Starting phenix.real_space_refine on Wed Mar 4 16:47:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy4_11549/03_2026/6zy4_11549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy4_11549/03_2026/6zy4_11549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zy4_11549/03_2026/6zy4_11549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy4_11549/03_2026/6zy4_11549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy4_11549/03_2026/6zy4_11549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy4_11549/03_2026/6zy4_11549.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9597 2.51 5 N 2504 2.21 5 O 2726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14902 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1013 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 793 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 999 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 999 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "K" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 794 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 941 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 724 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 734 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1982 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 243} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1972 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 243} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1946 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1949 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.26, per 1000 atoms: 0.22 Number of scatterers: 14902 At special positions: 0 Unit cell: (99.372, 126.75, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 4 15.00 Mg 2 11.99 O 2726 8.00 N 2504 7.00 C 9597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 750.8 milliseconds 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3610 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 24 sheets defined 35.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.572A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 26 removed outlier: 3.621A pdb=" N LEU A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 152 removed outlier: 3.653A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 152 removed outlier: 3.737A pdb=" N ILE D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 24 removed outlier: 3.865A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE I 13 " --> pdb=" O TRP I 9 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.622A pdb=" N LEU I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 23 removed outlier: 3.662A pdb=" N ILE J 8 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 16 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 Processing helix chain 'K' and resid 142 through 152 removed outlier: 3.545A pdb=" N LEU K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY K 148 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN K 149 " --> pdb=" O ASP K 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 24 removed outlier: 4.029A pdb=" N ILE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE L 13 " --> pdb=" O TRP L 9 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 152 removed outlier: 3.689A pdb=" N LEU L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.786A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.016A pdb=" N GLU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.934A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.926A pdb=" N THR F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.636A pdb=" N VAL F 106 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 107 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 4.125A pdb=" N GLU F 112 " --> pdb=" O TYR F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 126 removed outlier: 3.506A pdb=" N HIS F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 130 removed outlier: 3.853A pdb=" N GLU F 130 " --> pdb=" O MET F 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 127 through 130' Processing helix chain 'F' and resid 148 through 157 removed outlier: 3.685A pdb=" N ARG F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 removed outlier: 4.348A pdb=" N GLY F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL F 184 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.717A pdb=" N VAL F 208 " --> pdb=" O ASP F 204 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 204 through 209' Processing helix chain 'F' and resid 240 through 245 Processing helix chain 'G' and resid 47 through 56 removed outlier: 4.035A pdb=" N LEU G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 85 removed outlier: 3.985A pdb=" N TYR G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR G 82 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS G 85 " --> pdb=" O TYR G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 107 removed outlier: 3.750A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA G 107 " --> pdb=" O PHE G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 126 removed outlier: 3.507A pdb=" N HIS G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET G 126 " --> pdb=" O HIS G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 133 removed outlier: 3.963A pdb=" N VAL G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 157 removed outlier: 3.762A pdb=" N ARG G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG G 157 " --> pdb=" O ALA G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 181 removed outlier: 3.523A pdb=" N GLY G 181 " --> pdb=" O PRO G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 192 removed outlier: 3.730A pdb=" N LEU G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 245 removed outlier: 3.672A pdb=" N LEU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP G 245 " --> pdb=" O ARG G 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 240 through 245' Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.554A pdb=" N HIS E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 29 removed outlier: 3.552A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY E 24 " --> pdb=" O PHE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 58 through 74 removed outlier: 3.581A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 72 " --> pdb=" O MET E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.602A pdb=" N LEU E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 removed outlier: 3.877A pdb=" N LEU E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 97' Processing helix chain 'E' and resid 99 through 112 removed outlier: 3.565A pdb=" N VAL E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.540A pdb=" N THR E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 120 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 136 removed outlier: 4.032A pdb=" N MET E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E 136 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 150 through 175 removed outlier: 3.673A pdb=" N LEU E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Proline residue: E 156 - end of helix removed outlier: 3.668A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 166 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL E 173 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.971A pdb=" N MET E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 200 through 205 removed outlier: 3.697A pdb=" N LYS E 205 " --> pdb=" O ASN E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 223 removed outlier: 3.778A pdb=" N THR E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 247 removed outlier: 3.675A pdb=" N THR E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 11 Processing helix chain 'H' and resid 11 through 29 removed outlier: 3.540A pdb=" N LYS H 15 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY H 21 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY H 24 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 48 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.934A pdb=" N GLY H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU H 70 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 86 Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 99 through 112 removed outlier: 3.707A pdb=" N VAL H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA H 105 " --> pdb=" O PRO H 101 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 128 through 134 removed outlier: 3.675A pdb=" N MET H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 134' Processing helix chain 'H' and resid 144 through 153 removed outlier: 3.953A pdb=" N ILE H 153 " --> pdb=" O TRP H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 175 removed outlier: 