Starting phenix.real_space_refine on Sun May 3 21:38:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jy4_61887/05_2026/9jy4_61887.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jy4_61887/05_2026/9jy4_61887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jy4_61887/05_2026/9jy4_61887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jy4_61887/05_2026/9jy4_61887.map" model { file = "/net/cci-nas-00/data/ceres_data/9jy4_61887/05_2026/9jy4_61887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jy4_61887/05_2026/9jy4_61887.cif" } resolution = 3.29 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= 0.015 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 10042 2.51 5 N 2512 2.21 5 O 2984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15642 Number of models: 1 Model: "" Number of chains: 20 Chain: "a" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "b" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "m" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 285 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "n" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "P" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1505 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 3 Chain: "O" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1583 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "B" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "F" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "M" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 285 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "N" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "R" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1505 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 3 Chain: "Q" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1583 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 3.93, per 1000 atoms: 0.25 Number of scatterers: 15642 At special positions: 0 Unit cell: (170.568, 172.216, 123.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2984 8.00 N 2512 7.00 C 10042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 149 " - pdb=" SG CYS P 204 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 135 " - pdb=" SG CYS O 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 149 " - pdb=" SG CYS R 204 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 135 " - pdb=" SG CYS Q 195 " distance=2.03 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: 1.33 Conformation dependent library (CDL) restraints added in 712.5 milliseconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 36 sheets defined 27.6% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'a' and resid 28 through 32 Processing helix chain 'a' and resid 33 through 54 Processing helix chain 'b' and resid 28 through 54 Processing helix chain 'd' and resid 100 through 126 Processing helix chain 'e' and resid 126 through 153 Processing helix chain 'f' and resid 104 through 108 Processing helix chain 'f' and resid 126 through 154 Processing helix chain 'g' and resid 76 through 80 Processing helix chain 'g' and resid 111 through 140 Processing helix chain 'm' and resid 256 through 289 removed outlier: 4.300A pdb=" N MET m 261 " --> pdb=" O GLU m 257 " (cutoff:3.500A) Processing helix chain 'n' and resid 252 through 288 removed outlier: 3.609A pdb=" N CYS n 283 " --> pdb=" O ILE n 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.736A pdb=" N TYR P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 removed outlier: 3.518A pdb=" N SER P 91 " --> pdb=" O SER P 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.555A pdb=" N ILE O 83 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 184 through 189 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 33 through 54 Processing helix chain 'B' and resid 28 through 54 Processing helix chain 'D' and resid 100 through 126 Processing helix chain 'E' and resid 126 through 153 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 126 through 154 Processing helix chain 'G' and resid 76 through 80 Processing helix chain 'G' and resid 111 through 140 Processing helix chain 'M' and resid 256 through 289 removed outlier: 3.970A pdb=" N MET M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 288 removed outlier: 3.580A pdb=" N CYS N 283 " --> pdb=" O ILE N 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.745A pdb=" N TYR R 32 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.519A pdb=" N SER R 91 " --> pdb=" O SER R 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.622A pdb=" N ILE Q 83 " --> pdb=" O GLN Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 129 Processing helix chain 'Q' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'd' and resid 27 through 28 removed outlier: 3.767A pdb=" N GLU d 27 " --> pdb=" O PHE d 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 43 removed outlier: 3.856A pdb=" N THR d 42 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR