Starting phenix.real_space_refine on Sun Jul 5 05:10:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b2l_11987/07_2026/7b2l_11987.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b2l_11987/07_2026/7b2l_11987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b2l_11987/07_2026/7b2l_11987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b2l_11987/07_2026/7b2l_11987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b2l_11987/07_2026/7b2l_11987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b2l_11987/07_2026/7b2l_11987.map" } resolution = 3.9 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= 0.034 sd= 0.230 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: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 120 5.16 5 C 16400 2.51 5 N 4480 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26192 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "D" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "F" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "I" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "K" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "L" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "M" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "N" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "P" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "Q" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "R" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "S" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 6.15, per 1000 atoms: 0.23 Number of scatterers: 26192 At special positions: 0 Unit cell: (152.295, 154.425, 122.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 60 15.00 O 5132 8.00 N 4480 7.00 C 16400 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.0 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 0 sheets defined 85.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 35 through 46 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 69 through 87 removed outlier: 3.757A pdb=" N ILE A 73 " --> pdb=" O TYR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.748A pdb=" N VAL A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 removed outlier: 3.534A pdb=" N LYS A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 135 Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'B' and resid 4 through 16 removed outlier: 4.017A pdb=" N LEU B 8 " --> pdb=" O ILE B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 38 removed outlier: 3.673A pdb=" N VAL B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.784A pdb=" N PHE B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 74 removed outlier: 3.941A pdb=" N LEU B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 96 removed outlier: 5.864A pdb=" N ASP B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 Processing helix chain 'B' and resid 134 through 144 Processing helix chain 'B' and resid 144 through 176 Processing helix chain 'B' and resid 182 through 212 removed outlier: 3.531A pdb=" N ILE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Proline residue: B 189 - end of helix removed outlier: 3.610A pdb=" N ALA B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 245 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 17 through 27 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 51 through 65 removed outlier: 3.687A pdb=" N ILE C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 69 through 87 removed outlier: 3.604A pdb=" N ILE C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 98 removed outlier: 3.778A pdb=" N VAL C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 115 through 135 Processing helix chain 'C' and resid 135 through 147 Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.687A pdb=" N ASP D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 8 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'D' and resid 41 through 51 Processing helix chain 'D' and resid 52 through 55 removed outlier: 3.864A pdb=" N ASN D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 55' Processing helix chain 'D' and resid 56 through 74 Processing helix chain 'D' and resid 75 through 85 removed outlier: 4.172A pdb=" N LEU D 79 " --> pdb=" O HIS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 removed outlier: 3.646A pdb=" N ARG D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 123 removed outlier: 3.974A pdb=" N LYS D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 144 through 177 Processing helix chain 'D' and resid 180 through 212 Proline residue: D 189 - end of helix Processing helix chain 'D' and resid 223 through 244 Processing helix chain 'D' and resid 247 through 252 removed outlier: 4.359A pdb=" N LEU D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 252' Processing helix chain 'F' and resid 2 through 15 Processing helix chain 'F' and resid 17 through 27 Processing helix chain 'F' and resid 35 through 46 Processing helix chain 'F' and resid 51 through 65 Processing helix chain 'F' and resid 66 through 68 No H-bonds generated for 'chain 'F' and resid 66 through 68' Processing helix chain 'F' and resid 69 through 87 removed outlier: 3.757A pdb=" N ILE F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.748A pdb=" N VAL F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 106 removed outlier: 3.534A pdb=" N LYS F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 135 Processing helix chain 'F' and resid 135 through 147 Processing helix chain 'G' and resid 4 through 16 removed outlier: 4.017A pdb=" N LEU G 8 " --> pdb=" O ILE G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 38 removed outlier: 3.673A pdb=" N VAL G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 51 removed outlier: 3.784A pdb=" N PHE G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 74 removed outlier: 3.941A pdb=" N LEU G 60 " --> pdb=" O ASP G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 96 removed outlier: 5.864A pdb=" N ASP G 87 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP G 88 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G 93 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS G 96 " --> pdb=" O LEU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 Processing helix chain 'G' and resid 134 through 144 Processing helix chain 'G' and resid 144 through 176 Processing helix chain 'G' and resid 182 through 212 removed outlier: 3.531A pdb=" N ILE G 188 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Proline residue: G 189 - end of helix removed outlier: 3.610A pdb=" N ALA G 192 " --> pdb=" O ILE G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 245 Processing helix chain 'G' and resid 246 through 251 Processing helix chain 'H' and resid 2 through 14 Processing helix chain 'H' and resid 17 through 27 Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 51 through 65 removed outlier: 3.687A pdb=" N ILE H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 68 No H-bonds generated for 'chain 'H' and resid 66 through 68' Processing helix chain 'H' and resid 69 through 87 removed outlier: 3.604A pdb=" N ILE H 73 " --> pdb=" O TYR H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 removed outlier: 3.778A pdb=" N VAL H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 105 through 