc_final: 0.8152 (tppt) REVERT: G 99 ASP cc_start: 0.8029 (p0) cc_final: 0.7653 (p0) REVERT: G 101 ASP cc_start: 0.8455 (m-30) cc_final: 0.8118 (p0) REVERT: H 52 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7761 (mtp-110) REVERT: I 12 GLN cc_start: 0.8225 (mp10) cc_final: 0.7853 (mp10) REVERT: I 17 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8442 (ttp-170) REVERT: J 41 GLN cc_start: 0.8901 (mt0) cc_final: 0.8684 (mp10) outliers start: 34 outliers final: 25 residues processed: 265 average time/residue: 0.6230 time to fit residues: 175.5833 Evaluate side-chains 260 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 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 = 0.3959 r_free = 0.3959 target = 0.117434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089939 restraints weight = 18064.734| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.57 r_work: 0.3318 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10828 Z= 0.252 Angle : 0.700 10.186 14854 Z= 0.354 Chirality : 0.047 0.176 1594 Planarity : 0.005 0.054 1728 Dihedral : 11.884 169.225 1734 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.01 % Allowed : 30.96 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.25), residues: 1130 helix: 1.72 (0.27), residues: 376 sheet: 0.61 (0.28), residues: 322 loop : 0.90 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 90 TYR 0.011 0.001 TYR D 96 PHE 0.012 0.002 PHE J 69 TRP 0.008 0.001 TRP G 89 HIS 0.005 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (10822) covalent geometry : angle 0.69954 / 0.35 (14854) hydrogen bonds : bond 0.03397 / 2.24 ( 512) hydrogen bonds : angle 4.91355 / 3.42 ( 1566) metal coordination : bond 0.00506 / 0.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4634.15 seconds wall clock time: 79 minutes 43.65 seconds (4783.65 seconds total)