Starting phenix.real_space_refine on Wed Aug 5 15:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j62_35999/08_2026/8j62_35999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j62_35999/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2026/8j62_35999.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2026/8j62_35999.cif" model { file = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2026/8j62_35999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2026/8j62_35999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2026/8j62_35999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2026/8j62_35999.map" } 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-2.2rc3-6140/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: {'RNAv2': 19} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 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: 1.74, per 1000 atoms: 0.17 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: 0.73 Conformation dependent library (CDL) restraints added in 259.2 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: 1.23 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: 1.72 Time building geometry restraints manager: 0.92 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=" C1' G X 10 " pdb=" N9 G X 10 " ideal model delta sigma weight residual 1.478 1.463 0.015 2.00e-02 2.50e+03 5.30e-01 bond pdb=" C1' G X 3 " pdb=" N9 G X 3 " ideal model delta sigma weight residual 1.478 1.464 0.014 2.00e-02 2.50e+03 5.23e-01 bond pdb=" C1' G Y 10 " pdb=" N9 G Y 10 " ideal model delta sigma weight residual 1.478 1.464 0.014 2.00e-02 2.50e+03 5.22e-01 ... (remaining 10817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 14164 1.20 - 2.40: 409 2.40 - 3.60: 201 3.60 - 4.80: 63 4.80 - 6.00: 17 Bond angle restraints: 14854 Sorted by residual: angle pdb=" C3' U Y 11 " pdb=" O3' U Y 11 " pdb=" P U Y 12 " ideal model delta sigma weight residual 119.70 123.24 -3.54 1.20e+00 6.94e-01 8.71e+00 angle pdb=" C3' U X 11 " pdb=" O3' U X 11 " pdb=" P U X 12 " ideal model delta sigma weight residual 119.70 123.22 -3.52 1.20e+00 6.94e-01 8.62e+00 angle pdb=" C3' G X 3 " pdb=" C2' G X 3 " pdb=" O2' G X 3 " ideal model delta sigma weight residual 109.80 114.82 -5.02 2.00e+00 2.50e-01 6.29e+00 angle pdb=" C3' G Y 3 " pdb=" C2' G Y 3 " pdb=" O2' G Y 3 " ideal model delta sigma weight residual 109.80 114.80 -5.00 2.00e+00 2.50e-01 6.26e+00 angle pdb=" O3' A Y 15 " pdb=" C3' A Y 15 " pdb=" C2' A Y 15 " ideal model delta sigma weight residual 113.80 108.82 4.98 2.00e+00 2.50e-01 6.19e+00 ... (remaining 14849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 5160 18.03 - 36.06: 646 36.06 - 54.09: 213 54.09 - 72.12: 155 72.12 - 90.15: 16 Dihedral angle restraints: 6190 sinusoidal: 2738 harmonic: 3452 Sorted by residual: dihedral pdb=" C4' A Y 15 " pdb=" C3' A Y 15 " pdb=" C2' A Y 15 " pdb=" C1' A Y 15 " ideal model delta sinusoidal sigma weight residual 36.34 -37.36 73.70 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' A X 15 " pdb=" C3' A X 15 " pdb=" C2' A X 15 " pdb=" C1' A X 15 " ideal model delta sinusoidal sigma weight residual 36.35 -37.33 73.67 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' G Y 3 " pdb=" C3' G Y 3 " pdb=" C2' G Y 3 " pdb=" C1' G Y 3 " ideal model delta sinusoidal sigma weight residual 36.34 -36.19 72.53 1 3.10e+00 1.04e-01 6.99e+02 ... (remaining 6187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1280 0.059 - 0.119: 212 0.119 - 0.178: 10 0.178 - 0.237: 33 0.237 - 0.296: 59 Chirality restraints: 1594 Sorted by residual: chirality pdb=" P U X 12 " pdb=" OP1 U X 12 " pdb=" OP2 U X 12 " pdb=" O5' U X 12 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" P U Y 12 " pdb=" OP1 U Y 12 " pdb=" OP2 U Y 12 " pdb=" O5' U Y 12 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' U Y 12 " pdb=" C3' U Y 12 " pdb=" O2' U Y 12 " pdb=" C1' U Y 12 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (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: 0.01 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: 3.940 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- 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= 0.107 Angle : 0.630 6.001 14854 Z= 0.305 Chirality : 0.073 0.296 1594 Planarity : 0.003 0.027 1728 Dihedral : 20.551 90.147 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 0.00215 / 0.11 (10822) covalent geometry : angle 0.63003 / 0.31 (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 : 0.286 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: 0.5800 time to fit residues: 210.1237 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 : 0.377 ------------------------------------------------------------------------------- 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: 0.9990 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** E 