3.742A pdb=" N ALA H 164 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY H 166 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE H 167 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL H 173 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 175 " --> pdb=" O SER H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 189 removed outlier: 4.047A pdb=" N MET H 189 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 206 removed outlier: 3.573A pdb=" N LEU H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE H 204 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 221 removed outlier: 3.820A pdb=" N THR H 212 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE H 216 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE H 219 " --> pdb=" O TRP H 215 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 247 removed outlier: 4.389A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER H 242 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU H 244 " --> pdb=" O VAL H 240 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA H 245 " --> pdb=" O HIS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 255 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 removed outlier: 7.268A pdb=" N THR A 83 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE A 71 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG A 81 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N ILE A 134 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR A 43 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.014A pdb=" N VAL A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 60 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 66 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 59 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 99 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 60 removed outlier: 6.853A pdb=" N VAL D 58 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 63 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLY D 66 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU D 87 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP D 70 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 83 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 72 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ILE D 134 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR D 43 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 110 through 115 removed outlier: 3.520A pdb=" N ALA D 113 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 100 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU D 99 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 40 through 41 removed outlier: 3.903A pdb=" N TYR I 40 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 86 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL I 68 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 40 through 41 removed outlier: 3.903A pdb=" N TYR I 40 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 86 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR I 43 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.080A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 110 through 115 removed outlier: 6.320A pdb=" N LEU I 99 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 39 through 41 removed outlier: 3.615A pdb=" N THR J 83 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP J 70 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL J 68 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU J 87 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY J 66 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL J 58 " --> pdb=" O VAL J 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 43 through 44 removed outlier: 7.033A pdb=" N TYR J 43 " --> pdb=" O ILE J 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 40 through 41 removed outlier: 3.778A pdb=" N TYR K 40 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 71 through 73 removed outlier: 7.357A pdb=" N TYR K 43 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 64 through 66 removed outlier: 6.769A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER K 59 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 100 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU K 99 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 71 through 73 removed outlier: 3.601A pdb=" N LEU L 84 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ILE L 134 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR L 43 " --> pdb=" O ILE L 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 64 through 67 removed outlier: 3.865A pdb=" N GLY L 66 " --> pdb=" O VAL L 58 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU L 114 " --> pdb=" O PRO L 57 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AB8, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AB9, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AC1, first strand: chain 'F' and resid 28 through 30 removed outlier: 3.579A pdb=" N GLU F 64 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 165 through 168 removed outlier: 3.541A pdb=" N ILE F 166 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS F 214 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 218 through 219 removed outlier: 3.511A pdb=" N ALA F 219 " --> pdb=" O LYS F 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 7 through 11 removed outlier: 4.953A pdb=" N VAL G 9 " --> pdb=" O VAL G 31 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL G 31 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET G 11 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 29 " --> pdb=" O MET G 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 165 through 168 removed outlier: 3.621A pdb=" N HIS G 214 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 218 through 219 361 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4759 1.34 - 1.46: 2897 1.46 - 1.58: 7373 1.58 - 1.69: 6 1.69 - 1.81: 126 Bond restraints: 15161 Sorted by residual: bond pdb=" C TYR F 108 " pdb=" N PRO F 109 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C GLU K 37 " pdb=" N PRO K 38 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" CA THR J 39 " pdb=" C THR J 39 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.08e-02 8.57e+03 2.71e+00 bond pdb=" CA GLY B 11 " pdb=" C GLY B 11 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.34e+00 bond pdb=" N PHE G 172 " pdb=" CA PHE G 172 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.05e+00 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 20385 3.12 - 6.24: 204 6.24 - 9.36: 29 9.36 - 12.48: 9 12.48 - 15.61: 2 Bond angle restraints: 20629 Sorted by residual: angle pdb=" CA LEU F 265 " pdb=" CB LEU F 265 " pdb=" CG LEU F 265 " ideal model delta sigma weight residual 116.30 131.91 -15.61 3.50e+00 8.16e-02 1.99e+01 angle pdb=" N VAL F 205 " pdb=" CA VAL F 205 " pdb=" C VAL F 205 " ideal model delta sigma weight residual 108.88 118.36 -9.48 2.16e+00 2.14e-01 1.93e+01 angle pdb=" CA LEU G 265 " pdb=" CB LEU G 265 " pdb=" CG LEU G 265 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 angle pdb=" C ASP G 220 " pdb=" N LYS G 221 " pdb=" CA LYS G 221 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C ALA F 107 " pdb=" N TYR F 108 " pdb=" CA TYR F 108 " ideal model delta sigma weight residual 120.58 125.62 -5.04 1.32e+00 5.74e-01 1.46e+01 ... (remaining 20624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 8788 31.94 - 63.88: 205 63.88 - 95.83: 8 95.83 - 127.77: 2 127.77 - 159.71: 4 Dihedral angle restraints: 9007 sinusoidal: 3385 harmonic: 5622 Sorted by residual: dihedral pdb=" C5' ADP G 301 " pdb=" O5' ADP G 301 " pdb=" PA ADP G 301 " pdb=" O2A ADP G 301 " ideal model delta sinusoidal sigma weight residual -60.00 99.71 -159.71 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP F 301 " pdb=" O5' ADP F 301 " pdb=" PA ADP F 301 " pdb=" O2A ADP F 301 " ideal model delta sinusoidal sigma weight residual -60.00 99.68 -159.68 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP G 301 " pdb=" O3A ADP G 301 " pdb=" PA ADP G 301 " pdb=" PB ADP G 301 " ideal model delta sinusoidal sigma weight residual -60.00 74.69 -134.69 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 9004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1945 0.051 - 0.101: 434 0.101 - 0.152: 115 0.152 - 0.202: 25 0.202 - 0.253: 2 Chirality restraints: 2521 Sorted by residual: chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE G 65 " pdb=" CA ILE G 65 " pdb=" CG1 ILE G 65 " pdb=" CG2 ILE G 65 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2518 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 145 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO E 146 