108 Processing helix chain 'H' and resid 115 through 135 Processing helix chain 'H' and resid 135 through 147 Processing helix chain 'I' and resid 2 through 16 removed outlier: 3.687A pdb=" N ASP I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU I 8 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS I 14 " --> pdb=" O LYS I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 Processing helix chain 'I' and resid 41 through 51 Processing helix chain 'I' and resid 52 through 55 removed outlier: 3.864A pdb=" N ASN I 55 " --> pdb=" O PRO I 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 52 through 55' Processing helix chain 'I' and resid 56 through 74 Processing helix chain 'I' and resid 75 through 85 removed outlier: 4.172A pdb=" N LEU I 79 " --> pdb=" O HIS I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 96 removed outlier: 3.646A pdb=" N ARG I 94 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 123 removed outlier: 3.974A pdb=" N LYS I 104 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 143 Processing helix chain 'I' and resid 144 through 177 Processing helix chain 'I' and resid 180 through 212 Proline residue: I 189 - end of helix Processing helix chain 'I' and resid 223 through 244 Processing helix chain 'I' and resid 247 through 252 removed outlier: 4.359A pdb=" N LEU I 251 " --> pdb=" O TYR I 247 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL I 252 " --> pdb=" O LEU I 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 247 through 252' Processing helix chain 'K' and resid 2 through 15 Processing helix chain 'K' and resid 17 through 27 Processing helix chain 'K' and resid 35 through 46 Processing helix chain 'K' and resid 51 through 65 Processing helix chain 'K' and resid 66 through 68 No H-bonds generated for 'chain 'K' and resid 66 through 68' Processing helix chain 'K' and resid 69 through 87 removed outlier: 3.757A pdb=" N ILE K 73 " --> pdb=" O TYR K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 98 removed outlier: 3.748A pdb=" N VAL K 92 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 106 removed outlier: 3.534A pdb=" N LYS K 106 " --> pdb=" O ILE K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 135 Processing helix chain 'K' and resid 135 through 147 Processing helix chain 'L' and resid 4 through 16 removed outlier: 4.017A pdb=" N LEU L 8 " --> pdb=" O ILE L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 3.673A pdb=" N VAL L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 51 removed outlier: 3.784A pdb=" N PHE L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 74 removed outlier: 3.941A pdb=" N LEU L 60 " --> pdb=" O ASP L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 96 removed outlier: 5.864A pdb=" N ASP L 87 " --> pdb=" O ILE L 83 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP L 88 " --> pdb=" O ARG L 84 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY L 93 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 123 Processing helix chain 'L' and resid 134 through 144 Processing helix chain 'L' and resid 144 through 176 Processing helix chain 'L' and resid 182 through 212 removed outlier: 3.531A pdb=" N ILE L 188 " --> pdb=" O ILE L 184 " (cutoff:3.500A) Proline residue: L 189 - end of helix removed outlier: 3.610A pdb=" N ALA L 192 " --> pdb=" O ILE L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 245 Processing helix chain 'L' and resid 246 through 251 Processing helix chain 'M' and resid 2 through 14 Processing helix chain 'M' and resid 17 through 27 Processing helix chain 'M' and resid 35 through 46 Processing helix chain 'M' and resid 51 through 65 removed outlier: 3.687A pdb=" N ILE M 55 " --> pdb=" O ASP M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 68 No H-bonds generated for 'chain 'M' and resid 66 through 68' Processing helix chain 'M' and resid 69 through 87 removed outlier: 3.604A pdb=" N ILE M 73 " --> pdb=" O TYR M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 98 removed outlier: 3.778A pdb=" N VAL M 92 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 104 Processing helix chain 'M' and resid 105 through 108 Processing helix chain 'M' and resid 115 through 135 Processing helix chain 'M' and resid 135 through 147 Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.687A pdb=" N ASP N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU N 8 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 38 Processing helix chain 'N' and resid 41 through 51 Processing helix chain 'N' and resid 52 through 55 removed outlier: 3.864A pdb=" N ASN N 55 " --> pdb=" O PRO N 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 52 through 55' Processing helix chain 'N' and resid 56 through 74 Processing helix chain 'N' and resid 75 through 85 removed outlier: 4.172A pdb=" N LEU N 79 " --> pdb=" O HIS N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 96 removed outlier: 3.646A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 123 removed outlier: 3.974A pdb=" N LYS N 104 " --> pdb=" O SER N 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU N 105 " --> pdb=" O SER N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 143 Processing helix chain 'N' and resid 144 through 177 Processing helix chain 'N' and resid 180 through 212 Proline residue: N 189 - end of helix Processing helix chain 'N' and resid 223 through 244 Processing helix chain 'N' and resid 247 through 252 removed outlier: 4.359A pdb=" N LEU N 251 " --> pdb=" O TYR N 247 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 247 through 252' Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 17 through 27 Processing helix chain 'P' and resid 35 through 46 Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 66 through 68 No H-bonds generated for 'chain 'P' and resid 66 through 68' Processing helix chain 'P' and resid 69 through 87 removed outlier: 3.757A pdb=" N ILE P 73 " --> pdb=" O TYR P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 98 removed outlier: 3.748A pdb=" N VAL P 92 " --> pdb=" O SER P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 106 removed outlier: 3.534A pdb=" N LYS P 106 " --> pdb=" O ILE P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 135 Processing helix chain 'P' and resid 135 through 147 Processing helix chain 'Q' and resid 4 through 16 removed outlier: 4.017A pdb=" N LEU Q 8 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 38 removed outlier: 3.673A pdb=" N VAL Q 28 " --> pdb=" O LYS Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 51 removed outlier: 3.784A pdb=" N PHE Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 74 removed outlier: 3.941A pdb=" N LEU Q 60 " --> pdb=" O ASP Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 96 removed outlier: 5.864A pdb=" N ASP Q 87 " --> pdb=" O ILE Q 83 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP Q 88 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY Q 93 " --> pdb=" O ILE Q 89 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 123 Processing helix chain 'Q' and resid 134 through 144 Processing helix chain 'Q' and resid 144 through 176 Processing helix chain 'Q' and resid 182 through 212 removed outlier: 3.531A pdb=" N ILE Q 188 " --> pdb=" O ILE Q 184 " (cutoff:3.500A) Proline residue: Q 189 - end of helix removed outlier: 3.610A pdb=" N ALA Q 192 " --> pdb=" O ILE Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 223 through 245 Processing helix chain 'Q' and resid 246 through 251 Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 35 through 46 Processing helix chain 'R' and resid 51 through 65 removed outlier: 3.687A pdb=" N ILE R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 68 No H-bonds generated for 'chain 'R' and resid 66 through 68' Processing helix chain 'R' and resid 69 through 87 removed outlier: 3.604A pdb=" N ILE R 73 " --> pdb=" O TYR R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 98 removed outlier: 3.778A pdb=" N VAL R 92 " --> pdb=" O SER R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 104 Processing helix chain 'R' and resid 105 through 108 Processing helix chain 'R' and resid 115 through 135 Processing helix chain 'R' and resid 135 through 147 Processing helix chain 'S' and resid 2 through 16 removed outlier: 3.687A pdb=" N ASP S 7 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU S 8 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 38 Processing helix chain 'S' and resid 41 through 51 Processing helix chain 'S' and resid 52 through 55 removed outlier: 3.864A pdb=" N ASN S 55 " --> pdb=" O PRO S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 55' Processing helix chain 'S' and resid 56 through 74 Processing helix chain 'S' and resid 75 through 85 removed outlier: 4.172A pdb=" N LEU S 79 " --> pdb=" O HIS S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 96 removed outlier: 3.646A pdb=" N ARG S 94 " --> pdb=" O ARG S 90 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 123 removed outlier: 3.974A pdb=" N LYS S 104 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU S 105 " --> pdb=" O SER S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 134 through 143 Processing helix chain 'S' and resid 144 through 177 Processing helix chain 'S' and resid 180 through 212 Proline residue: S 189 - end of helix Processing helix chain 'S' and resid 223 through 244 Processing helix chain 'S' and resid 247 through 252 removed outlier: 4.359A pdb=" N LEU S 251 " --> pdb=" O TYR S 247 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL S 252 " --> pdb=" O LEU S 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 247 through 252' 1853 hydrogen bonds defined for protein. 5511 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: 4.27 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 4036 1.25 - 1.39: 4956 1.39 - 1.54: 14844 1.54 - 1.68: 2620 1.68 - 1.82: 192 Bond restraints: 26648 Sorted by residual: bond pdb=" C VAL K 23 " pdb=" O VAL K 23 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" C VAL P 23 " pdb=" O VAL P 23 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" C VAL F 23 " pdb=" O VAL F 23 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" O11 PIO F 202 " pdb=" P1 PIO F 202 " ideal model delta sigma weight residual 1.495 1.648 -0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 26643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 29758 2.65 - 5.30: 5610 5.30 - 7.95: 556 7.95 - 10.59: 40 10.59 - 13.24: 40 Bond angle restraints: 36004 Sorted by residual: angle pdb=" CA SER P 28 " pdb=" C SER P 28 " pdb=" O SER P 28 " ideal model delta sigma weight residual 120.60 110.51 10.09 1.20e+00 6.94e-01 7.06e+01 angle pdb=" CA SER A 28 " pdb=" C SER A 28 " pdb=" O SER A 28 " ideal model delta sigma weight residual 120.60 110.51 10.09 1.20e+00 6.94e-01 7.06e+01 angle pdb=" CA SER F 28 " pdb=" C SER F 28 " pdb=" O SER F 28 " ideal model delta sigma weight residual 120.60 110.51 10.09 1.20e+00 6.94e-01 7.06e+01 angle pdb=" CA SER K 28 " pdb=" C SER K 28 " pdb=" O SER K 28 " ideal model delta sigma weight residual 120.60 110.51 10.09 1.20e+00 6.94e-01 7.06e+01 angle pdb=" CA ASP L 7 " pdb=" CB ASP L 7 " pdb=" CG ASP L 7 " ideal model delta sigma weight residual 112.60 120.72 -8.12 1.00e+00 1.00e+00 6.59e+01 ... (remaining 35999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14344 17.77 - 35.53: 1280 35.53 - 53.30: 240 53.30 - 71.06: 132 71.06 - 88.83: 64 Dihedral angle restraints: 16060 sinusoidal: 6700 harmonic: 9360 Sorted by residual: dihedral pdb=" CA VAL L 252 " pdb=" C VAL L 252 " pdb=" N THR L 253 " pdb=" CA THR L 253 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL B 252 " pdb=" C VAL B 252 " pdb=" N THR B 253 " pdb=" CA THR B 253 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL G 252 " pdb=" C VAL G 252 " pdb=" N THR G 253 " pdb=" CA THR G 253 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 16057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2704 0.096 - 0.193: 1096 0.193 - 0.289: 204 0.289 - 0.385: 36 0.385 - 0.482: 16 Chirality restraints: 4056 Sorted by residual: chirality pdb=" CA ASN M 31 " pdb=" N ASN M 31 " pdb=" C ASN M 31 " pdb=" CB ASN M 31 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ASN C 31 " pdb=" N ASN C 31 " pdb=" C ASN C 31 " pdb=" CB ASN C 31 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ASN R 31 " pdb=" N ASN R 31 " pdb=" C ASN R 31 " pdb=" CB ASN R 31 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 4053 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 133 " -0.166 2.00e-02 2.50e+03 9.72e-02 1.89e+02 pdb=" CG TYR I 133 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR I 133 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR I 133 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR I 133 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TYR I 133 " 0.065 2.00e-02 2.50e+03 pdb=" CZ TYR I 133 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR I 133 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 133 " -0.166 2.00e-02 2.50e+03 9.72e-02 1.89e+02 pdb=" CG TYR N 133 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR N 133 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR N 133 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR N 133 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TYR N 133 " 0.065 2.00e-02 2.50e+03 pdb=" CZ TYR N 133 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR N 133 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 133 " 0.166 2.00e-02 2.50e+03 9.72e-02 1.89e+02 pdb=" CG TYR S 133 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR S 133 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR S 133 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR S 133 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 TYR S 133 " -0.065 2.00e-02 2.50e+03 pdb=" CZ TYR S 133 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR S 133 " 0.165 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 208 2.63 - 3.20: 23532 3.20 - 3.76: 41267 3.76 - 4.33: 54521 4.33 - 4.90: 89076 Nonbonded interactions: 208604 Sorted by model distance: nonbonded pdb=" O51 PIO C 301 " pdb=" O6 PIO C 301 " model vdw 2.060 3.040 nonbonded pdb=" O51 PIO H 301 " pdb=" O6 PIO H 301 " model vdw 2.060 3.040 nonbonded pdb=" O52 PIO M 301 " pdb=" O6 PIO M 301 " model vdw 2.060 3.040 nonbonded pdb=" O52 PIO R 301 " pdb=" O6 PIO R 301 " model vdw 2.060 3.040 nonbonded pdb=" O52 PIO F 202 " pdb=" O6 PIO F 202 " model vdw 2.103 3.040 ... (remaining 208599 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 