e 113 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG e 115 " --> pdb=" O HIS d 89 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG d 91 " --> pdb=" O ARG e 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 38 through 41 removed outlier: 3.644A pdb=" N THR e 44 " --> pdb=" O SER e 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.830A pdb=" N LYS f 37 " --> pdb=" O THR f 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 65 through 66 removed outlier: 4.244A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN g 98 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE g 56 " --> pdb=" O GLN g 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 122 through 123 Processing sheet with id=AA9, first strand: chain 'g' and resid 31 through 33 removed outlier: 6.960A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.897A pdb=" N GLU P 10 " --> pdb=" O THR P 117 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR P 119 " --> pdb=" O GLU P 10 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N MET P 34 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.897A pdb=" N GLU P 10 " --> pdb=" O THR P 117 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR P 119 " --> pdb=" O GLU P 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL P 111 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 129 through 133 removed outlier: 3.540A pdb=" N GLY P 153 " --> pdb=" O TYR P 184 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR P 184 " --> pdb=" O GLY P 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.531A pdb=" N CYS O 23 " --> pdb=" O TYR O 71 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.568A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 118 through 119 removed outlier: 3.694A pdb=" N VAL O 134 " --> pdb=" O PHE O 119 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER O 175 " --> pdb=" O THR O 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 154 through 155 removed outlier: 3.778A pdb=" N ASN O 146 " --> pdb=" O THR O 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 27 through 28 removed outlier: 3.769A pdb=" N GLU D 27 " --> pdb=" O PHE D 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.853A pdb=" N THR D 42 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR E 113 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG E 115 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG D 91 " --> pdb=" O ARG E 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 41 removed outlier: 3.592A pdb=" N THR E 44 " --> pdb=" O SER E 41 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AC6, first strand: chain 'F' and resid 37 through 41 removed outlier: 3.837A pdb=" N LYS F 37 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 65 through 66 removed outlier: 4.299A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN G 98 " --> pdb=" O TYR F 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE G 56 " --> pdb=" O GLN G 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.515A pdb=" N ILE G 108 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.962A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.897A pdb=" N GLU R 10 " --> pdb=" O THR R 117 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR R 119 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N MET R 34 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.897A pdb=" N GLU R 10 " --> pdb=" O THR R 117 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR R 119 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL R 111 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 129 through 133 removed outlier: 3.540A pdb=" N GLY R 153 " --> pdb=" O TYR R 184 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR R 184 " --> pdb=" O GLY R 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 160 through 162 Processing sheet with id=AD6, first strand: chain 'Q' and resid 4 through 6 removed outlier: 3.522A pdb=" N CYS Q 23 " --> pdb=" O TYR Q 71 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP Q 70 " --> pdb=" O SER Q 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 118 through 119 removed outlier: 3.695A pdb=" N VAL Q 134 " --> pdb=" O PHE Q 119 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER Q 175 " --> pdb=" O THR Q 165 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 154 through 155 removed outlier: 3.776A pdb=" N ASN Q 146 " --> pdb=" O THR Q 198 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2088 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: 2.71 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4864 1.34 - 1.47: 3946 1.47 - 1.59: 7012 1.59 - 1.71: 0 1.71 - 1.83: 146 Bond restraints: 15968 Sorted by residual: bond pdb=" C GLU R 157 " pdb=" N PRO R 158 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.63e+00 bond pdb=" C GLU P 157 " pdb=" N PRO P 158 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.59e+00 bond pdb=" C ARG O 108 " pdb=" N