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 205 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO G 206 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO G 206 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 206 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 145 " -0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO H 146 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " -0.030 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4650 2.83 - 3.35: 11934 3.35 - 3.87: 23578 3.87 - 4.38: 25608 4.38 - 4.90: 43735 Nonbonded interactions: 109505 Sorted by model distance: nonbonded pdb=" OG1 THR I 39 " pdb=" O ILE I 86 " model vdw 2.314 3.040 nonbonded pdb=" O ASN B 89 " pdb=" OH TYR G 261 " model vdw 2.322 3.040 nonbonded pdb=" O LEU H 90 " pdb=" OG SER H 94 " model vdw 2.323 3.040 nonbonded pdb=" O ILE H 58 " pdb=" OG SER H 62 " model vdw 2.331 3.040 nonbonded pdb=" O ILE E 58 " pdb=" OG SER E 62 " model vdw 2.333 3.040 ... (remaining 109500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 25 or resid 40 through 69 or (resid 70 through 7 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 73 or (resid \ 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or r \ esid 86 or (resid 87 through 88 and (name N or name CA or name C or name O or na \ me CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or name CA o \ r name C or name O or name CB )) or resid 93 through 94 or (resid 95 and (name N \ or name CA or name C or name O or name CB )) or resid 96 through 108 or (resid \ 109 and (name N or name CA or name C or name O or name CB )) or resid 110 throug \ h 116 or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 140 or (resid 141 and (name N or name CA or name C or name O o \ r name CB )) or resid 142 through 143 or (resid 144 through 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 152)) selection = (chain 'I' and (resid 3 through 25 or resid 40 through 66 or (resid 67 and (name \ N or name CA or name C or name O or name CB )) or resid 68 through 71 or (resid \ 72 and (name N or name CA or name C or name O or name CB )) or resid 73 or (res \ id 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (r \ esid 76 and (name N or name CA or name C or name O or name CB )) or resid 77 thr \ ough 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or \ resid 86 through 87 or (resid 88 and (name N or name CA or name C or name O or \ name CB )) or resid 89 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 116 or (resid 130 throu \ gh 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thr \ ough 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) \ or resid 142 or (resid 143 through 145 and (name N or name CA or name C or name \ O or name CB )) or resid 146 through 152)) selection = (chain 'J' and (resid 3 through 25 or resid 40 through 70 or (resid 71 through 7 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 73 or (resid \ 74 and (name N or name CA or name C or name O or name CB )) or resid 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 86 or (resid 87 through 88 and (name N or name CA or name C or name O or name \ CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 116 or (resid 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 or (resid 132 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 142 or (r \ esid 143 through 145 and (name N or name CA or name C or name O or name CB )) or \ resid 146 through 152)) selection = (chain 'L' and (resid 3 through 25 or resid 40 through 66 or (resid 67 and (name \ N or name CA or name C or name O or name CB )) or resid 68 through 70 or (resid \ 71 through 72 and (name N or name CA or name C or name O or name CB )) or resid \ 73 through 84 or (resid 85 and (name N or name CA or name C or name O or name C \ B )) or resid 86 or (resid 87 through 88 and (name N or name CA or name C or nam \ e O or name CB )) or resid 89 through 90 or (resid 91 through 92 and (name N or \ name CA or name C or name O or name CB )) or resid 93 through 116 or (resid 130 \ and (name N or name CA or name C or name O or name CB )) or resid 131 through 14 \ 0 or (resid 141 and (name N or name CA or name C or name O or name CB )) or resi \ d 142 through 143 or (resid 144 through 145 and (name N or name CA or name C or \ name O or name CB )) or resid 146 through 152)) } ncs_group { reference = (chain 'B' and (resid 4 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB )) or resid 98)) selection = (chain 'C' and (resid 4 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 98)) } ncs_group { reference = (chain 'D' and (resid 37 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 88 or (resid 89 and ( \ name N or name CA or name C or name O or name CB )) or resid 90 through 94 or (r \ esid 95 and (name N or name CA or name C or name O or name CB )) or resid 96 thr \ ough 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) \ or resid 108 through 117 or (resid 129 and (name N or name CA or name C or name \ O or name CB )) or resid 130 through 152)) selection = (chain 'K' and (resid 37 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 117 or resid 129 through 152)) } ncs_group { reference = chain 'E' selection = (chain 'H' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 through 259)) } ncs_group { reference = (chain 'F' and (resid 6 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 134 or (resid 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 302)) selection = (chain 'G' and (resid 6 through 248 or (resid 249 and (name N or name CA or name \ C or name O or name CB )) or resid 250 through 302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.003 0.044 15161 Z= 0.155 Angle : 0.797 15.605 20629 Z= 0.393 Chirality : 0.049 0.253 2521 Planarity : 0.005 0.057 2568 Dihedral : 13.498 159.710 5397 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % 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: -5.91 (0.13), residues: 1934 helix: -5.17 (0.04), residues: 649 sheet: -3.13 (0.27), residues: 233 loop : -3.32 (0.15), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 102 TYR 0.010 0.001 TYR I 40 PHE 0.008 0.001 PHE G 172 TRP 0.015 0.001 TRP H 195 HIS 0.004 0.000 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00292 (15161) covalent geometry : angle 0.79741 (20629) hydrogen bonds : bond 0.34396 ( 361) hydrogen bonds : angle 10.92594 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 0.539 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8991 (m-10) cc_final: 0.8748 (m-10) REVERT: A 46 PHE cc_start: 0.7031 (m-80) cc_final: 0.6753 (m-80) REVERT: A 95 ASP cc_start: 0.7357 (p0) cc_final: 0.6830 (p0) REVERT: A 138 LYS cc_start: 0.8110 (tttt) cc_final: 0.7642 (tptp) REVERT: A 141 MET cc_start: 0.7644 (mmt) cc_final: 0.7279 (tpt) REVERT: A 144 GLU cc_start: 0.7877 (pp20) cc_final: 0.7567 (mp0) REVERT: D 43 TYR cc_start: 0.8898 (m-80) cc_final: 0.8535 (m-80) REVERT: D 95 ASP cc_start: 0.5560 (m-30) cc_final: 0.4095 (t0) REVERT: D 136 ASP cc_start: 0.8096 (t0) cc_final: 0.7821 (m-30) REVERT: I 7 GLU cc_start: 0.8919 (pt0) cc_final: 0.7666 (tm-30) REVERT: I 8 ILE cc_start: 0.9530 (mt) cc_final: 0.8700 (mt) REVERT: I 60 ILE cc_start: 0.9209 (mt) cc_final: 0.8784 (tt) REVERT: J 4 LYS cc_start: 0.7840 (tppt) cc_final: 0.7221 (tttt) REVERT: J 60 ILE cc_start: 0.9125 (pt) cc_final: 0.8683 (mm) REVERT: J 92 HIS cc_start: 0.8173 (m90) cc_final: 0.7878 (m-70) REVERT: J 102 ARG cc_start: 0.9164 (mtt180) cc_final: 0.8433 (ttp-110) REVERT: J 111 TYR cc_start: 0.8752 (p90) cc_final: 0.8504 (p90) REVERT: J 138 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6301 (tptp) REVERT: K 53 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8085 (mmtt) REVERT: K 145 ASP cc_start: 0.9274 (m-30) cc_final: 0.8942 (p0) REVERT: L 85 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7721 (mp0) REVERT: B 8 MET cc_start: 0.8986 (tpt) cc_final: 0.8737 (tpp) REVERT: B 87 LEU cc_start: 0.9413 (tp) cc_final: 0.9187 (tp) REVERT: B 89 ASN cc_start: 0.9327 (t0) cc_final: 0.8953 (t0) REVERT: C 8 MET cc_start: 0.7718 (tpt) cc_final: 0.7303 (tpp) REVERT: C 23 ASP cc_start: 0.8201 (m-30) cc_final: 0.7929 (p0) REVERT: C 52 THR cc_start: 0.8380 (t) cc_final: 0.7645 (t) REVERT: F 24 PHE cc_start: 0.8626 (m-80) cc_final: 0.8345 (m-80) REVERT: F 29 LEU cc_start: 0.8778 (mm) cc_final: 0.8556 (mm) REVERT: F 35 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8010 (mmmt) REVERT: F 47 LYS cc_start: 0.8042 (mmmm) cc_final: 0.7635 (mptt) REVERT: F 84 ARG cc_start: 0.8812 (ttm170) cc_final: 0.8453 (ptp-110) REVERT: F 165 LEU cc_start: 0.9378 (tp) cc_final: 0.8738 (tp) REVERT: F 184 VAL cc_start: 0.8300 (p) cc_final: 0.8081 (p) REVERT: F 207 GLU cc_start: 0.8362 (mp0) cc_final: 