'C' selection = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'B' and resid 1 through 256) selection = chain 'D' selection = (chain 'G' and resid 1 through 256) selection = chain 'I' selection = (chain 'L' and resid 1 through 256) selection = chain 'N' selection = (chain 'Q' and resid 1 through 256) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.910 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.018 0.881 26652 Z= 1.379 Angle : 2.043 13.242 36004 Z= 1.352 Chirality : 0.106 0.482 4056 Planarity : 0.019 0.219 4464 Dihedral : 16.432 88.826 9964 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.80 % Favored : 93.56 % Rotamer: Outliers : 3.78 % Allowed : 8.40 % Favored : 87.82 % Cbeta Deviations : 1.05 % 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: -1.26 (0.12), residues: 3104 helix: -0.46 (0.08), residues: 2432 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 24 TYR 0.184 0.030 TYR L 112 PHE 0.107 0.018 PHE S 200 TRP 0.158 0.029 TRP R 70 HIS 0.029 0.006 HIS M 32 Details of bonding type rmsd/Z covalent geometry : bond 0.01412 / 0.86 (26648) covalent geometry : angle 2.04265 / 1.35 (36004) hydrogen bonds : bond 0.20251 / 13.41 ( 1853) hydrogen bonds : angle 7.66209 / 5.58 ( 5511) Misc. bond : bond 0.88133 / 44.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 808 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.8007 (m110) cc_final: 0.7784 (t0) REVERT: B 9 GLN cc_start: 0.7739 (mt0) cc_final: 0.7337 (mt0) REVERT: B 136 TYR cc_start: 0.6985 (t80) cc_final: 0.6634 (t80) REVERT: B 152 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6506 (tt) REVERT: B 195 TYR cc_start: 0.6686 (t80) cc_final: 0.6396 (t80) REVERT: C 14 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8695 (mmtm) REVERT: C 66 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8382 (mtmt) REVERT: C 136 ASP cc_start: 0.7124 (p0) cc_final: 0.6900 (p0) REVERT: D 59 GLN cc_start: 0.8730 (mt0) cc_final: 0.8522 (mt0) REVERT: D 63 MET cc_start: 0.8875 (ttp) cc_final: 0.8579 (tmm) REVERT: F 11 ASN cc_start: 0.8007 (m110) cc_final: 0.7786 (t0) REVERT: G 9 GLN cc_start: 0.7729 (mt0) cc_final: 0.7318 (mt0) REVERT: G 136 TYR cc_start: 0.6987 (t80) cc_final: 0.6634 (t80) REVERT: G 152 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6513 (tt) REVERT: G 195 TYR cc_start: 0.6684 (t80) cc_final: 0.6392 (t80) REVERT: H 14 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8693 (mmtm) REVERT: H 66 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8397 (mtmt) REVERT: H 136 ASP cc_start: 0.7130 (p0) cc_final: 0.6905 (p0) REVERT: I 59 GLN cc_start: 0.8732 (mt0) cc_final: 0.8523 (mt0) REVERT: I 63 MET cc_start: 0.8876 (ttp) cc_final: 0.8576 (tmm) REVERT: K 11 ASN cc_start: 0.8008 (m110) cc_final: 0.7788 (t0) REVERT: L 9 GLN cc_start: 0.7732 (mt0) cc_final: 0.7327 (mt0) REVERT: L 136 TYR cc_start: 0.6991 (t80) cc_final: 0.6639 (t80) REVERT: L 152 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6506 (tt) REVERT: L 195 TYR cc_start: 0.6682 (t80) cc_final: 0.6388 (t80) REVERT: M 14 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8695 (mmtm) REVERT: M 66 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8396 (mtmt) REVERT: M 136 ASP cc_start: 0.7132 (p0) cc_final: 0.6906 (p0) REVERT: N 59 GLN cc_start: 0.8728 (mt0) cc_final: 0.8521 (mt0) REVERT: N 63 MET cc_start: 0.8872 (ttp) cc_final: 0.8579 (tmm) REVERT: P 11 ASN cc_start: 0.8009 (m110) cc_final: 0.7794 (t0) REVERT: Q 9 GLN cc_start: 0.7728 (mt0) cc_final: 0.7316 (mt0) REVERT: Q 136 TYR cc_start: 0.6990 (t80) cc_final: 0.6636 (t80) REVERT: Q 152 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6510 (tt) REVERT: Q 195 TYR cc_start: 0.6684 (t80) cc_final: 0.6394 (t80) REVERT: R 14 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8696 (mmtm) REVERT: R 66 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8399 (mtmt) REVERT: R 136 ASP cc_start: 0.7130 (p0) cc_final: 0.6903 (p0) REVERT: S 59 GLN cc_start: 0.8729 (mt0) cc_final: 0.8524 (mt0) REVERT: S 63 MET cc_start: 0.8875 (ttp) cc_final: 0.8580 (tmm) outliers start: 108 outliers final: 8 residues processed: 876 average time/residue: 0.1850 time to fit residues: 248.7900 Evaluate side-chains 380 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 360 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 152 ILE Chi-restraints excluded: chain R residue 14 LYS Chi-restraints excluded: chain R residue 66 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN A 146 ASN B 38 HIS B 55 ASN C 4 GLN C 11 ASN C 20 GLN C 29 ASN C 98 ASN D 38 HIS D 167 GLN D 179 ASN F 25 ASN F 146 ASN G 38 HIS G 55 ASN H 4 GLN H 11 ASN H 20 GLN H 29 ASN H 98 ASN I 38 HIS I 167 GLN K 25 ASN K 146 ASN L 38 HIS L 55 ASN M 4 GLN M 11 ASN M 20 GLN M 29 ASN M 98 ASN N 38 HIS N 167 GLN P 25 ASN P 146 ASN Q 38 HIS Q 55 ASN R 4 GLN R 11 ASN R 20 GLN R 29 ASN R 98 ASN S 38 HIS S 167 GLN S 179 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100805 restraints weight = 68044.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.100920 restraints weight = 67745.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101633 restraints weight = 57879.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101848 restraints weight = 50767.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101862 restraints weight = 48437.738| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 26652 Z= 0.176 Angle : 0.736 8.201 36004 Z= 0.397 Chirality : 0.042 0.174 4056 Planarity : 0.005 0.049 4464 Dihedral : 8.274 66.829 3592 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.58 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 15.97 % Favored : 82.14 % 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: 0.83 (0.14), residues: 3104 helix: 1.01 (0.09), residues: 2468 sheet: None (None), residues: 0 loop : -1.05 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 29 TYR 0.043 0.002 TYR B 109 PHE 0.025 0.003 PHE G 61 TRP 0.010 0.002 TRP C 70 HIS 0.008 0.001 HIS N 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (26648) covalent geometry : angle 0.73591 / 0.40 (36004) hydrogen bonds : bond 0.05654 / 3.78 ( 1853) hydrogen bonds : angle 4.63250 / 3.35 ( 5511) Misc. bond : bond 0.00082 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 484 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7837 (m-30) cc_final: 0.7576 (m-30) REVERT: A 69 TYR cc_start: 0.8814 (m-80) cc_final: 0.8559 (m-80) REVERT: A 114 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7111 (pt0) REVERT: C 20 GLN cc_start: 0.8584 (mt0) cc_final: 0.8332 (mt0) REVERT: C 49 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.7988 (t) REVERT: D 9 GLN cc_start: 0.7536 (mt0) cc_final: 0.7330 (mt0) REVERT: F 30 ASP cc_start: 0.7826 (m-30) cc_final: 0.7571 (m-30) REVERT: F 69 TYR cc_start: 0.8811 (m-80) cc_final: 0.8556 (m-80) REVERT: F 114 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: H 20 GLN cc_start: 0.8586 (mt0) cc_final: 0.8329 (mt0) REVERT: H 49 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.7972 (t) REVERT: K 30 ASP cc_start: 0.7828 (m-30) cc_final: 0.7571 (m-30) REVERT: K 69 TYR cc_start: 0.8786 (m-80) cc_final: 0.8535 (m-80) REVERT: K 114 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: M 20 GLN cc_start: 0.8585 (mt0) cc_final: 