ALA O 110 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.52e+00 bond pdb=" C ARG Q 108 " pdb=" N ALA Q 110 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.45e+00 bond pdb=" N ALA Q 110 " pdb=" CA ALA Q 110 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.18e+00 ... (remaining 15963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 21296 2.33 - 4.67: 294 4.67 - 7.00: 51 7.00 - 9.34: 18 9.34 - 11.67: 9 Bond angle restraints: 21668 Sorted by residual: angle pdb=" C ARG O 108 " pdb=" N ALA O 110 " pdb=" CA ALA O 110 " ideal model delta sigma weight residual 121.70 132.45 -10.75 1.80e+00 3.09e-01 3.57e+01 angle pdb=" C ARG Q 108 " pdb=" N ALA Q 110 " pdb=" CA ALA Q 110 " ideal model delta sigma weight residual 121.70 132.41 -10.71 1.80e+00 3.09e-01 3.54e+01 angle pdb=" C ASN m 260 " pdb=" N MET m 261 " pdb=" CA MET m 261 " ideal model delta sigma weight residual 122.56 113.65 8.91 1.72e+00 3.38e-01 2.68e+01 angle pdb=" C TYR Q 50 " pdb=" N THR Q 51 " pdb=" CA THR Q 51 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C TYR O 50 " pdb=" N THR O 51 " pdb=" CA THR O 51 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 ... (remaining 21663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 8376 17.78 - 35.57: 873 35.57 - 53.35: 227 53.35 - 71.14: 36 71.14 - 88.92: 14 Dihedral angle restraints: 9526 sinusoidal: 3698 harmonic: 5828 Sorted by residual: dihedral pdb=" CB CYS f 119 " pdb=" SG CYS f 119 " pdb=" SG CYS f 122 " pdb=" CB CYS f 122 " ideal model delta sinusoidal sigma weight residual -86.00 -157.90 71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 122 " pdb=" CB CYS F 122 " ideal model delta sinusoidal sigma weight residual -86.00 -157.03 71.03 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CA MET m 261 " pdb=" C MET m 261 " pdb=" N MET m 262 " pdb=" CA MET m 262 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 9523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2150 0.060 - 0.120: 330 0.120 - 0.180: 22 0.180 - 0.239: 3 0.239 - 0.299: 1 Chirality restraints: 2506 Sorted by residual: chirality pdb=" CA MET m 261 " pdb=" N MET m 261 " pdb=" C MET m 261 " pdb=" CB MET m 261 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CG LEU A 49 " pdb=" CB LEU A 49 " pdb=" CD1 LEU A 49 " pdb=" CD2 LEU A 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU a 49 " pdb=" CB LEU a 49 " pdb=" CD1 LEU a 49 " pdb=" CD2 LEU a 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2503 not shown) Planarity restraints: 2690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 121 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C ASN F 121 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN F 121 " 0.017 2.00e-02 2.50e+03 pdb=" N CYS F 122 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN f 121 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ASN f 121 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN f 121 " 0.017 2.00e-02 2.50e+03 pdb=" N CYS f 122 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 28 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 29 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " 0.026 5.00e-02 4.00e+02 ... (remaining 2687 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 167 2.59 - 3.17: 13180 3.17 - 3.75: 24011 3.75 - 4.32: 32064 4.32 - 4.90: 53619 Nonbonded interactions: 123041 Sorted by model distance: nonbonded pdb=" O GLY f 67 " pdb=" OH TYR P 102 " model vdw 2.018 3.040 nonbonded pdb=" N GLN F 33 " pdb=" NE2 GLN F 33 " model vdw 2.047 3.200 nonbonded pdb=" O GLY F 67 " pdb=" OH TYR R 102 " model vdw 2.120 3.040 nonbonded pdb=" O ILE D 24 " pdb=" OH TYR E 95 " model vdw 2.183 3.040 nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.184 3.040 ... (remaining 123036 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 27 through 55) selection = chain 'B' selection = (chain 'a' and resid 27 through 55) selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = (chain 'F' and resid 33 through 153) selection = chain 'e' selection = (chain 'f' and resid 33 through 153) } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'P' selection = chain 'R' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.600 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 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 0.040 15990 Z= 0.151 Angle : 0.752 11.673 21712 Z= 0.384 Chirality : 0.044 0.299 2506 Planarity : 0.003 0.047 2690 Dihedral : 15.456 88.924 5720 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % Rotamer: Outliers : 2.45 % Allowed : 17.33 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1946 helix: 2.19 (0.23), residues: 482 sheet: -0.35 (0.20), residues: 636 loop : -1.35 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 30 TYR 0.016 0.001 TYR n 264 PHE 0.022 0.001 PHE a 40 TRP 0.016 0.001 TRP R 163 HIS 0.007 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00320 (15968) covalent geometry : angle 0.74973 (21668) SS BOND : bond 