0.7903 (mp0) REVERT: F 261 TYR cc_start: 0.6251 (t80) cc_final: 0.5850 (t80) REVERT: G 26 ASN cc_start: 0.7697 (t0) cc_final: 0.7460 (m-40) REVERT: G 40 MET cc_start: 0.8444 (mpp) cc_final: 0.8146 (mpp) REVERT: G 103 PHE cc_start: 0.8059 (t80) cc_final: 0.7640 (t80) REVERT: G 115 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8511 (pm20) REVERT: G 127 MET cc_start: 0.8302 (ptp) cc_final: 0.7919 (ptp) REVERT: E 119 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7089 (tm-30) REVERT: E 123 MET cc_start: 0.8200 (mtp) cc_final: 0.7970 (mtm) REVERT: E 135 MET cc_start: 0.8261 (mtm) cc_final: 0.8032 (mtm) REVERT: E 178 LYS cc_start: 0.8816 (tppt) cc_final: 0.8579 (mmmm) REVERT: E 185 PHE cc_start: 0.8076 (t80) cc_final: 0.7767 (t80) REVERT: E 205 LYS cc_start: 0.8817 (ptpt) cc_final: 0.8308 (ptmt) REVERT: E 219 PHE cc_start: 0.8900 (t80) cc_final: 0.8678 (t80) REVERT: E 223 ASP cc_start: 0.8473 (t0) cc_final: 0.7696 (t70) REVERT: H 47 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8748 (tp40) REVERT: H 54 LEU cc_start: 0.8893 (mt) cc_final: 0.8348 (mt) REVERT: H 58 ILE cc_start: 0.9390 (pt) cc_final: 0.9157 (tp) REVERT: H 134 MET cc_start: 0.7786 (ptm) cc_final: 0.6621 (ppp) REVERT: H 149 TRP cc_start: 0.8650 (m100) cc_final: 0.8245 (m-10) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.1403 time to fit residues: 125.6340 Evaluate side-chains 393 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 115 ASN L 135 GLN B 75 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 75 GLN F 105 ASN F 214 HIS G 105 ASN G 113 HIS G 235 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.092505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.070726 restraints weight = 61542.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.072574 restraints weight = 40454.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.073875 restraints weight = 29407.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.074775 restraints weight = 23072.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.075551 restraints weight = 19275.901| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15161 Z= 0.157 Angle : 0.684 10.558 20629 Z= 0.334 Chirality : 0.044 0.203 2521 Planarity : 0.005 0.061 2568 Dihedral : 8.313 155.210 2121 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % 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: -4.51 (0.15), residues: 1934 helix: -3.41 (0.14), residues: 652 sheet: -2.84 (0.27), residues: 256 loop : -2.74 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 111 TYR 0.021 0.001 TYR F 261 PHE 0.034 0.002 PHE F 254 TRP 0.013 0.001 TRP H 168 HIS 0.011 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00334 (15161) covalent geometry : angle 0.68357 (20629) hydrogen bonds : bond 0.03647 ( 361) hydrogen bonds : angle 5.61605 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 465 time to evaluate : 0.682 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7070 (pt) cc_final: 0.6123 (tt) REVERT: A 138 LYS cc_start: 0.8102 (tttt) cc_final: 0.7677 (tppt) REVERT: A 141 MET cc_start: 0.7872 (mmt) cc_final: 0.7493 (tpt) REVERT: D 43 TYR cc_start: 0.8792 (m-80) cc_final: 0.8448 (m-80) REVERT: D 95 ASP cc_start: 0.5698 (m-30) cc_final: 0.4668 (t0) REVERT: I 138 LYS cc_start: 0.8867 (tptp) cc_final: 0.8574 (mmtm) REVERT: I 150 PHE cc_start: 0.7283 (m-80) cc_final: 0.6831 (m-80) REVERT: J 4 LYS cc_start: 0.7822 (tppt) cc_final: 0.7283 (tttt) REVERT: J 92 HIS cc_start: 0.8042 (m90) cc_final: 0.7675 (m-70) REVERT: J 102 ARG cc_start: 0.8713 (mtt180) cc_final: 0.8419 (ttm170) REVERT: J 111 TYR cc_start: 0.8624 (p90) cc_final: 0.8307 (p90) REVERT: J 138 LYS cc_start: 0.7413 (mmtt) cc_final: 0.6527 (tptp) REVERT: K 53 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8375 (mmtt) REVERT: L 85 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7532 (mp0) REVERT: L 135 GLN cc_start: 0.7684 (mm110) cc_final: 0.7315 (pm20) REVERT: B 60 HIS cc_start: 0.8094 (m-70) cc_final: 0.7865 (m170) REVERT: B 87 LEU cc_start: 0.9421 (tp) cc_final: 0.9189 (tp) REVERT: C 8 MET cc_start: 0.8080 (tpt) cc_final: 0.7848 (tpt) REVERT: C 23 ASP cc_start: 0.8136 (m-30) cc_final: 0.7853 (p0) REVERT: F 47 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7809 (mptt) REVERT: F 85 LYS cc_start: 0.8601 (pttt) cc_final: 0.8375 (ptpp) REVERT: F 130 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7490 (tp30) REVERT: F 165 LEU cc_start: 0.9125 (tp) cc_final: 0.8626 (tp) REVERT: F 180 MET cc_start: 0.8681 (mmp) cc_final: 0.8368 (mmm) REVERT: F 183 LEU cc_start: 0.9402 (mp) cc_final: 0.9028 (mt) REVERT: G 35 LYS cc_start: 0.8394 (mmtm) cc_final: 0.7920 (mmmt) REVERT: G 40 MET cc_start: 0.8212 (mpp) cc_final: 0.7773 (mpp) REVERT: G 90 LEU cc_start: 0.9401 (pp) cc_final: 0.8901 (pp) REVERT: G 98 THR cc_start: 0.8822 (p) cc_final: 0.8455 (t) REVERT: G 126 MET cc_start: 0.8245 (mmm) cc_final: 0.7854 (mmm) REVERT: G 127 MET cc_start: 0.8286 (ptp) cc_final: 0.7851 (ptp) REVERT: E 68 MET cc_start: 0.8590 (mtp) cc_final: 0.8037 (mtp) REVERT: E 127 GLU cc_start: 0.8576 (tp30) cc_final: 0.8216 (tp30) REVERT: E 205 LYS cc_start: 0.8823 (ptpt) cc_final: 0.8322 (ptmt) REVERT: E 220 ASN cc_start: 0.9323 (m-40) cc_final: 0.9089 (m-40) REVERT: E 223 ASP cc_start: 0.8228 (t0) cc_final: 0.7153 (t0) REVERT: H 29 ASN cc_start: 0.9110 (m110) cc_final: 0.8712 (m110) REVERT: H 72 LEU cc_start: 0.9379 (mm) cc_final: 0.9170 (mm) REVERT: H 93 LEU cc_start: 0.8682 (tt) cc_final: 0.8423 (tp) REVERT: H 127 GLU cc_start: 0.8290 (mp0) cc_final: 0.7853 (mp0) REVERT: H 149 TRP cc_start: 0.8542 (m100) cc_final: 0.8242 (m-10) REVERT: H 201 ASN cc_start: 0.8024 (t0) cc_final: 0.7792 (t0) REVERT: H 205 LYS cc_start: 0.8840 (pttm) cc_final: 0.8390 (pttp) REVERT: H 220 ASN cc_start: 0.9183 (m-40) cc_final: 0.8747 (m-40) outliers start: 2 outliers final: 0 residues processed: 466 average time/residue: 0.1218 time to fit residues: 83.4303 Evaluate side-chains 346 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 179 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 148 optimal weight: 0.0980 chunk 130 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS K 48 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN F 105 ASN F 242 GLN G 235 ASN E 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.090464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.069062 restraints weight = 60842.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070920 restraints weight = 40033.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.072283 restraints weight = 29066.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.073253 restraints weight = 22691.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.073911 restraints weight = 18674.249| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 15161 Z= 0.112 Angle : 0.619 9.468 20629 Z= 0.293 Chirality : 0.042 0.156 2521 Planarity : 0.004 0.043 2568 Dihedral : 7.944 144.336 2121 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.67 % 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: -3.68 (0.17), residues: 1934 helix: -2.28 (0.18), residues: 678 sheet: -2.51 (0.29), residues: 253 loop : -2.53 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 111 TYR 0.012 0.001 TYR D 40 PHE 0.018 0.001 PHE E 148 TRP 0.014 0.001 TRP C 29 HIS 0.007 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00261 (15161) covalent geometry : angle 0.61926 (20629) hydrogen bonds : bond 0.02975 ( 361) hydrogen bonds : angle 4.90019 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 436 time to evaluate : 0.566 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7255 (pt) cc_final: 0.6386 (tt) REVERT: A 138 LYS cc_start: 0.8085 (tttt) cc_final: 0.7533 (tppt) REVERT: A 141 MET cc_start: 0.7901 (mmt) cc_final: 0.7584 (tpt) REVERT: A 144 GLU cc_start: 0.8846 (tt0) cc_final: 0.7724 (mp0) REVERT: D 43 TYR cc_start: 0.8781 (m-80) cc_final: 0.8469 (m-80) REVERT: D 95 ASP cc_start: 0.5645 (m-30) cc_final: 0.4672 (t0) REVERT: D 144 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8195 (mt-10) REVERT: I 7 GLU cc_start: 0.8850 (pt0) cc_final: 0.7364 (tm-30) REVERT: I 111 TYR cc_start: 0.9150 (p90) cc_final: 0.8895 (p90) REVERT: I 138 LYS cc_start: 0.8795 (tptp) cc_final: 0.8566 (mmtm) REVERT: I 150 PHE cc_start: 0.7216 (m-80) cc_final: 0.6782 (m-80) REVERT: J 4 LYS cc_start: 0.7857 (tppt) cc_final: 0.7291 (ttpt) REVERT: J 92 HIS cc_start: 0.8024 (m90) cc_final: 0.7659 (m-70) REVERT: J 102 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8552 (ttm110) REVERT: J 138 LYS cc_start: 0.7262 (mmtt) cc_final: 0.6342 (tptp) REVERT: L 85 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7519 (mp0) REVERT: L 102 ARG cc_start: 0.9116 (mmt90) cc_final: 0.8901 (mtp85) REVERT: L 114 LEU cc_start: 0.7624 (mm) cc_final: 0.7188 (mm) REVERT: L 146 LEU cc_start: 0.8596 (mt) cc_final: 0.8366 (mt) REVERT: B 60 HIS cc_start: 0.8057 (m-70) cc_final: 0.7700 (m-70) REVERT: B 88 TYR cc_start: 0.8862 (m-80) cc_final: 0.8655 (m-10) REVERT: C 8 MET cc_start: 0.8046 (tpt) cc_final: 0.7785 (tpt) REVERT: C 17 SER cc_start: 0.8788 (m) cc_final: 0.8459 (p) REVERT: C 23 ASP cc_start: 0.8453 (m-30) cc_final: 0.7959 (p0) REVERT: F 47 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7951 (mptt) REVERT: F 130 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7571 (tp30) REVERT: F 165 LEU cc_start: 0.8935 (tp) cc_final: 0.8505 (tp) REVERT: F 180 MET cc_start: 0.8764 (mmp) cc_final: 0.8415 (mmm) REVERT: F 183 LEU cc_start: 0.9450 (mp) cc_final: 0.9243 (mm) REVERT: G 40 MET cc_start: 0.8326 (mpp) cc_final: 0.7767 (mpp) REVERT: G 75 MET cc_start: 0.6406 (ptt) cc_final: 0.5882 (ptt) REVERT: G 90 LEU cc_start: 0.9300 (pp) cc_final: 0.8816 (pp) REVERT: G 101 ASN cc_start: 0.8976 (t0) cc_final: 0.8299 (t0) REVERT: G 127 MET cc_start: 0.8253 (ptp) cc_final: 0.7820 (ptp) REVERT: E 46 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8431 (tpm170) REVERT: E 68 MET cc_start: 0.8526 (mtp) cc_final: 0.8173 (mtp) REVERT: E 127 GLU cc_start: 0.8545 (tp30) cc_final: 0.8155 (tp30) REVERT: E 133 GLU cc_start: 0.8909 (pp20) cc_final: 0.8482 (tm-30) REVERT: E 204 ILE cc_start: 0.9269 (pt) cc_final: 0.9056 (pt) REVERT: E 220 ASN cc_start: 0.9362 (m-40) cc_final: 0.9157 (m-40) REVERT: E 223 ASP cc_start: 0.8202 (t0) cc_final: 0.7476 (t70) REVERT: H 72 LEU cc_start: 0.9474 (mm) cc_final: 0.9152 (mm) REVERT: H 127 GLU cc_start: 0.8344 (mp0) cc_final: 0.7884 (mp0) REVERT: H 149 TRP cc_start: 0.8635 (m100) cc_final: 0.8275 (m-10) REVERT: H 201 ASN cc_start: 0.8038 (t0) cc_final: 0.7791 (t0) REVERT: H 205 LYS cc_start: 0.8883 (pttm) cc_final: 0.8396 (pttp) REVERT: H 220 ASN cc_start: 0.9163 (m-40) cc_final: 0.8661 (m-40) REVERT: H 223 ASP cc_start: 0.8445 (t70) cc_final: 0.8130 (t0) outliers start: 4 outliers final: 0 residues processed: 438 average time/residue: 0.1210 time to fit residues: 78.2142 Evaluate side-chains 346 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 180 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 189 optimal weight: 0.7980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS F 214 HIS F 226 HIS G 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.087890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.065446 restraints weight = 63737.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067345 restraints weight = 41319.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.068670 restraints weight = 29521.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.069544 restraints weight = 22975.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.070218 restraints weight = 19180.436| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15161 Z= 0.124 Angle : 0.622 9.054 20629 Z= 0.293 Chirality : 0.042 0.148 2521 Planarity : 0.004 0.048 2568 Dihedral : 7.355 138.554 2121 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.13 % Allowed : 4.76 % Favored : 95.11 % 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: -2.85 (0.18), residues: 1934 helix: -1.28 (0.20), residues: 666 sheet: -2.27 (0.30), residues: 247 loop : -2.22 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 89 TYR 0.012 0.001 TYR D 40 PHE 0.013 0.001 PHE E 148 TRP 0.008 0.001 TRP B 7 HIS 0.006 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00267 (15161) covalent geometry : angle 0.62214 (20629) hydrogen bonds : bond 0.02385 ( 361) hydrogen bonds : angle 4.43840 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 426 time to evaluate : 0.572 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7238 (mp10) cc_final: 0.6802 (tp-100) REVERT: A 83 THR cc_start: 0.8475 (p) cc_final: 0.8249 (p) REVERT: A 84 LEU cc_start: 0.7283 (pt) cc_final: 0.6456 (tt) REVERT: A 138 LYS cc_start: 0.8130 (tttt) cc_final: 0.7590 (tptp) REVERT: D 95 ASP cc_start: 0.5771 (m-30) cc_final: 0.4760 (t0) REVERT: D 144 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8126 (mt-10) REVERT: I 7 GLU cc_start: 0.9045 (pt0) cc_final: 0.7462 (tm-30) REVERT: I 13 PHE cc_start: 0.8744 (t80) cc_final: 0.8544 (t80) REVERT: I 111 TYR cc_start: 0.9154 (p90) cc_final: 0.8813 (p90) REVERT: I 138 LYS cc_start: 0.8989 (tptp) cc_final: 0.8618 (mmtm) REVERT: I 150 PHE cc_start: 0.7278 (m-80) cc_final: 0.6898 (m-80) REVERT: J 4 LYS cc_start: 0.8028 (tppt) cc_final: 0.7452 (ttpt) REVERT: J 92 HIS cc_start: 0.8056 (m90) cc_final: 0.7676 (m-70) REVERT: J 111 TYR cc_start: 0.8671 (p90) cc_final: 0.8463 (p90) REVERT: J 138 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6462 (tptp) REVERT: K 48 ASN cc_start: 0.8761 (t0) cc_final: 0.7682 (p0) REVERT: K 67 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8422 (mmm-85) REVERT: L 85 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7478 (mp0) REVERT: L 107 LEU cc_start: 0.7062 (tp) cc_final: 0.6616 (pt) REVERT: L 114 LEU cc_start: 0.7564 (mm) cc_final: 0.7105 (mm) REVERT: B 60 HIS cc_start: 0.8327 (m-70) cc_final: 0.7973 (m-70) REVERT: C 8 MET cc_start: 0.8122 (tpt) cc_final: 0.7898 (tpp) REVERT: C 16 LEU cc_start: 0.8968 (mt) cc_final: 0.8695 (mt) REVERT: C 17 SER cc_start: 0.8891 (m) cc_final: 0.8229 (p) REVERT: C 23 ASP cc_start: 0.8676 (m-30) cc_final: 0.8064 (p0) REVERT: F 29 LEU cc_start: 0.8719 (mm) cc_final: 0.7859 (mm) REVERT: F 40 MET cc_start: 0.8275 (mpp) cc_final: 0.8075 (mpp) REVERT: F 47 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8039 (mppt) REVERT: F 130 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7787 (tp30) REVERT: F 139 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7579 (mmmt) REVERT: F 180 MET cc_start: 0.8815 (mmp) cc_final: 0.8410 (mmm) REVERT: G 40 MET cc_start: 0.8306 (mpp) cc_final: 0.7810 (mpp) REVERT: G 90 LEU cc_start: 0.9303 (pp) cc_final: 0.8688 (pp) REVERT: G 101 ASN cc_start: 0.9011 (t0) cc_final: 0.8647 (t0) REVERT: G 127 MET cc_start: 0.8332 (ptp) cc_final: 0.7850 (ptp) REVERT: G 134 LEU cc_start: 0.9319 (mt) cc_final: 0.9107 (mm) REVERT: G 169 ASP cc_start: 0.8701 (t0) cc_final: 0.8438 (t0) REVERT: E 68 MET cc_start: 0.8671 (mtp) cc_final: 0.8176 (mtp) REVERT: E 127 GLU cc_start: 0.8588 (tp30) cc_final: 0.8209 (tp30) REVERT: E 133 GLU cc_start: 0.9087 (pp20) cc_final: 0.8757 (tm-30) REVERT: E 223 ASP cc_start: 0.8187 (t0) cc_final: 0.7482 (t70) REVERT: H 72 LEU cc_start: 0.9542 (mm) cc_final: 0.9306 (mm) REVERT: H 127 GLU cc_start: 0.8479 (mp0) cc_final: 0.7946 (mp0) REVERT: H 149 TRP cc_start: 0.8791 (m100) cc_final: 0.8269 (m-10) REVERT: H 201 ASN cc_start: 0.8192 (t0) cc_final: 0.7896 (t0) REVERT: H 205 LYS cc_start: 0.9106 (pttm) cc_final: 0.8524 (pttp) REVERT: H 220 ASN cc_start: 0.9177 (m-40) cc_final: 0.8721 (m-40) REVERT: H 223 ASP cc_start: 0.8607 (t70) cc_final: 0.8231 (t0) outliers start: 2 outliers final: 0 residues processed: 427 average time/residue: 0.1108 time to fit residues: 70.5926 Evaluate side-chains 340 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 102 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 11 optimal weight: 0.0040 chunk 79 optimal weight: 0.0060 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.086026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.063348 restraints weight = 64195.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065309 restraints weight = 40114.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066665 restraints weight = 28220.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.067618 restraints weight = 21642.