0.8333 (mt0) REVERT: M 49 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.7984 (t) REVERT: N 9 GLN cc_start: 0.7540 (mt0) cc_final: 0.7338 (mt0) REVERT: P 30 ASP cc_start: 0.7826 (m-30) cc_final: 0.7578 (m-30) REVERT: P 69 TYR cc_start: 0.8786 (m-80) cc_final: 0.8536 (m-80) REVERT: P 114 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: R 20 GLN cc_start: 0.8569 (mt0) cc_final: 0.8319 (mt0) REVERT: R 49 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.7981 (t) REVERT: S 9 GLN cc_start: 0.7541 (mt0) cc_final: 0.7333 (mt0) outliers start: 54 outliers final: 16 residues processed: 522 average time/residue: 0.1614 time to fit residues: 133.4298 Evaluate side-chains 339 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 315 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain P residue 64 ASN Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 133 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 283 optimal weight: 0.5980 chunk 156 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN C 64 ASN C 98 ASN G 9 GLN H 64 ASN H 98 ASN I 179 ASN L 9 GLN M 64 ASN M 98 ASN N 179 ASN Q 9 GLN R 64 ASN R 98 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.124960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100852 restraints weight = 67234.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101090 restraints weight = 71020.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101665 restraints weight = 59043.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101909 restraints weight = 51982.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101914 restraints weight = 48956.060| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26652 Z= 0.149 Angle : 0.650 8.093 36004 Z= 0.347 Chirality : 0.038 0.152 4056 Planarity : 0.004 0.040 4464 Dihedral : 7.302 62.467 3544 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.65 % Rotamer: Outliers : 2.07 % Allowed : 18.21 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.14), residues: 3104 helix: 1.31 (0.10), residues: 2468 sheet: None (None), residues: 0 loop : -1.07 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 7 TYR 0.031 0.002 TYR Q 109 PHE 0.031 0.003 PHE G 165 TRP 0.011 0.001 TRP A 94 HIS 0.008 0.001 HIS N 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (26648) covalent geometry : angle 0.64959 / 0.35 (36004) hydrogen bonds : bond 0.04872 / 3.24 ( 1853) hydrogen bonds : angle 4.34970 / 3.14 ( 5511) Misc. bond : bond 0.00007 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 386 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.7765 (t80) cc_final: 0.7551 (t80) REVERT: A 72 HIS cc_start: 0.7553 (m170) cc_final: 0.7079 (m170) REVERT: B 9 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: B 126 PHE cc_start: 0.4588 (p90) cc_final: 0.4369 (p90) REVERT: C 20 GLN cc_start: 0.8610 (mt0) cc_final: 0.8060 (mt0) REVERT: C 58 MET cc_start: 0.8839 (tpp) cc_final: 0.8608 (tpp) REVERT: D 72 GLN cc_start: 0.8192 (tt0) cc_final: 0.7961 (mt0) REVERT: F 72 HIS cc_start: 0.7552 (m170) cc_final: 0.7088 (m170) REVERT: G 9 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7285 (mt0) REVERT: G 126 PHE cc_start: 0.4559 (p90) cc_final: 0.4347 (p90) REVERT: H 20 GLN cc_start: 0.8593 (mt0) cc_final: 0.8064 (mt0) REVERT: H 58 MET cc_start: 0.8836 (tpp) cc_final: 0.8566 (tpp) REVERT: I 72 GLN cc_start: 0.8203 (tt0) cc_final: 0.7965 (mt0) REVERT: K 72 HIS cc_start: 0.7548 (m170) cc_final: 0.7065 (m170) REVERT: L 9 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7283 (mt0) REVERT: L 126 PHE cc_start: 0.4549 (p90) cc_final: 0.4337 (p90) REVERT: M 20 GLN cc_start: 0.8619 (mt0) cc_final: 0.8063 (mt0) REVERT: M 58 MET cc_start: 0.8835 (tpp) cc_final: 0.8572 (tpp) REVERT: N 72 GLN cc_start: 0.8200 (tt0) cc_final: 0.7962 (mt0) REVERT: P 72 HIS cc_start: 0.7546 (m170) cc_final: 0.7068 (m170) REVERT: Q 9 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: Q 126 PHE cc_start: 0.4557 (p90) cc_final: 0.4335 (p90) REVERT: R 20 GLN cc_start: 0.8592 (mt0) cc_final: 0.8031 (mt0) REVERT: R 58 MET cc_start: 0.8830 (tpp) cc_final: 0.8568 (tpp) REVERT: S 72 GLN cc_start: 0.8184 (tt0) cc_final: 0.7948 (mt0) outliers start: 59 outliers final: 28 residues processed: 437 average time/residue: 0.1675 time to fit residues: 117.0297 Evaluate side-chains 342 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 9 GLN Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 89 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 265 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 HIS C 98 ASN D 59 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS H 98 ASN I 59 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 HIS M 98 ASN N 59 GLN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 HIS R 98 ASN S 59 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.122943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098332 restraints weight = 66505.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097387 restraints weight = 71771.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098294 restraints weight = 68424.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098524 restraints weight = 55907.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098711 restraints weight = 51107.898| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26652 Z= 0.180 Angle : 0.650 8.997 36004 Z= 0.342 Chirality : 0.039 0.144 4056 Planarity : 0.004 0.043 4464 Dihedral : 6.867 58.736 3532 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 2.49 % Allowed : 19.47 % Favored : 78.05 % 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: 1.30 (0.15), residues: 3104 helix: 1.37 (0.10), residues: 2432 sheet: None (None), residues: 0 loop : -0.89 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 109 TYR 0.033 0.002 TYR B 109 PHE 0.027 0.002 PHE G 165 TRP 0.009 0.002 TRP F 94 HIS 0.007 0.001 HIS N 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (26648) covalent geometry : angle 0.65028 / 0.34 (36004) hydrogen bonds : bond 0.04695 / 3.12 ( 1853) hydrogen bonds : angle 4.34412 / 3.14 ( 5511) Misc. bond : bond 0.00004 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 352 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.7812 (t80) cc_final: 0.7522 (t80) REVERT: A 53 PHE cc_start: 0.6887 (m-10) cc_final: 0.6327 (m-10) REVERT: B 59 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: C 49 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8042 (t) REVERT: D 9 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: G 59 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: H 49 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8031 (t) REVERT: K 53 PHE cc_start: 0.6883 (m-10) cc_final: 0.6329 (m-10) REVERT: L 59 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: M 49 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8035 (t) REVERT: N 9 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7030 (tt0) REVERT: P 53 PHE cc_start: 0.6885 (m-10) cc_final: 0.6317 (m-10) REVERT: Q 59 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: R 49 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8046 (t) REVERT: S 9 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7019 (tt0) outliers start: 71 outliers final: 28 residues processed: 415 average time/residue: 0.1615 time to fit residues: 109.2227 Evaluate side-chains 326 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 9 GLN Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 89 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 202 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN C 98 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN H 98 ASN I 9 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN M 98 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 98 ASN S 179 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.124061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098877 restraints weight = 66754.