42 HIS B 96 GLN G 43 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.125815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.098452 restraints weight = 17793.415| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.58 r_work: 0.3469 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2227 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= 0.150 Angle : 0.896 11.628 14854 Z= 0.392 Chirality : 0.072 0.589 1594 Planarity : 0.004 0.027 1728 Dihedral : 17.593 150.322 1748 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.31 % Allowed : 27.96 % Favored : 68.74 % 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: 1.68 (0.25), residues: 1130 helix: 1.75 (0.27), residues: 374 sheet: 0.72 (0.27), residues: 328 loop : 1.09 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 49 TYR 0.017 0.001 TYR J 29 PHE 0.008 0.001 PHE B 113 TRP 0.022 0.001 TRP J 113 HIS 0.004 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (10822) covalent geometry : angle 0.89583 / 0.39 (14854) hydrogen bonds : bond 0.03191 / 2.09 ( 512) hydrogen bonds : angle 5.01823 / 3.59 ( 1566) metal coordination : bond 0.00133 / 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 299 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.7901 (m110) cc_final: 0.7630 (m110) REVERT: D 122 MET cc_start: 0.8849 (mmp) cc_final: 0.8635 (mmp) REVERT: E 17 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8270 (ttp80) REVERT: E 88 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: G 99 ASP cc_start: 0.7731 (p0) cc_final: 0.7418 (p0) REVERT: G 101 ASP cc_start: 0.8600 (m-30) cc_final: 0.8205 (p0) REVERT: G 108 HIS cc_start: 0.8428 (m-70) cc_final: 0.8105 (t-90) REVERT: H 122 MET cc_start: 0.8806 (mmp) cc_final: 0.8554 (mmp) REVERT: I 17 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8338 (ttp-170) REVERT: I 88 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6569 (tm-30) outliers start: 33 outliers final: 15 residues processed: 278 average time/residue: 0.5860 time to fit residues: 173.5806 Evaluate side-chains 270 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 253 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 67 THR 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 50 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 88 GLU 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: 0.9990 chunk 101 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.125661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097542 restraints weight = 17766.550| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.63 r_work: 0.3454 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10828 Z= 0.131 Angle : 0.699 9.376 14854 Z= 0.326 Chirality : 0.060 0.383 1594 Planarity : 0.004 0.030 1728 Dihedral : 17.473 152.836 1736 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 5.51 % Allowed : 28.26 % Favored : 66.23 % 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: 1.78 (0.25), residues: 1130 helix: 1.88 (0.26), residues: 374 sheet: 0.80 (0.27), residues: 324 loop : 1.06 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 49 TYR 0.010 0.001 TYR G 69 PHE 0.011 0.001 PHE B 113 TRP 0.022 0.001 TRP F 113 HIS 0.003 0.001 HIS B 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10822) covalent geometry : angle 0.69949 / 0.33 (14854) hydrogen bonds : bond 0.02958 / 1.92 ( 512) hydrogen bonds : angle 4.78770 / 3.41 ( 1566) metal coordination : bond 0.00175 / 0.11 ( 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 322 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7741 (m110) REVERT: A 166 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: C 167 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8198 (ttm-80) REVERT: D 21 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8291 (mp) REVERT: E 12 GLN cc_start: 0.8383 (mp10) cc_final: 0.8170 (mp10) REVERT: E 45 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8673 (mt-10) REVERT: E 88 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: B 50 LEU cc_start: 0.8769 (mt) cc_final: 0.8548 (mm) REVERT: G 91 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8210 (tppt) REVERT: G 99 ASP cc_start: 0.7958 (p0) cc_final: 0.7653 (p0) REVERT: G 101 ASP cc_start: 0.8577 (m-30) cc_final: 0.8192 (p0) REVERT: G 108 HIS cc_start: 0.8453 (m-70) cc_final: 0.8179 (t-90) REVERT: H 21 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8221 (mp) REVERT: H 52 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8176 (mtp-110) REVERT: I 17 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8442 (ttp-170) REVERT: I 88 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6572 (tm-30) outliers start: 55 outliers final: 27 residues processed: 285 average time/residue: 0.6500 time to fit residues: 197.1781 Evaluate side-chains 285 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 67 THR 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 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 8 MET 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 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 G residue 96 THR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 52 ARG 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 88 GLU 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: 8.