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068330 restraints weight = 17722.902| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15161 Z= 0.131 Angle : 0.631 8.524 20629 Z= 0.298 Chirality : 0.043 0.172 2521 Planarity : 0.004 0.042 2568 Dihedral : 6.921 147.336 2121 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.57 % 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: -2.43 (0.19), residues: 1934 helix: -0.80 (0.21), residues: 671 sheet: -2.20 (0.31), residues: 239 loop : -2.05 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 81 TYR 0.018 0.001 TYR H 222 PHE 0.020 0.001 PHE H 209 TRP 0.012 0.001 TRP F 216 HIS 0.009 0.001 HIS F 203 Details of bonding type rmsd covalent geometry : bond 0.00291 (15161) covalent geometry : angle 0.63053 (20629) hydrogen bonds : bond 0.02321 ( 361) hydrogen bonds : angle 4.32032 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 0.494 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7625 (mp10) cc_final: 0.7054 (tp-100) REVERT: A 84 LEU cc_start: 0.7233 (pt) cc_final: 0.6654 (tt) REVERT: A 112 LEU cc_start: 0.8296 (mm) cc_final: 0.8012 (mm) REVERT: A 138 LYS cc_start: 0.8076 (tttt) cc_final: 0.7564 (tptp) REVERT: D 95 ASP cc_start: 0.5793 (m-30) cc_final: 0.4781 (t0) REVERT: D 144 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8197 (mt-10) REVERT: I 7 GLU cc_start: 0.9087 (pt0) cc_final: 0.7638 (tm-30) REVERT: I 111 TYR cc_start: 0.9163 (p90) cc_final: 0.8718 (p90) REVERT: I 138 LYS cc_start: 0.9062 (tptp) cc_final: 0.8669 (mmtm) REVERT: I 150 PHE cc_start: 0.7306 (m-80) cc_final: 0.6889 (m-80) REVERT: J 4 LYS cc_start: 0.8078 (tppt) cc_final: 0.7517 (ttpt) REVERT: J 92 HIS cc_start: 0.8112 (m90) cc_final: 0.7709 (m-70) REVERT: J 138 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6618 (tptp) REVERT: K 48 ASN cc_start: 0.8789 (t0) cc_final: 0.7772 (p0) REVERT: L 85 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7556 (mp0) REVERT: L 107 LEU cc_start: 0.7192 (tp) cc_final: 0.6746 (pt) REVERT: L 146 LEU cc_start: 0.8717 (mt) cc_final: 0.8410 (mt) REVERT: B 60 HIS cc_start: 0.8366 (m-70) cc_final: 0.7995 (m-70) REVERT: C 8 MET cc_start: 0.8109 (tpt) cc_final: 0.7902 (tpp) REVERT: C 23 ASP cc_start: 0.8652 (m-30) cc_final: 0.8141 (p0) REVERT: C 60 HIS cc_start: 0.8531 (m-70) cc_final: 0.8204 (m-70) REVERT: F 40 MET cc_start: 0.8426 (mpp) cc_final: 0.8110 (mpp) REVERT: F 47 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8352 (mppt) REVERT: F 89 MET cc_start: 0.8637 (ppp) cc_final: 0.8337 (ppp) REVERT: F 128 LYS cc_start: 0.9517 (mmtp) cc_final: 0.9287 (mttt) REVERT: F 130 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8026 (tp30) REVERT: F 167 MET cc_start: 0.8803 (mpp) cc_final: 0.8312 (mpp) REVERT: F 180 MET cc_start: 0.8936 (mmp) cc_final: 0.8386 (mmm) REVERT: F 202 SER cc_start: 0.9192 (t) cc_final: 0.8743 (m) REVERT: G 40 MET cc_start: 0.8391 (mpp) cc_final: 0.7776 (mpp) REVERT: G 127 MET cc_start: 0.8589 (ptp) cc_final: 0.8158 (ptp) REVERT: G 169 ASP cc_start: 0.8879 (t0) cc_final: 0.8527 (t0) REVERT: E 15 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8680 (mmtm) REVERT: E 68 MET cc_start: 0.8771 (mtp) cc_final: 0.8322 (mtp) REVERT: E 111 ARG cc_start: 0.8632 (tpt170) cc_final: 0.8323 (tpt90) REVERT: E 127 GLU cc_start: 0.8742 (tp30) cc_final: 0.8243 (tp30) REVERT: E 132 MET cc_start: 0.8788 (ppp) cc_final: 0.8552 (tmm) REVERT: E 223 ASP cc_start: 0.8282 (t0) cc_final: 0.7666 (t70) REVERT: H 20 PHE cc_start: 0.8537 (m-10) cc_final: 0.8139 (t80) REVERT: H 56 MET cc_start: 0.8733 (tpp) cc_final: 0.8164 (tmm) REVERT: H 72 LEU cc_start: 0.9620 (mm) cc_final: 0.9292 (mm) REVERT: H 127 GLU cc_start: 0.8614 (mp0) cc_final: 0.7932 (mp0) REVERT: H 149 TRP cc_start: 0.8947 (m100) cc_final: 0.8187 (m-10) REVERT: H 201 ASN cc_start: 0.8361 (t0) cc_final: 0.8008 (t0) REVERT: H 205 LYS cc_start: 0.9190 (pttm) cc_final: 0.8551 (pttm) REVERT: H 220 ASN cc_start: 0.9259 (m-40) cc_final: 0.8679 (m-40) REVERT: H 223 ASP cc_start: 0.8774 (t70) cc_final: 0.8367 (t0) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.1184 time to fit residues: 72.7595 Evaluate side-chains 332 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 30 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 30.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 ASN F 92 GLN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.084601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063806 restraints weight = 62940.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065473 restraints weight = 40871.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.066674 restraints weight = 29656.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.067494 restraints weight = 23158.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068117 restraints weight = 19278.814| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15161 Z= 0.120 Angle : 0.634 7.966 20629 Z= 0.298 Chirality : 0.043 0.180 2521 Planarity : 0.004 0.052 2568 Dihedral : 6.647 143.809 2121 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.95 % 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: -2.21 (0.19), residues: 1934 helix: -0.52 (0.21), residues: 669 sheet: -2.05 (0.32), residues: 239 loop : -1.99 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 46 TYR 0.018 0.001 TYR H 222 PHE 0.024 0.001 PHE A 150 TRP 0.011 0.001 TRP C 29 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00270 (15161) covalent geometry : angle 0.63402 (20629) hydrogen bonds : bond 0.02304 ( 361) hydrogen bonds : angle 4.30361 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.491 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7600 (mp10) cc_final: 0.7259 (tp-100) REVERT: A 84 LEU cc_start: 0.7644 (pt) cc_final: 0.6707 (tt) REVERT: A 112 LEU cc_start: 0.8207 (mm) cc_final: 0.7951 (mm) REVERT: D 95 ASP cc_start: 0.5755 (m-30) cc_final: 0.4798 (t0) REVERT: D 144 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8302 (mt-10) REVERT: I 7 GLU cc_start: 0.8990 (pt0) cc_final: 0.7481 (tm-30) REVERT: I 13 PHE cc_start: 0.8829 (t80) cc_final: 0.8621 (t80) REVERT: I 111 TYR cc_start: 0.9119 (p90) cc_final: 0.8638 (p90) REVERT: I 138 LYS cc_start: 0.9041 (tptp) cc_final: 0.8658 (mmtm) REVERT: I 150 PHE cc_start: 0.7297 (m-10) cc_final: 0.6940 (m-80) REVERT: J 4 LYS cc_start: 0.8042 (tppt) cc_final: 0.7526 (ttpt) REVERT: J 92 HIS cc_start: 0.8071 (m90) cc_final: 0.7685 (m-70) REVERT: J 138 LYS cc_start: 0.7449 (mmtt) cc_final: 0.6722 (tptp) REVERT: K 48 ASN cc_start: 0.8777 (t0) cc_final: 0.7766 (p0) REVERT: K 53 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8060 (mmtt) REVERT: K 67 ARG cc_start: 0.8891 (mmm160) cc_final: 0.8478 (mmm-85) REVERT: L 67 ARG cc_start: 0.8894 (ptm160) cc_final: 0.8495 (ptm160) REVERT: L 85 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7686 (mp0) REVERT: L 107 LEU cc_start: 0.7265 (tp) cc_final: 0.6821 (pt) REVERT: B 60 HIS cc_start: 0.8355 (m-70) cc_final: 0.7912 (m-70) REVERT: C 8 MET cc_start: 0.8160 (tpt) cc_final: 0.7910 (tpp) REVERT: C 23 ASP cc_start: 0.8607 (m-30) cc_final: 0.8093 (p0) REVERT: C 60 HIS cc_start: 0.8486 (m-70) cc_final: 0.8171 (m-70) REVERT: F 29 LEU cc_start: 0.8458 (mm) cc_final: 0.8070 (mm) REVERT: F 40 MET cc_start: 0.8258 (mpp) cc_final: 0.8022 (mpp) REVERT: F 47 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8382 (mppt) REVERT: F 89 MET cc_start: 0.8844 (ppp) cc_final: 0.8521 (ppp) REVERT: F 128 LYS cc_start: 0.9497 (mmtp) cc_final: 0.9288 (mttt) REVERT: F 130 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8104 (tp30) REVERT: F 180 MET cc_start: 0.8878 (mmp) cc_final: 0.8398 (mmm) REVERT: F 202 SER cc_start: 0.9164 (t) cc_final: 0.8327 (m) REVERT: G 40 MET cc_start: 0.8284 (mpp) cc_final: 0.7933 (mpp) REVERT: G 90 LEU cc_start: 0.9191 (pp) cc_final: 0.8707 (pp) REVERT: G 127 MET cc_start: 0.8635 (ptp) cc_final: 0.8247 (ptp) REVERT: G 169 ASP cc_start: 0.8794 (t0) cc_final: 0.8407 (t70) REVERT: E 15 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8720 (mmtm) REVERT: E 68 MET cc_start: 0.8722 (mtp) cc_final: 0.8239 (mtp) REVERT: E 111 ARG cc_start: 0.8612 (tpt170) cc_final: 0.8387 (tpt90) REVERT: E 127 GLU cc_start: 0.8618 (tp30) cc_final: 0.8173 (tp30) REVERT: E 132 MET cc_start: 0.8868 (ppp) cc_final: 0.8627 (tmm) REVERT: E 207 VAL cc_start: 0.9618 (m) cc_final: 0.9348 (p) REVERT: E 223 ASP cc_start: 0.8195 (t0) cc_final: 0.7589 (t70) REVERT: H 56 MET cc_start: 0.8518 (tpp) cc_final: 0.8127 (tmm) REVERT: H 91 VAL cc_start: 0.9116 (p) cc_final: 0.8893 (p) REVERT: H 127 GLU cc_start: 0.8574 (mp0) cc_final: 0.7944 (mp0) REVERT: H 149 TRP cc_start: 0.8918 (m100) cc_final: 0.8186 (m-10) REVERT: H 201 ASN cc_start: 0.8313 (t0) cc_final: 0.7978 (t0) REVERT: H 205 LYS cc_start: 0.9163 (pttm) cc_final: 0.8531 (pttm) REVERT: H 220 ASN cc_start: 0.9201 (m-40) cc_final: 0.8639 (m-40) REVERT: H 223 ASP cc_start: 0.8742 (t70) cc_final: 0.8366 (t0) outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.1094 time to fit residues: 67.9283 Evaluate side-chains 328 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 0.0030 chunk 166 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 176 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 HIS F 92 GLN F 101 ASN F 105 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.080644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059522 restraints weight = 65019.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061213 restraints weight = 41719.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062367 restraints weight = 29550.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063215 restraints weight = 22826.