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099214 restraints weight = 66678.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099877 restraints weight = 55212.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099983 restraints weight = 49409.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.100291 restraints weight = 45781.536| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26652 Z= 0.139 Angle : 0.626 8.992 36004 Z= 0.327 Chirality : 0.037 0.142 4056 Planarity : 0.004 0.042 4464 Dihedral : 6.645 58.809 3532 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.64 % Favored : 97.23 % Rotamer: Outliers : 3.01 % Allowed : 19.99 % Favored : 77.00 % 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: 1.44 (0.15), residues: 3104 helix: 1.47 (0.10), residues: 2448 sheet: None (None), residues: 0 loop : -0.92 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 109 TYR 0.028 0.002 TYR N 195 PHE 0.024 0.002 PHE G 165 TRP 0.008 0.001 TRP A 94 HIS 0.005 0.001 HIS L 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (26648) covalent geometry : angle 0.62558 / 0.33 (36004) hydrogen bonds : bond 0.04343 / 2.87 ( 1853) hydrogen bonds : angle 4.16780 / 3.01 ( 5511) Misc. bond : bond 0.00005 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 372 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7713 (m170) cc_final: 0.7319 (m170) REVERT: B 59 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: B 195 TYR cc_start: 0.6806 (t80) cc_final: 0.6367 (t80) REVERT: B 208 MET cc_start: 0.6341 (tpp) cc_final: 0.5598 (ptt) REVERT: D 195 TYR cc_start: 0.7225 (t80) cc_final: 0.6669 (t80) REVERT: F 53 PHE cc_start: 0.6767 (m-10) cc_final: 0.6366 (m-10) REVERT: F 72 HIS cc_start: 0.7719 (m170) cc_final: 0.7317 (m170) REVERT: G 59 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: G 195 TYR cc_start: 0.6778 (t80) cc_final: 0.6350 (t80) REVERT: G 208 MET cc_start: 0.6324 (tpp) cc_final: 0.5594 (ptt) REVERT: I 182 CYS cc_start: 0.7027 (p) cc_final: 0.6731 (t) REVERT: K 72 HIS cc_start: 0.7731 (m170) cc_final: 0.7368 (m170) REVERT: L 59 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: L 195 TYR cc_start: 0.6787 (t80) cc_final: 0.6360 (t80) REVERT: L 208 MET cc_start: 0.6329 (tpp) cc_final: 0.5588 (ptt) REVERT: N 182 CYS cc_start: 0.7032 (p) cc_final: 0.6735 (t) REVERT: P 72 HIS cc_start: 0.7718 (m170) cc_final: 0.7362 (m170) REVERT: Q 59 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: Q 195 TYR cc_start: 0.6784 (t80) cc_final: 0.6354 (t80) REVERT: Q 208 MET cc_start: 0.6330 (tpp) cc_final: 0.5594 (ptt) REVERT: S 195 TYR cc_start: 0.7220 (t80) cc_final: 0.6674 (t80) outliers start: 86 outliers final: 37 residues processed: 447 average time/residue: 0.1519 time to fit residues: 112.7106 Evaluate side-chains 328 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 185 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 HIS C 98 ASN D 122 HIS D 179 ASN G 68 HIS H 98 ASN I 9 GLN ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS L 68 HIS M 98 ASN N 122 HIS Q 68 HIS R 98 ASN S 122 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.120350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.096445 restraints weight = 66094.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095269 restraints weight = 66270.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096031 restraints weight = 67148.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.096245 restraints weight = 52134.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096379 restraints weight = 49851.379| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26652 Z= 0.238 Angle : 0.692 9.479 36004 Z= 0.361 Chirality : 0.041 0.175 4056 Planarity : 0.004 0.042 4464 Dihedral : 6.774 59.968 3532 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.42 % Rotamer: Outliers : 3.08 % Allowed : 20.94 % Favored : 75.98 % 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: 1.23 (0.15), residues: 3104 helix: 1.33 (0.10), residues: 2448 sheet: None (None), residues: 0 loop : -1.00 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 109 TYR 0.021 0.002 TYR S 195 PHE 0.023 0.003 PHE G 165 TRP 0.008 0.002 TRP F 94 HIS 0.011 0.002 HIS N 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (26648) covalent geometry : angle 0.69243 / 0.36 (36004) hydrogen bonds : bond 0.04807 / 3.17 ( 1853) hydrogen bonds : angle 4.43980 / 3.21 ( 5511) Misc. bond : bond 0.00003 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 286 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6551 (mt0) REVERT: C 49 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.7973 (t) REVERT: D 182 CYS cc_start: 0.7164 (p) cc_final: 0.6953 (t) REVERT: F 53 PHE cc_start: 0.6884 (m-10) cc_final: 0.6540 (m-10) REVERT: G 59 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.6565 (mt0) REVERT: H 49 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.7957 (t) REVERT: I 109 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8026 (t80) REVERT: L 59 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.6569 (mt0) REVERT: M 49 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.7969 (t) REVERT: N 109 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8018 (t80) REVERT: Q 59 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.6573 (mt0) REVERT: R 49 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.7976 (t) outliers start: 88 outliers final: 48 residues processed: 366 average time/residue: 0.1417 time to fit residues: 86.8960 Evaluate side-chains 318 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 89 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 275 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 299 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 98 ASN D 122 HIS H 98 ASN I 122 HIS M 98 ASN ** N 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 HIS R 98 ASN S 122 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.122051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098205 restraints weight = 66700.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097157 restraints weight = 69297.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097961 restraints weight = 64755.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098193 restraints weight = 52228.