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.0040 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.122273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094264 restraints weight = 17947.815| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.57 r_work: 0.3391 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10828 Z= 0.167 Angle : 0.721 8.259 14854 Z= 0.339 Chirality : 0.060 0.429 1594 Planarity : 0.004 0.033 1728 Dihedral : 17.156 154.718 1734 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 5.91 % Allowed : 27.66 % Favored : 66.43 % 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: 1.72 (0.25), residues: 1130 helix: 1.84 (0.26), residues: 378 sheet: 0.72 (0.27), residues: 332 loop : 1.06 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 49 TYR 0.020 0.001 TYR J 29 PHE 0.010 0.001 PHE A 113 TRP 0.018 0.001 TRP J 113 HIS 0.003 0.001 HIS G 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (10822) covalent geometry : angle 0.72058 / 0.34 (14854) hydrogen bonds : bond 0.03034 / 1.98 ( 512) hydrogen bonds : angle 4.85839 / 3.42 ( 1566) metal coordination : bond 0.00294 / 0.19 ( 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 309 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 250 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9004 (mt) cc_final: 0.8740 (mm) REVERT: A 57 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7891 (ttm110) REVERT: A 97 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: A 166 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: E 12 GLN cc_start: 0.8241 (mp10) cc_final: 0.7993 (mp10) REVERT: E 17 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8247 (ttp-170) REVERT: E 88 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: E 97 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: F 41 GLN cc_start: 0.8883 (mt0) cc_final: 0.8669 (mp10) REVERT: B 50 LEU cc_start: 0.8855 (mt) cc_final: 0.8643 (mm) REVERT: B 166 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: G 91 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8229 (tppt) REVERT: I 97 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7101 (mp10) outliers start: 59 outliers final: 29 residues processed: 279 average time/residue: 0.6983 time to fit residues: 206.8217 Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 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 17 ARG Chi-restraints excluded: chain E residue 88 GLU 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 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 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 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: 0.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.119048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090965 restraints weight = 17789.182| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.54 r_work: 0.3334 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10828 Z= 0.246 Angle : 0.775 9.582 14854 Z= 0.367 Chirality : 0.063 0.525 1594 Planarity : 0.005 0.074 1728 Dihedral : 17.327 154.612 1734 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 6.11 % Allowed : 28.06 % 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: 1.62 (0.25), residues: 1130 helix: 1.77 (0.26), residues: 378 sheet: 0.62 (0.27), residues: 326 loop : 1.02 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 15 TYR 0.011 0.001 TYR C 69 PHE 0.011 0.002 PHE A 140 TRP 0.009 0.001 TRP C 89 HIS 0.003 0.001 HIS G 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (10822) covalent geometry : angle 0.77517 / 0.37 (14854) hydrogen bonds : bond 0.03350 / 2.18 ( 512) hydrogen bonds : angle 5.02478 / 3.52 ( 1566) metal coordination : bond 0.00491 / 0.33 ( 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 304 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 243 time to evaluate : 0.369 Fit side-chains REVERT: A 50 LEU cc_start: 0.9060 (mt) cc_final: 0.8799 (mm) REVERT: A 57 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7879 (ttm110) REVERT: A 89 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8266 (mtm110) REVERT: A 97 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: A 166 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: D 52 ARG cc_start: 0.8602 (mtp-110) cc_final: 0.8364 (mtp-110) REVERT: E 12 GLN cc_start: 0.8197 (mp10) cc_final: 0.7900 (mp10) REVERT: E 17 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8162 (ttp-170) REVERT: E 45 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8661 (mt-10) REVERT: E 88 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6877 (tm-30) REVERT: E 97 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: E 104 ASP cc_start: 0.7670 (m-30) cc_final: 0.7420 (m-30) REVERT: F 41 GLN cc_start: 0.8899 (mt0) cc_final: 0.8682 (mp10) REVERT: B 89 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8262 (mtm110) REVERT: B 166 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: G 88 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: H 21 LEU cc_start: 0.8901 (mp) cc_final: 0.8655 (mp) REVERT: H 30 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8019 (m) REVERT: H 52 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8357 (mtp-110) REVERT: I 12 GLN cc_start: 0.8400 (mm110) cc_final: 0.8040 (mp10) REVERT: J 68 PHE cc_start: 0.8133 (m-80) cc_final: 0.6061 (t80) outliers start: 61 outliers final: 29 residues processed: 273 average time/residue: 0.6126 time to fit residues: 177.8268 Evaluate side-chains 271 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 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 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 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 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 17 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 170 THR 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 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 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 107 ILE 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: 1.9990 chunk 16 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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** E 43 HIS B 96 GLN G 110 HIS H 45 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.118137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.090052 restraints weight = 17896.465| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.54 r_work: 0.3314 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10828 Z= 0.266 Angle : 0.790 10.874 14854 Z= 0.373 Chirality : 0.064 0.519 1594 Planarity : 0.004 0.053 1728 Dihedral : 17.379 154.645 1734 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 6.01 % Allowed : 28.56 % Favored : 65.43 % 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: 1.49 (0.25), residues: 1130 helix: 1.71 (0.26), residues: 378 sheet: 0.55 (0.28), residues: 326 loop : 0.91 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 23 TYR 0.024 0.002 TYR J 29 PHE 0.011 0.002 PHE A 140 TRP 0.012 0.001 TRP G 89 HIS 0.003 0.001 HIS G 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.27 (10822) covalent geometry : angle 0.78999 / 0.37 (14854) hydrogen bonds : bond 0.03402 / 2.23 ( 512) hydrogen bonds : angle 5.06765 / 3.55 ( 1566) metal coordination : bond 0.00542 / 0.36 ( 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 311 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.400 Fit side-chains REVERT: A 50 LEU cc_start: 0.9063 (mt) cc_final: 0.8795 (mm) REVERT: A 57 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7865 (ttm110) REVERT: A 89 ARG cc_start: 0.8691 (ttp-110) cc_final: 0.8278 (mtm110) REVERT: A 97 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: A 136 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.8025 (m110) REVERT: A 166 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: C 61 ASP cc_start: 0.8187 (p0) cc_final: 0.7933 (p0) REVERT: C 88 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: D 88 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8143 (mm) REVERT: E 12 GLN cc_start: 0.8186 (mp10) cc_final: 0.7710 (mp10) REVERT: E 17 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7987 (ttp-170) REVERT: E 88 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: E 97 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: F 41 GLN cc_start: 0.8909 (mt0) cc_final: 0.8691 (mp10) REVERT: B 66 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8886 (mttp) REVERT: B 89 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8296 (mtm110) REVERT: B 166 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: G 88 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: I 12 GLN cc_start: 0.8377 (mm110) cc_final: 0.8003 (mp10) REVERT: I 17 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8143 (mtp85) REVERT: I 97 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: J 41 GLN cc_start: 0.8917 (mt0) cc_final: 0.8666 (mp10) outliers start: 60 outliers final: 32 residues processed: 287 average time/residue: 0.6681 time to fit residues: 203.8224 Evaluate side-chains 283 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER 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 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 17 