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063778 restraints weight = 18777.357| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15161 Z= 0.190 Angle : 0.706 11.317 20629 Z= 0.337 Chirality : 0.045 0.169 2521 Planarity : 0.004 0.060 2568 Dihedral : 6.474 149.940 2121 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.13 % Allowed : 2.47 % Favored : 97.40 % 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: -2.03 (0.19), residues: 1934 helix: -0.30 (0.21), residues: 680 sheet: -1.89 (0.30), residues: 273 loop : -1.95 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 81 TYR 0.013 0.001 TYR E 75 PHE 0.018 0.002 PHE J 13 TRP 0.018 0.002 TRP F 216 HIS 0.008 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00412 (15161) covalent geometry : angle 0.70564 (20629) hydrogen bonds : bond 0.02775 ( 361) hydrogen bonds : angle 4.51540 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 406 time to evaluate : 0.414 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7731 (pt) cc_final: 0.6737 (tt) REVERT: A 112 LEU cc_start: 0.8190 (mm) cc_final: 0.7896 (mm) REVERT: D 95 ASP cc_start: 0.5483 (m-30) cc_final: 0.4722 (t0) REVERT: I 18 LEU cc_start: 0.9209 (tt) cc_final: 0.9006 (mt) REVERT: I 111 TYR cc_start: 0.9119 (p90) cc_final: 0.8482 (p90) REVERT: I 150 PHE cc_start: 0.7296 (m-10) cc_final: 0.6868 (m-80) REVERT: J 4 LYS cc_start: 0.8236 (tppt) cc_final: 0.7745 (ttpt) REVERT: J 92 HIS cc_start: 0.8138 (m90) cc_final: 0.7770 (m-70) REVERT: J 138 LYS cc_start: 0.7539 (mmtt) cc_final: 0.6884 (tptp) REVERT: K 48 ASN cc_start: 0.8711 (t0) cc_final: 0.7834 (p0) REVERT: L 67 ARG cc_start: 0.8915 (ptm160) cc_final: 0.8523 (ptm160) REVERT: L 85 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7809 (mp0) REVERT: B 60 HIS cc_start: 0.8439 (m-70) cc_final: 0.7969 (m-70) REVERT: C 8 MET cc_start: 0.8412 (tpt) cc_final: 0.8143 (tpp) REVERT: C 23 ASP cc_start: 0.8761 (m-30) cc_final: 0.8245 (p0) REVERT: C 60 HIS cc_start: 0.8587 (m-70) cc_final: 0.8183 (m-70) REVERT: F 29 LEU cc_start: 0.8594 (mm) cc_final: 0.8227 (mm) REVERT: F 47 LYS cc_start: 0.9373 (mmmm) cc_final: 0.8745 (mppt) REVERT: F 89 MET cc_start: 0.9138 (ppp) cc_final: 0.8605 (ppp) REVERT: F 130 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8223 (tp30) REVERT: F 167 MET cc_start: 0.8833 (mpp) cc_final: 0.8502 (mpp) REVERT: G 40 MET cc_start: 0.8216 (mpp) cc_final: 0.7992 (mpp) REVERT: G 127 MET cc_start: 0.8619 (ptp) cc_final: 0.8150 (ptp) REVERT: G 169 ASP cc_start: 0.8560 (t0) cc_final: 0.8297 (t0) REVERT: E 15 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8895 (mmtm) REVERT: E 68 MET cc_start: 0.8572 (mtp) cc_final: 0.8080 (mtp) REVERT: E 111 ARG cc_start: 0.8708 (tpt170) cc_final: 0.8481 (tpt90) REVERT: E 127 GLU cc_start: 0.8546 (tp30) cc_final: 0.8043 (tp30) REVERT: E 132 MET cc_start: 0.9066 (ppp) cc_final: 0.8676 (ppp) REVERT: E 181 ASP cc_start: 0.7812 (m-30) cc_final: 0.7399 (m-30) REVERT: E 223 ASP cc_start: 0.8195 (t0) cc_final: 0.7582 (t70) REVERT: E 257 MET cc_start: 0.5104 (mtm) cc_final: 0.3782 (mmm) REVERT: H 47 GLN cc_start: 0.9123 (tp40) cc_final: 0.8874 (tp-100) REVERT: H 49 TYR cc_start: 0.8982 (t80) cc_final: 0.8758 (t80) REVERT: H 56 MET cc_start: 0.8396 (tpp) cc_final: 0.8121 (tmm) REVERT: H 91 VAL cc_start: 0.9181 (p) cc_final: 0.8923 (p) REVERT: H 127 GLU cc_start: 0.8632 (mp0) cc_final: 0.8182 (mp0) REVERT: H 201 ASN cc_start: 0.8444 (t0) cc_final: 0.8031 (t0) REVERT: H 205 LYS cc_start: 0.9236 (pttm) cc_final: 0.8660 (pttp) REVERT: H 220 ASN cc_start: 0.9260 (m-40) cc_final: 0.8745 (m110) REVERT: H 223 ASP cc_start: 0.8764 (t70) cc_final: 0.8361 (t0) outliers start: 2 outliers final: 0 residues processed: 407 average time/residue: 0.1113 time to fit residues: 68.1064 Evaluate side-chains 311 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 162 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.078996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058286 restraints weight = 65076.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059949 restraints weight = 41607.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.060965 restraints weight = 29550.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061832 restraints weight = 23408.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062464 restraints weight = 19250.814| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15161 Z= 0.187 Angle : 0.712 8.892 20629 Z= 0.341 Chirality : 0.045 0.152 2521 Planarity : 0.004 0.073 2568 Dihedral : 6.217 136.176 2121 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -2.01 (0.19), residues: 1934 helix: -0.15 (0.20), residues: 706 sheet: -2.03 (0.29), residues: 283 loop : -2.04 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 135 TYR 0.023 0.001 TYR F 81 PHE 0.023 0.002 PHE I 13 TRP 0.018 0.002 TRP F 216 HIS 0.017 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00404 (15161) covalent geometry : angle 0.71191 (20629) hydrogen bonds : bond 0.02655 ( 361) hydrogen bonds : angle 4.46560 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 84 LEU cc_start: 0.7887 (pt) cc_final: 0.6891 (tt) REVERT: A 112 LEU cc_start: 0.8211 (mm) cc_final: 0.7872 (mm) REVERT: A 138 LYS cc_start: 0.8115 (tttt) cc_final: 0.7599 (tptp) REVERT: D 95 ASP cc_start: 0.5567 (m-30) cc_final: 0.4833 (t0) REVERT: D 144 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8437 (pt0) REVERT: I 138 LYS cc_start: 0.8939 (tptp) cc_final: 0.8560 (mmtm) REVERT: I 150 PHE cc_start: 0.7239 (m-10) cc_final: 0.6778 (m-80) REVERT: J 4 LYS cc_start: 0.8194 (tppt) cc_final: 0.7761 (tttt) REVERT: J 92 HIS cc_start: 0.8157 (m90) cc_final: 0.7788 (m-70) REVERT: J 138 LYS cc_start: 0.7582 (mmtt) cc_final: 0.6979 (tptp) REVERT: K 48 ASN cc_start: 0.8700 (t0) cc_final: 0.7924 (p0) REVERT: K 53 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8439 (mmtt) REVERT: L 67 ARG cc_start: 0.8895 (ptm160) cc_final: 0.8492 (ptm160) REVERT: L 85 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7815 (mp0) REVERT: L 102 ARG cc_start: 0.8815 (mtp85) cc_final: 0.8177 (mmp80) REVERT: B 60 HIS cc_start: 0.8383 (m-70) cc_final: 0.7836 (m-70) REVERT: C 8 MET cc_start: 0.8586 (tpt) cc_final: 0.8290 (tpp) REVERT: C 23 ASP cc_start: 0.8725 (m-30) cc_final: 0.8297 (p0) REVERT: C 60 HIS cc_start: 0.8706 (m-70) cc_final: 0.8127 (m-70) REVERT: C 63 ASP cc_start: 0.8772 (p0) cc_final: 0.7675 (p0) REVERT: F 47 LYS cc_start: 0.9437 (mmmm) cc_final: 0.8747 (mppt) REVERT: F 89 MET cc_start: 0.9123 (ppp) cc_final: 0.8756 (ppp) REVERT: F 130 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8271 (tp30) REVERT: F 167 MET cc_start: 0.8599 (mpp) cc_final: 0.8296 (mpp) REVERT: F 180 MET cc_start: 0.8895 (mmp) cc_final: 0.8368 (mmm) REVERT: G 43 SER cc_start: 0.9293 (m) cc_final: 0.9053 (p) REVERT: G 52 ARG cc_start: 0.9287 (mtp180) cc_final: 0.9048 (mtp85) REVERT: G 87 MET cc_start: 0.8685 (mpp) cc_final: 0.8304 (mpp) REVERT: G 90 LEU cc_start: 0.9238 (pp) cc_final: 0.8713 (pp) REVERT: G 127 MET cc_start: 0.8722 (ptp) cc_final: 0.8315 (ptp) REVERT: G 170 GLU cc_start: 0.8925 (tp30) cc_final: 0.8447 (tm-30) REVERT: G 203 HIS cc_start: 0.8756 (p-80) cc_final: 0.8455 (p-80) REVERT: E 68 MET cc_start: 0.8616 (mtp) cc_final: 0.8280 (mtp) REVERT: E 111 ARG cc_start: 0.8715 (tpt170) cc_final: 0.8508 (tpt90) REVERT: E 127 GLU cc_start: 0.8469 (tp30) cc_final: 0.7983 (tp30) REVERT: E 223 ASP cc_start: 0.8203 (t0) cc_final: 0.7626 (t70) REVERT: E 257 MET cc_start: 0.5706 (mtt) cc_final: 0.4441 (mmm) REVERT: H 49 TYR cc_start: 0.8979 (t80) cc_final: 0.8724 (t80) REVERT: H 127 GLU cc_start: 0.8577 (mp0) cc_final: 0.8210 (mp0) REVERT: H 220 ASN cc_start: 0.9280 (m-40) cc_final: 0.8725 (m110) REVERT: H 223 ASP cc_start: 0.8752 (t70) cc_final: 0.8359 (t0) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.1087 time to fit residues: 64.8249 Evaluate side-chains 312 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 6.9990 chunk 62 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 135 GLN F 92 GLN F 233 GLN H 47 GLN H 201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.077880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.057111 restraints weight = 66400.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058718 restraints weight = 41995.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.059807 restraints weight = 29696.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060619 restraints weight = 23179.