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098330 restraints weight = 49403.314| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26652 Z= 0.156 Angle : 0.644 10.500 36004 Z= 0.335 Chirality : 0.038 0.175 4056 Planarity : 0.004 0.042 4464 Dihedral : 6.565 59.335 3532 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.07 % Rotamer: Outliers : 3.05 % Allowed : 21.81 % Favored : 75.14 % 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: 1.41 (0.15), residues: 3104 helix: 1.48 (0.10), residues: 2448 sheet: None (None), residues: 0 loop : -1.06 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 94 TYR 0.019 0.002 TYR B 109 PHE 0.022 0.002 PHE L 165 TRP 0.007 0.001 TRP F 94 HIS 0.012 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (26648) covalent geometry : angle 0.64370 / 0.34 (36004) hydrogen bonds : bond 0.04384 / 2.90 ( 1853) hydrogen bonds : angle 4.28759 / 3.10 ( 5511) Misc. bond : bond 0.00005 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 316 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 HIS cc_start: 0.5086 (m90) cc_final: 0.4690 (m-70) REVERT: B 208 MET cc_start: 0.6345 (tpp) cc_final: 0.6016 (ppp) REVERT: C 49 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8003 (t) REVERT: D 9 GLN cc_start: 0.7578 (mt0) cc_final: 0.7331 (mt0) REVERT: D 109 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8017 (t80) REVERT: F 53 PHE cc_start: 0.6869 (m-10) cc_final: 0.6495 (m-10) REVERT: G 123 HIS cc_start: 0.5110 (m90) cc_final: 0.4707 (m-70) REVERT: G 208 MET cc_start: 0.6325 (tpp) cc_final: 0.6025 (ppp) REVERT: H 49 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.7984 (t) REVERT: I 9 GLN cc_start: 0.7750 (tt0) cc_final: 0.7490 (tt0) REVERT: L 123 HIS cc_start: 0.5062 (m90) cc_final: 0.4673 (m-70) REVERT: L 208 MET cc_start: 0.6350 (tpp) cc_final: 0.6027 (ppp) REVERT: M 49 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.7999 (t) REVERT: N 9 GLN cc_start: 0.7559 (mt0) cc_final: 0.7319 (mt0) REVERT: Q 123 HIS cc_start: 0.5082 (m90) cc_final: 0.4682 (m-70) REVERT: Q 208 MET cc_start: 0.6336 (tpp) cc_final: 0.6007 (ppp) REVERT: R 49 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8015 (t) REVERT: S 9 GLN cc_start: 0.7534 (mt0) cc_final: 0.7280 (mt0) REVERT: S 109 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8004 (t80) outliers start: 87 outliers final: 69 residues processed: 390 average time/residue: 0.1453 time to fit residues: 93.5835 Evaluate side-chains 359 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 284 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 109 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 189 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 0.0870 chunk 186 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 233 optimal weight: 0.9980 chunk 299 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 122 HIS ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN I 122 HIS ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 122 HIS ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN S 122 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.122340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097447 restraints weight = 66646.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097104 restraints weight = 66898.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097616 restraints weight = 61656.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097978 restraints weight = 54139.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098085 restraints weight = 50260.284| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26652 Z= 0.160 Angle : 0.635 10.767 36004 Z= 0.333 Chirality : 0.038 0.193 4056 Planarity : 0.004 0.052 4464 Dihedral : 6.513 59.387 3532 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.84 % Favored : 97.04 % Rotamer: Outliers : 3.26 % Allowed : 22.27 % Favored : 74.47 % 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: 1.43 (0.15), residues: 3104 helix: 1.50 (0.10), residues: 2448 sheet: None (None), residues: 0 loop : -1.09 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG S 227 TYR 0.020 0.002 TYR Q 109 PHE 0.022 0.002 PHE L 165 TRP 0.007 0.001 TRP A 94 HIS 0.014 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (26648) covalent geometry : angle 0.63550 / 0.33 (36004) hydrogen bonds : bond 0.04306 / 2.84 ( 1853) hydrogen bonds : angle 4.27577 / 3.09 ( 5511) Misc. bond : bond 0.00001 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 316 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 HIS cc_start: 0.5140 (m90) cc_final: 0.4692 (m-70) REVERT: B 208 MET cc_start: 0.6300 (tpp) cc_final: 0.5973 (ppp) REVERT: C 49 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.7956 (t) REVERT: F 53 PHE cc_start: 0.6831 (m-10) cc_final: 0.6522 (m-10) REVERT: G 123 HIS cc_start: 0.5136 (m90) cc_final: 0.4689 (m-70) REVERT: G 208 MET cc_start: 0.6311 (tpp) cc_final: 0.5979 (ppp) REVERT: H 49 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.7961 (t) REVERT: I 9 GLN cc_start: 0.7813 (tt0) cc_final: 0.7594 (tt0) REVERT: I 102 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7175 (t80) REVERT: I 109 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7992 (t80) REVERT: I 156 MET cc_start: 0.8075 (ttp) cc_final: 0.7843 (ttp) REVERT: L 123 HIS cc_start: 0.5116 (m90) cc_final: 0.4676 (m-70) REVERT: L 208 MET cc_start: 0.6303 (tpp) cc_final: 0.5974 (ppp) REVERT: M 49 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.7960 (t) REVERT: N 102 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7177 (t80) REVERT: N 109 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7981 (t80) REVERT: N 156 MET cc_start: 0.8084 (ttp) cc_final: 0.7845 (ttp) REVERT: Q 123 HIS cc_start: 0.5133 (m90) cc_final: 0.4685 (m-70) REVERT: Q 208 MET cc_start: 0.6304 (tpp) cc_final: 0.5976 (ppp) REVERT: R 49 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.7973 (t) REVERT: S 102 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7181 (t80) outliers start: 93 outliers final: 68 residues processed: 393 average time/residue: 0.1630 time to fit residues: 105.4093 Evaluate side-chains 358 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 281 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 102 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 252 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 9 GLN D 122 HIS ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN I 122 HIS ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 9 GLN N 122 HIS ** Q 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN S 9 GLN S 122 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096028 restraints weight = 66631.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095158 restraints weight = 68394.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095823 restraints weight = 67252.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096012 restraints weight = 53829.