ARG Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 97 GLN 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 66 LYS 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 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 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 85 VAL Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 107 ILE 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: 3.9990 chunk 39 optimal weight: 0.0030 chunk 101 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN 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 = 0.4014 r_free = 0.4014 target = 0.121291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093582 restraints weight = 17638.758| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.52 r_work: 0.3378 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10828 Z= 0.152 Angle : 0.731 8.167 14854 Z= 0.346 Chirality : 0.058 0.379 1594 Planarity : 0.004 0.045 1728 Dihedral : 17.304 154.635 1734 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.51 % Allowed : 29.36 % 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: 1.58 (0.25), residues: 1130 helix: 1.82 (0.26), residues: 376 sheet: 0.65 (0.28), residues: 324 loop : 0.86 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 23 TYR 0.010 0.001 TYR C 69 PHE 0.011 0.001 PHE B 113 TRP 0.015 0.001 TRP C 89 HIS 0.008 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (10822) covalent geometry : angle 0.73084 / 0.35 (14854) hydrogen bonds : bond 0.03012 / 1.99 ( 512) hydrogen bonds : angle 4.89812 / 3.43 ( 1566) metal coordination : bond 0.00213 / 0.14 ( 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 299 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8967 (mt) cc_final: 0.8745 (mm) REVERT: A 57 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7845 (ttm110) REVERT: A 89 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8290 (mtm110) REVERT: A 136 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7954 (m110) REVERT: A 166 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: C 23 ARG cc_start: 0.8241 (mtm110) cc_final: 0.7846 (mtt-85) REVERT: C 88 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: E 12 GLN cc_start: 0.8236 (mp10) cc_final: 0.7807 (mp10) REVERT: E 88 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: E 171 GLU cc_start: 0.8382 (pp20) cc_final: 0.7820 (pm20) REVERT: F 41 GLN cc_start: 0.8916 (mt0) cc_final: 0.8682 (mp10) REVERT: B 86 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8292 (pttm) REVERT: B 89 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8303 (mtm110) REVERT: B 166 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: G 23 ARG cc_start: 0.8248 (mtm110) cc_final: 0.7847 (mtt-85) REVERT: G 88 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: H 54 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8504 (pt0) REVERT: H 88 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8162 (mm) REVERT: I 12 GLN cc_start: 0.8388 (mm110) cc_final: 0.8029 (mp10) REVERT: I 17 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8008 (mtt180) REVERT: J 41 GLN cc_start: 0.8911 (mt0) cc_final: 0.8656 (mp10) outliers start: 55 outliers final: 27 residues processed: 276 average time/residue: 0.6786 time to fit residues: 198.8793 Evaluate side-chains 273 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER 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 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 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 E residue 88 GLU 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 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 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 I residue 15 ARG Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 107 ILE 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: 5.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.124338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.096515 restraints weight = 17704.511| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.58 r_work: 0.3436 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10828 Z= 0.120 Angle : 0.720 9.778 14854 Z= 0.338 Chirality : 0.056 0.281 1594 Planarity : 0.004 0.033 1728 Dihedral : 17.200 154.932 1734 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.81 % Allowed : 31.96 % Favored : 64.23 % 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: 1.72 (0.26), residues: 1130 helix: 1.97 (0.27), residues: 376 sheet: 0.73 (0.28), residues: 326 loop : 0.90 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 23 TYR 0.021 0.001 TYR F 29 PHE 0.012 0.001 PHE B 113 TRP 0.016 0.001 TRP C 89 HIS 0.009 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10822) covalent geometry : angle 0.72027 / 0.34 (14854) hydrogen bonds : bond 0.02791 / 1.85 ( 512) hydrogen bonds : angle 4.71797 / 3.30 ( 