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060969 restraints weight = 19052.618| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.7593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15161 Z= 0.190 Angle : 0.736 9.388 20629 Z= 0.353 Chirality : 0.046 0.191 2521 Planarity : 0.004 0.051 2568 Dihedral : 6.195 131.377 2121 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.56 % 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: -1.94 (0.19), residues: 1934 helix: -0.05 (0.20), residues: 712 sheet: -2.18 (0.29), residues: 285 loop : -1.97 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG I 102 TYR 0.012 0.001 TYR G 256 PHE 0.020 0.002 PHE H 209 TRP 0.016 0.002 TRP F 216 HIS 0.014 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00415 (15161) covalent geometry : angle 0.73574 (20629) hydrogen bonds : bond 0.02774 ( 361) hydrogen bonds : angle 4.72250 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.548 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8292 (mm) cc_final: 0.7863 (mm) REVERT: A 138 LYS cc_start: 0.8071 (tttt) cc_final: 0.7545 (tptp) REVERT: D 84 LEU cc_start: 0.8113 (mp) cc_final: 0.7486 (pp) REVERT: D 95 ASP cc_start: 0.5627 (m-30) cc_final: 0.4880 (t0) REVERT: D 144 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8249 (pt0) REVERT: I 111 TYR cc_start: 0.9090 (p90) cc_final: 0.8450 (p90) REVERT: I 138 LYS cc_start: 0.8840 (tptp) cc_final: 0.8606 (mppt) REVERT: I 150 PHE cc_start: 0.7305 (m-10) cc_final: 0.6861 (m-80) REVERT: J 4 LYS cc_start: 0.8235 (tppt) cc_final: 0.7931 (ttpt) REVERT: J 92 HIS cc_start: 0.8243 (m90) cc_final: 0.7822 (m-70) REVERT: J 138 LYS cc_start: 0.7549 (mmtt) cc_final: 0.7105 (tptp) REVERT: K 48 ASN cc_start: 0.8794 (t0) cc_final: 0.8107 (p0) REVERT: K 53 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8541 (mmtt) REVERT: L 67 ARG cc_start: 0.8817 (ptm160) cc_final: 0.8408 (ptm160) REVERT: L 85 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7820 (mp0) REVERT: L 102 ARG cc_start: 0.8853 (mtp85) cc_final: 0.8172 (mmp80) REVERT: L 135 GLN cc_start: 0.7808 (mm110) cc_final: 0.7177 (pm20) REVERT: B 60 HIS cc_start: 0.8520 (m-70) cc_final: 0.7983 (m-70) REVERT: C 8 MET cc_start: 0.8765 (tpt) cc_final: 0.8473 (tpp) REVERT: C 23 ASP cc_start: 0.8746 (m-30) cc_final: 0.8347 (p0) REVERT: C 60 HIS cc_start: 0.8713 (m-70) cc_final: 0.8120 (m-70) REVERT: C 63 ASP cc_start: 0.8885 (p0) cc_final: 0.8450 (p0) REVERT: F 29 LEU cc_start: 0.8572 (mm) cc_final: 0.8294 (mm) REVERT: F 89 MET cc_start: 0.9154 (ppp) cc_final: 0.8758 (ppp) REVERT: F 128 LYS cc_start: 0.9581 (mmtp) cc_final: 0.9305 (mttt) REVERT: F 130 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8329 (tp30) REVERT: F 167 MET cc_start: 0.8715 (mpp) cc_final: 0.8461 (mpp) REVERT: G 43 SER cc_start: 0.9342 (m) cc_final: 0.9128 (p) REVERT: G 52 ARG cc_start: 0.9266 (mtp180) cc_final: 0.9038 (mtp85) REVERT: G 127 MET cc_start: 0.8810 (ptp) cc_final: 0.8479 (ptp) REVERT: E 127 GLU cc_start: 0.8486 (tp30) cc_final: 0.7848 (tp30) REVERT: E 181 ASP cc_start: 0.8169 (m-30) cc_final: 0.7880 (m-30) REVERT: E 223 ASP cc_start: 0.8135 (t0) cc_final: 0.7548 (t70) REVERT: E 257 MET cc_start: 0.5660 (mtt) cc_final: 0.4617 (tpp) REVERT: H 89 MET cc_start: 0.8604 (mpp) cc_final: 0.8361 (mmt) REVERT: H 123 MET cc_start: 0.9392 (ttp) cc_final: 0.8769 (ttm) REVERT: H 127 GLU cc_start: 0.8670 (mp0) cc_final: 0.8364 (mp0) REVERT: H 220 ASN cc_start: 0.9307 (m-40) cc_final: 0.8688 (m110) REVERT: H 223 ASP cc_start: 0.8728 (t70) cc_final: 0.8361 (t0) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.1041 time to fit residues: 61.2530 Evaluate side-chains 305 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 158 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.080519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059012 restraints weight = 65001.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060732 restraints weight = 40630.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.061901 restraints weight = 28766.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.062671 restraints weight = 22302.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063272 restraints weight = 18543.058| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15161 Z= 0.109 Angle : 0.690 11.459 20629 Z= 0.320 Chirality : 0.044 0.181 2521 Planarity : 0.004 0.047 2568 Dihedral : 5.868 127.583 2121 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.79 (0.19), residues: 1934 helix: 0.06 (0.21), residues: 708 sheet: -2.02 (0.29), residues: 285 loop : -1.88 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 81 TYR 0.013 0.001 TYR B 88 PHE 0.022 0.001 PHE I 13 TRP 0.010 0.001 TRP J 9 HIS 0.003 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00254 (15161) covalent geometry : angle 0.69047 (20629) hydrogen bonds : bond 0.02263 ( 361) hydrogen bonds : angle 4.30370 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.564 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 TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. REVERT: A 112 LEU cc_start: 0.8230 (mm) cc_final: 0.7913 (mm) REVERT: A 138 LYS cc_start: 0.7992 (tttt) cc_final: 0.7524 (tptp) REVERT: D 84 LEU cc_start: 0.8115 (mp) cc_final: 0.7518 (pp) REVERT: D 95 ASP cc_start: 0.5641 (m-30) cc_final: 0.4839 (t0) REVERT: D 144 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8378 (pt0) REVERT: I 111 TYR cc_start: 0.9037 (p90) cc_final: 0.8369 (p90) REVERT: I 150 PHE cc_start: 0.7331 (m-10) cc_final: 0.6966 (m-80) REVERT: J 92 HIS cc_start: 0.8152 (m90) cc_final: 0.7736 (m-70) REVERT: J 138 LYS cc_start: 0.7523 (mmtt) cc_final: 0.7034 (tptp) REVERT: K 48 ASN cc_start: 0.8766 (t0) cc_final: 0.8070 (p0) REVERT: K 53 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8594 (mmtt) REVERT: L 67 ARG cc_start: 0.8816 (ptm160) cc_final: 0.8436 (ptm160) REVERT: L 85 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7808 (mp0) REVERT: L 102 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8333 (mmp80) REVERT: B 60 HIS cc_start: 0.8260 (m-70) cc_final: 0.7720 (m-70) REVERT: C 8 MET cc_start: 0.8642 (tpt) cc_final: 0.8327 (tpp) REVERT: C 23 ASP cc_start: 0.8629 (m-30) cc_final: 0.8249 (p0) REVERT: C 63 ASP cc_start: 0.8829 (p0) cc_final: 0.8218 (p0) REVERT: F 29 LEU cc_start: 0.8509 (mm) cc_final: 0.7814 (mm) REVERT: F 47 LYS cc_start: 0.9448 (mttt) cc_final: 0.9049 (mttp) REVERT: F 128 LYS cc_start: 0.9510 (mmtp) cc_final: 0.9277 (mttt) REVERT: F 130 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8271 (tp30) REVERT: F 141 MET cc_start: 0.8781 (tpt) cc_final: 0.8548 (tpp) REVERT: G 43 SER cc_start: 0.9292 (m) cc_final: 0.8965 (p) REVERT: G 52 ARG cc_start: 0.9215 (mtp180) cc_final: 0.8901 (mtp85) REVERT: G 75 MET cc_start: 0.6641 (ptm) cc_final: 0.5943 (ppp) REVERT: G 127 MET cc_start: 0.8835 (ptp) cc_final: 0.8490 (ptp) REVERT: G 202 SER cc_start: 0.9374 (m) cc_final: 0.9107 (m) REVERT: E 223 ASP cc_start: 0.8055 (t0) cc_final: 0.7418 (t70) REVERT: E 257 MET cc_start: 0.5235 (mtt) cc_final: 0.4296 (tpp) REVERT: H 89 MET cc_start: 0.8635 (mpp) cc_final: 0.8418 (mmt) REVERT: H 127 GLU cc_start: 0.8613 (mp0) cc_final: 0.8320 (mp0) REVERT: H 205 LYS cc_start: 0.9093 (pttm) cc_final: 0.8362 (pttm) REVERT: H 216 ILE cc_start: 0.9647 (mt) cc_final: 0.9273 (mp) REVERT: H 220 ASN cc_start: 0.9232 (m-40) cc_final: 0.8588 (m110) REVERT: H 223 ASP cc_start: 0.8671 (t70) cc_final: 0.8323 (t0) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1046 time to fit residues: 65.4680 Evaluate side-chains 325 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 136 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 150 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 98 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 GLN F 191 ASN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.080373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059641 restraints weight = 64427.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061262 restraints weight = 41369.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062425 restraints weight = 29644.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.063200 restraints weight = 23044.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.063820 restraints weight = 19153.745| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15161 Z= 0.116 Angle : 0.684 9.190 20629 Z= 0.320 Chirality : 0.045 0.166 2521 Planarity : 0.004 0.063 2568 Dihedral : 5.824 126.446 2121 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.06 % Allowed : 0.32 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.19), residues: 1934 helix: 0.10 (0.20), residues: 718 sheet: -2.01 (0.29), residues: 287 loop : -1.84 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 81 TYR 0.029 0.001 TYR B 88 PHE 0.020 0.001 PHE H 209 TRP 0.010 0.001 TRP C 7 HIS 0.003 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00270 (15161) covalent geometry : angle 0.68350 (20629) hydrogen bonds : bond 0.02271 ( 361) hydrogen bonds : angle 4.28260 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.96 seconds wall clock time: 48 minutes 35.35 seconds (2915.35 seconds total)