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096114 restraints weight = 50960.866| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26652 Z= 0.248 Angle : 0.726 11.300 36004 Z= 0.374 Chirality : 0.042 0.197 4056 Planarity : 0.005 0.050 4464 Dihedral : 6.667 59.769 3532 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 2.91 % Allowed : 22.86 % Favored : 74.23 % 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: 1.16 (0.15), residues: 3104 helix: 1.32 (0.10), residues: 2448 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 227 TYR 0.018 0.002 TYR Q 109 PHE 0.043 0.003 PHE N 126 TRP 0.008 0.002 TRP C 70 HIS 0.014 0.002 HIS I 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (26648) covalent geometry : angle 0.72572 / 0.37 (36004) hydrogen bonds : bond 0.04765 / 3.14 ( 1853) hydrogen bonds : angle 4.50136 / 3.25 ( 5511) Misc. bond : bond 0.00001 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 271 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 HIS cc_start: 0.5006 (m90) cc_final: 0.4645 (m-70) REVERT: B 208 MET cc_start: 0.6290 (tpp) cc_final: 0.6016 (ppp) REVERT: C 49 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8006 (t) REVERT: F 53 PHE cc_start: 0.6954 (m-10) cc_final: 0.6467 (m-10) REVERT: G 123 HIS cc_start: 0.4980 (m90) cc_final: 0.4640 (m-70) REVERT: G 208 MET cc_start: 0.6289 (tpp) cc_final: 0.6015 (ppp) REVERT: H 49 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.7993 (t) REVERT: I 9 GLN cc_start: 0.7894 (tt0) cc_final: 0.7599 (tt0) REVERT: I 102 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.7271 (t80) REVERT: I 109 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8027 (t80) REVERT: L 123 HIS cc_start: 0.4963 (m90) cc_final: 0.4617 (m-70) REVERT: L 208 MET cc_start: 0.6305 (tpp) cc_final: 0.6015 (ppp) REVERT: M 49 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8010 (t) REVERT: N 102 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.7242 (t80) REVERT: N 109 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8025 (t80) REVERT: Q 123 HIS cc_start: 0.5003 (m90) cc_final: 0.4641 (m-70) REVERT: Q 208 MET cc_start: 0.6265 (tpp) cc_final: 0.5997 (ppp) REVERT: R 49 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8006 (t) REVERT: S 102 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7258 (t80) outliers start: 83 outliers final: 66 residues processed: 342 average time/residue: 0.1538 time to fit residues: 88.9628 Evaluate side-chains 334 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 259 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain N residue 122 HIS Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain S residue 122 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 38 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 270 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 238 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 122 HIS ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN I 122 HIS ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 122 HIS ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN S 122 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097983 restraints weight = 66350.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.097461 restraints weight = 65943.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098115 restraints weight = 64344.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.098287 restraints weight = 51437.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098423 restraints weight = 47376.108| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26652 Z= 0.170 Angle : 0.677 12.018 36004 Z= 0.353 Chirality : 0.039 0.209 4056 Planarity : 0.004 0.056 4464 Dihedral : 6.552 59.155 3532 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 3.01 % Allowed : 23.11 % Favored : 73.88 % 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: 1.27 (0.15), residues: 3104 helix: 1.42 (0.10), residues: 2448 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 227 TYR 0.021 0.002 TYR Q 109 PHE 0.041 0.003 PHE D 236 TRP 0.007 0.001 TRP R 70 HIS 0.016 0.002 HIS I 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (26648) covalent geometry : angle 0.67744 / 0.35 (36004) hydrogen bonds : bond 0.04448 / 2.93 ( 1853) hydrogen bonds : angle 4.38238 / 3.17 ( 5511) Misc. bond : bond 0.00003 / 0.00 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 293 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 HIS cc_start: 0.4910 (m90) cc_final: 0.4593 (m-70) REVERT: B 208 MET cc_start: 0.6303 (tpp) cc_final: 0.6024 (ppp) REVERT: C 49 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.7948 (t) REVERT: D 102 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7649 (t80) REVERT: G 123 HIS cc_start: 0.4883 (m90) cc_final: 0.4581 (m-70) REVERT: G 208 MET cc_start: 0.6306 (tpp) cc_final: 0.6028 (ppp) REVERT: H 49 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.7939 (t) REVERT: I 102 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7196 (t80) REVERT: I 109 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.7826 (t80) REVERT: L 123 HIS cc_start: 0.4832 (m90) cc_final: 0.4543 (m-70) REVERT: L 208 MET cc_start: 0.6296 (tpp) cc_final: 0.6025 (ppp) REVERT: M 49 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.7951 (t) REVERT: N 102 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7171 (t80) REVERT: N 109 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7806 (t80) REVERT: Q 123 HIS cc_start: 0.4884 (m90) cc_final: 0.4571 (m-70) REVERT: Q 208 MET cc_start: 0.6264 (tpp) cc_final: 0.6007 (ppp) REVERT: R 49 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.7948 (t) REVERT: S 102 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7134 (t80) outliers start: 86 outliers final: 72 residues processed: 363 average time/residue: 0.1564 time to fit residues: 95.3779 Evaluate side-chains 351 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain N residue 122 HIS Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain S residue 122 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 166 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 294 optimal weight: 0.0870 chunk 298 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 122 HIS D 128 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN I 122 HIS I 232 HIS ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 122 HIS N 232 HIS ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN S 122 HIS S 128 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.123941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.099538 restraints weight = 65595.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099369 restraints weight = 66650.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100007 restraints weight = 57891.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100265 restraints weight = 50727.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100326 restraints weight = 47313.366| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26652 Z= 0.136 Angle : 0.643 11.843 36004 Z= 0.340 Chirality : 0.038 0.341 4056 Planarity : 0.004 0.054 4464 Dihedral : 6.379 59.536 3532 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.24 % Allowed : 24.68 % Favored : 73.07 % 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: 1.46 (0.15), residues: 3104 helix: 1.55 (0.10), residues: 2448 sheet: None (None), residues: 0 loop : -1.21 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 227 TYR 0.017 0.001 TYR L 109 PHE 0.044 0.003 PHE D 236 TRP 0.008 0.001 TRP R 70 HIS 0.007 0.001 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (26648) covalent geometry : angle 0.64327 / 0.34 (36004) hydrogen bonds : bond 0.04143 / 2.73 ( 1853) hydrogen bonds : angle 4.25949 / 3.08 ( 5511) Misc. bond : bond 0.00001 / 0.00 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3805.97 seconds wall clock time: 67 minutes 49.88 seconds (4069.88 seconds total)