1566) metal coordination : bond 0.00081 / 0.05 ( 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 290 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7860 (ttm110) REVERT: A 86 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8344 (pttm) REVERT: A 89 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8278 (mtm110) REVERT: A 136 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7951 (m110) REVERT: C 23 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7828 (mtt-85) REVERT: D 52 ARG cc_start: 0.8572 (mtp-110) cc_final: 0.8250 (mtp-110) REVERT: D 88 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8089 (mm) REVERT: E 12 GLN cc_start: 0.8178 (mp10) cc_final: 0.7803 (mp10) REVERT: E 17 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7873 (ttm170) REVERT: E 171 GLU cc_start: 0.8371 (pp20) cc_final: 0.7756 (pm20) REVERT: B 86 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8347 (pttm) REVERT: B 89 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8266 (mtm110) REVERT: G 23 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7838 (mtt-85) REVERT: H 39 GLU cc_start: 0.8384 (tt0) cc_final: 0.8163 (tt0) REVERT: H 52 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8234 (mtp-110) REVERT: I 12 GLN cc_start: 0.8347 (mm110) cc_final: 0.7995 (mp10) REVERT: I 17 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7959 (ttt180) REVERT: I 97 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: J 41 GLN cc_start: 0.8912 (mt0) cc_final: 0.8686 (mp10) outliers start: 38 outliers final: 25 residues processed: 273 average time/residue: 0.6435 time to fit residues: 186.8127 Evaluate side-chains 266 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 102 THR 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 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 E residue 17 ARG 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 G residue 67 THR 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 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU 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 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: 0.9980 chunk 21 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 ** 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 = 0.4028 r_free = 0.4028 target = 0.121877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.094023 restraints weight = 17783.614| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.53 r_work: 0.3392 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10828 Z= 0.170 Angle : 0.773 10.434 14854 Z= 0.362 Chirality : 0.059 0.377 1594 Planarity : 0.004 0.047 1728 Dihedral : 17.224 155.449 1734 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.01 % Allowed : 32.16 % Favored : 63.83 % 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: 1.69 (0.26), residues: 1130 helix: 1.87 (0.27), residues: 376 sheet: 0.77 (0.28), residues: 324 loop : 0.92 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 90 TYR 0.011 0.001 TYR C 69 PHE 0.010 0.001 PHE A 113 TRP 0.010 0.001 TRP C 89 HIS 0.005 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (10822) covalent geometry : angle 0.77294 / 0.36 (14854) hydrogen bonds : bond 0.03104 / 2.05 ( 512) hydrogen bonds : angle 4.79148 / 3.34 ( 1566) metal coordination : bond 0.00281 / 0.18 ( 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 281 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7876 (ttm110) REVERT: A 86 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8311 (pttm) REVERT: A 89 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8303 (mtm110) REVERT: A 136 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7893 (m110) REVERT: C 23 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7815 (mtt-85) REVERT: D 52 ARG cc_start: 0.8564 (mtp-110) cc_final: 0.8227 (mtp-110) REVERT: E 12 GLN cc_start: 0.8197 (mp10) cc_final: 0.7793 (mp10) REVERT: E 17 ARG cc_start: 0.8652 (ttp-170) cc_final: 0.7946 (ttm170) REVERT: E 97 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: E 171 GLU cc_start: 0.8313 (pp20) cc_final: 0.8072 (pp20) REVERT: B 86 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8304 (pttm) REVERT: B 89 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8299 (mtm110) REVERT: G 88 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: H 52 ARG cc_start: 0.8550 (mtp-110) cc_final: 0.8196 (mtp-110) REVERT: I 12 GLN cc_start: 0.8364 (mm110) cc_final: 0.8000 (mp10) REVERT: I 17 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7940 (ttt180) REVERT: J 41 GLN cc_start: 0.8909 (mt0) cc_final: 0.8683 (mp10) outliers start: 40 outliers final: 29 residues processed: 265 average time/residue: 0.6623 time to fit residues: 186.5240 Evaluate side-chains 267 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER 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 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 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 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 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 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 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 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: 2.9990 chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN B 96 GLN H 41 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 = 0.3985 r_free = 0.3985 target = 0.119158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091064 restraints weight = 17713.391| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.53 r_work: 0.3332 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10828 Z= 0.235 Angle : 0.816 10.257 14854 Z= 0.385 Chirality : 0.062 0.468 1594 Planarity : 0.004 0.057 1728 Dihedral : 17.336 155.947 1734 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.01 % Allowed : 32.36 % Favored : 63.63 % 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: 1.49 (0.25), residues: 1130 helix: 1.65 (0.27), residues: 376 sheet: 0.59 (0.28), residues: 322 loop : 0.92 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 23 TYR 0.024 0.002 TYR F 29 PHE 0.011 0.002 PHE J 69 TRP 0.009 0.001 TRP G 79 HIS 0.005 0.001 HIS G 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.24 (10822) covalent geometry : angle 0.81568 / 0.38 (14854) hydrogen bonds : bond 0.03336 / 2.20 ( 512) hydrogen bonds : angle 4.94890 / 3.45 ( 1566) metal coordination : bond 0.00453 / 0.30 ( 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: 40 poor density : 237 time to evaluate : 0.409 Fit side-chains REVERT: A 57 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7870 (ttm110) REVERT: A 89 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8290 (mtm110) REVERT: A 136 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7858 (m110) REVERT: A 166 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: C 88 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: D 88 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (mm) REVERT: E 12 GLN cc_start: 0.8191 (mp10) cc_final: 0.7734 (mp10) REVERT: E 17 ARG cc_start: 0.8658 (ttp-170) cc_final: 0.7748 (ttp-170) REVERT: E 171 GLU cc_start: 0.8296 (pp20) cc_final: 0.7764 (pm20) REVERT: B 89 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8301 (mtm110) REVERT: B 166 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: G 23 ARG cc_start: 0.8246 (mtm110) cc_final: 0.7820 (mtt-85) REVERT: G 61 ASP cc_start: 0.8196 (p0) cc_final: 0.7871 (p0) REVERT: G 88 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: H 54 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: H 88 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8207 (mm) REVERT: I 12 GLN cc_start: 0.8387 (mm110) cc_final: 0.7998 (mp10) REVERT: I 17 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8197 (ttp-170) REVERT: I 171 GLU cc_start: 0.8200 (pm20) cc_final: 0.7927 (pm20) REVERT: J 41 GLN cc_start: 0.8910 (mt0) cc_final: 0.8660 (mp10) outliers start: 40 outliers final: 26 residues processed: 263 average time/residue: 0.6728 time to fit residues: 188.0307 Evaluate side-chains 270 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER 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 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 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG 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 166 GLN 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 17 ARG 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: 0.8980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.122611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094970 restraints weight = 17751.752| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.53 r_work: 0.3400 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10828 Z= 0.145 Angle : 0.763 10.060 14854 Z= 0.359 Chirality : 0.057 0.335 1594 Planarity : 0.005 0.055 1728 Dihedral : 17.227 156.159 1734 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.31 % Allowed : 32.67 % Favored : 64.03 % 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: 1.53 (0.26), residues: 1130 helix: 1.68 (0.27), residues: 378 sheet: 0.61 (0.28), residues: 324 loop : 0.95 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 23 TYR 0.010 0.001 TYR C 69 PHE 0.010 0.001 PHE B 113 TRP 0.015 0.001 TRP C 89 HIS 0.006 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (10822) covalent geometry : angle 0.76307 / 0.36 (14854) hydrogen bonds : bond 0.02973 / 1.97 ( 512) hydrogen bonds : angle 4.80550 / 3.36 ( 1566) metal coordination : bond 0.00160 / 0.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4510.06 seconds wall clock time: 77 minutes 22.42 seconds (4642.42 seconds total)