0.00241 ( 22) SS BOND : angle 1.38443 ( 44) hydrogen bonds : bond 0.19828 ( 759) hydrogen bonds : angle 7.19692 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 51 LEU cc_start: 0.3857 (OUTLIER) cc_final: 0.3553 (tt) REVERT: g 67 GLU cc_start: 0.6815 (mp0) cc_final: 0.6202 (pm20) REVERT: g 115 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.6843 (tp) REVERT: P 144 MET cc_start: 0.2631 (mtm) cc_final: 0.2426 (mtt) REVERT: A 35 LEU cc_start: 0.6991 (pp) cc_final: 0.6663 (pp) REVERT: B 51 LEU cc_start: 0.3943 (OUTLIER) cc_final: 0.3681 (tt) REVERT: F 125 MET cc_start: 0.6014 (pmm) cc_final: 0.5057 (pmm) REVERT: G 67 GLU cc_start: 0.6801 (mp0) cc_final: 0.6184 (pm20) REVERT: G 115 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.6876 (tp) REVERT: Q 3 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8386 (mp10) outliers start: 43 outliers final: 32 residues processed: 332 average time/residue: 0.1195 time to fit residues: 60.8766 Evaluate side-chains 288 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 107 ASP Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 119 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 166 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.216760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.172928 restraints weight = 25720.550| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.71 r_work: 0.3771 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15990 Z= 0.160 Angle : 0.714 10.665 21712 Z= 0.361 Chirality : 0.044 0.208 2506 Planarity : 0.004 0.030 2690 Dihedral : 6.702 57.760 2202 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.42 % Allowed : 17.27 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1946 helix: 2.40 (0.22), residues: 482 sheet: -0.21 (0.20), residues: 664 loop : -1.21 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.035 0.002 TYR B 33 PHE 0.012 0.001 PHE F 110 TRP 0.017 0.001 TRP G 55 HIS 0.005 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00356 (15968) covalent geometry : angle 0.71297 (21668) SS BOND : bond 0.00430 ( 22) SS BOND : angle 1.09802 ( 44) hydrogen bonds : bond 0.03850 ( 759) hydrogen bonds : angle 5.23831 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 35 LEU cc_start: 0.7526 (pp) cc_final: 0.7314 (pp) REVERT: b 51 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.3922 (tt) REVERT: d 100 ASP cc_start: 0.7213 (p0) cc_final: 0.6868 (p0) REVERT: f 41 SER cc_start: 0.7218 (m) cc_final: 0.6814 (p) REVERT: f 119 CYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7423 (p) REVERT: f 121 ASN cc_start: 0.7235 (t0) cc_final: 0.6916 (t0) REVERT: f 125 MET cc_start: 0.5098 (pmm) cc_final: 0.4486 (pmm) REVERT: g 115 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7016 (tp) REVERT: P 144 MET cc_start: 0.3391 (mtm) cc_final: 0.3071 (mtt) REVERT: B 51 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3879 (tt) REVERT: D 91 ARG cc_start: 0.5661 (tmt170) cc_final: 0.4788 (tmm160) REVERT: F 41 SER cc_start: 0.7215 (m) cc_final: 0.6807 (p) REVERT: F 119 CYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7387 (p) REVERT: F 121 ASN cc_start: 0.7082 (t0) cc_final: 0.6740 (t0) REVERT: G 115 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7027 (tp) REVERT: N 265 MET cc_start: 0.7912 (tmm) cc_final: 0.7707 (tmm) outliers start: 60 outliers final: 31 residues processed: 321 average time/residue: 0.1118 time to fit residues: 55.4711 Evaluate side-chains 302 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 265 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain n residue 252 THR Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 119 CYS Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 1 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 92 GLN f 33 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.214991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.170071 restraints weight = 25827.570| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.71 r_work: 0.3717 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15990 Z= 0.233 Angle : 0.710 10.595 21712 Z= 0.359 Chirality : 0.045 0.200 2506 Planarity : 0.004 0.030 2690 Dihedral : 6.550 60.654 2176 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 4.56 % Allowed : 19.04 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 1946 helix: 2.33 (0.22), residues: 482 sheet: -0.23 (0.20), residues: 636 loop : -1.33 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.038 0.002 TYR N 266 PHE 0.023 0.002 PHE Q 136 TRP 0.015 0.002 TRP P 36 HIS 0.005 0.002 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00536 (15968) covalent geometry : angle 0.70843 (21668) SS BOND : bond 0.00638 ( 22) SS BOND : angle 1.22928 ( 44) hydrogen bonds : bond 0.03766 ( 759) hydrogen bonds : angle 4.89375 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 265 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: f 121 ASN cc_start: 0.7557 (t0) cc_final: 0.7020 (t0) REVERT: g 70 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6763 (mtmm) REVERT: g 115 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7177 (tp) REVERT: P 144 MET cc_start: 0.3431 (mtm) cc_final: 0.3105 (mtt) REVERT: P 205 ASN cc_start: 0.6264 (OUTLIER) cc_final: 0.5859 (m-40) REVERT: F 121 ASN cc_start: 0.7450 (t0) cc_final: 0.7155 (t0) REVERT: G 70 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6774 (mtmm) REVERT: G 115 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7104 (tp) REVERT: N 265 MET cc_start: 0.7751 (tmm) cc_final: 0.7448 (tmm) REVERT: N 266 TYR cc_start: 0.8565 (m-80) cc_final: 0.8349 (m-80) REVERT: R 205 ASN cc_start: 0.6285 (OUTLIER) cc_final: 0.5873 (m-40) outliers start: 80 outliers final: 49 residues processed: 323 average time/residue: 0.1069 time to fit residues: 53.7641 Evaluate side-chains 305 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain e residue 92 GLN Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** 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 = 0.4716 r_free = 0.4716 target = 0.216698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.173060 restraints weight = 25881.960| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.88 r_work: 0.3733 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15990 Z= 0.147 Angle : 0.682 10.973 21712 Z= 0.341 Chirality : 0.044 0.198 2506 Planarity : 0.003 0.029 2690 Dihedral : 6.219 59.395 2174 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 4.56 % Allowed : 19.90 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1946 helix: 2.21 (0.22), residues: 482 sheet: -0.20 (0.20), residues: 650 loop : -1.25 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 82 TYR 0.028 0.001 TYR N 266 PHE 0.019 0.001 PHE O 136 TRP 0.012 0.001 TRP P 36 HIS 0.005 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00330 (15968) covalent geometry : angle 0.68089 (21668) SS BOND : bond 0.00477 ( 22) SS BOND : angle 1.13473 ( 44) hydrogen bonds : bond 0.03387 ( 759) hydrogen bonds : angle 4.66242 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 265 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 41 SER cc_start: 0.7293 (m) cc_final: 0.6849 (p) REVERT: g 70 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6767 (mtmm) REVERT: g 105 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7263 (pt0) REVERT: g 111 ASN cc_start: 0.5439 (p0) cc_final: 0.5104 (p0) REVERT: g 114 THR cc_start: 0.7203 (p) cc_final: 0.6984 (t) REVERT: g 115 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7272 (tp) REVERT: n 266 TYR cc_start: 0.8687 (m-80) cc_final: 0.8457 (m-80) REVERT: P 144 MET cc_start: 0.3418 (mtm) cc_final: 0.3120 (mtt) REVERT: F 41 SER cc_start: 0.7275 (m) cc_final: 0.6834 (p) REVERT: F 121 ASN cc_start: 0.7374 (t0) cc_final: 0.6970 (t0) REVERT: G 70 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6762 (mtmm) REVERT: G 115 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7216 (tp) REVERT: N 265 MET cc_start: 0.7814 (tmm) cc_final: 0.7465 (tmm) REVERT: N 266 TYR cc_start: 0.8697 (m-80) cc_final: 0.8420 (m-80) outliers start: 80 outliers final: 53 residues processed: 324 average time/residue: 0.1144 time to fit residues: 56.9518 Evaluate side-chains 304 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 33 GLN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 145 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** 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 = 0.4708 r_free = 0.4708 target = 0.215852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.172572 restraints weight = 25845.559| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.65 r_work: 0.3734 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15990 Z= 0.183 Angle : 0.701 10.504 21712 Z= 0.350 Chirality : 0.044 0.223 2506 Planarity : 0.003 0.036 2690 Dihedral : 5.972 59.236 2166 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 4.79 % Allowed : 20.98 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1946 helix: 2.17 (0.22), residues: 482 sheet: -0.09 (0.21), residues: 622 loop : -1.21 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 117 TYR 0.028 0.002 TYR n 264 PHE 0.018 0.001 PHE O 136 TRP 0.013 0.002 TRP P 36 HIS 0.005 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00416 (15968) covalent geometry : angle 0.69944 (21668) SS BOND : bond 0.00549 ( 22) SS BOND : angle 1.25614 ( 44) hydrogen bonds : bond 0.03399 ( 759) hydrogen bonds : angle 4.61310 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 256 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 100 ASP cc_start: 0.7140 (p0) cc_final: 0.6689 (p0) REVERT: f 134 VAL cc_start: 0.7522 (m) cc_final: 0.7270 (p) REVERT: g 70 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6736 (mtmm) REVERT: g 111 ASN cc_start: 0.5543 (p0) cc_final: 0.5223 (p0) REVERT: g 114 THR cc_start: 0.7132 (p) cc_final: 0.6903 (t) REVERT: g 115 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7348 (tp) REVERT: P 144 MET cc_start: 0.3734 (mtm) cc_final: 0.3360 (mtt) REVERT: P 154 TYR cc_start: 0.7346 (p90) cc_final: 0.7145 (p90) REVERT: D 91 ARG cc_start: 0.5504 (tmt170) cc_final: 0.4521 (tmm160) REVERT: G 70 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6740 (mtmm) REVERT: M 261 MET cc_start: 0.9072 (mmt) cc_final: 0.8797 (mmt) REVERT: N 260 THR cc_start: 0.8851 (t) cc_final: 0.8629 (t) REVERT: N 265 MET cc_start: 0.7856 (tmm) cc_final: 0.7318 (tmm) REVERT: N 266 TYR cc_start: 0.8718 (m-80) cc_final: 0.8265 (m-80) REVERT: R 154 TYR cc_start: 0.7334 (p90) cc_final: 0.7134 (p90) outliers start: 84 outliers final: 65 residues processed: 318 average time/residue: 0.1097 time to fit residues: 53.9112 Evaluate side-chains 318 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 250 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 33 GLN Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain g residue 115 ILE Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 175 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 135 optimal weight: 0.0570 chunk 144 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 51 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 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 = 0.4710 r_free = 0.4710 target = 0.216158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.174855 restraints weight = 25715.824| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.98 r_work: 0.3725 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15990 Z= 0.155 Angle : 0.693 10.504 21712 Z= 0.347 Chirality : 0.044 0.260 2506 Planarity : 0.003 0.042 2690 Dihedral : 5.813 58.924 2164 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 4.45 % Allowed : 21.84 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1946 helix: 2.14 (0.22), residues: 480 sheet: -0.07 (0.21), residues: 626 loop : -1.18 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 117 TYR 0.032 0.001 TYR n 266 PHE 0.016 0.001 PHE O 136 TRP 0.011 0.001 TRP P 36 HIS 0.005 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00349 (15968) covalent geometry : angle 0.69238 (21668) SS BOND : bond 0.00454 ( 22) SS BOND : angle 1.05243 ( 44) hydrogen bonds : bond 0.03356 ( 759) hydrogen bonds : angle 4.53383 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 262 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 134 VAL cc_start: 0.7468 (m) cc_final: 0.7209 (p) REVERT: g 70 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6713 (mtmm) REVERT: g 111 ASN cc_start: 0.5316 (p0) cc_final: 0.4999 (p0) REVERT: g 114 THR cc_start: 0.7272 (p) cc_final: 0.7027 (t) REVERT: g 115 ILE cc_start: 0.7762 (mt) cc_final: 0.7399 (tp) REVERT: n 266 TYR cc_start: 0.8532 (m-80) cc_final: 0.8268 (m-80) REVERT: P 144 MET cc_start: 0.3474 (mtm) cc_final: 0.3187 (mtt) REVERT: P 154 TYR cc_start: 0.7335 (p90) cc_final: 0.7083 (p90) REVERT: A 32 CYS cc_start: 0.7811 (p) cc_final: 0.7437 (t) REVERT: E 123 MET cc_start: 0.6634 (ppp) cc_final: 0.5245 (tpp) REVERT: F 134 VAL cc_start: 0.7460 (m) cc_final: 0.7190 (p) REVERT: G 70 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6719 (mtmm) REVERT: M 261 MET cc_start: 0.9047 (mmt) cc_final: 0.8807 (mmt) REVERT: M 262 MET cc_start: 0.8173 (tpt) cc_final: 0.7906 (tpp) REVERT: N 260 THR cc_start: 0.8837 (t) cc_final: 0.8590 (t) REVERT: N 265 MET cc_start: 0.7732 (tmm) cc_final: 0.7173 (tmm) REVERT: N 266 TYR cc_start: 0.8656 (m-80) cc_final: 0.8159 (m-80) REVERT: R 154 TYR cc_start: 0.7339 (p90) cc_final: 0.7090 (p90) outliers start: 78 outliers final: 61 residues processed: 315 average time/residue: 0.1099 time to fit residues: 53.4581 Evaluate side-chains 311 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain m residue 270 ARG Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 81 MET Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 28 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 259 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.214474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.179102 restraints weight = 25722.678| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 3.10 r_work: 0.3681 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15990 Z= 0.208 Angle : 0.725 10.480 21712 Z= 0.364 Chirality : 0.045 0.267 2506 Planarity : 0.004 0.042 2690 Dihedral : 5.922 59.265 2160 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.12 % Rotamer: Outliers : 4.56 % Allowed : 21.84 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1946 helix: 2.15 (0.22), residues: 478 sheet: -0.13 (0.21), residues: 626 loop : -1.21 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 117 TYR 0.024 0.002 TYR n 264 PHE 0.026 0.002 PHE O 136 TRP 0.014 0.002 TRP R 36 HIS 0.005 0.002 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00480 (15968) covalent geometry : angle 0.72331 (21668) SS BOND : bond 0.00673 ( 22) SS BOND : angle 1.33154 ( 44) hydrogen bonds : bond 0.03427 ( 759) hydrogen bonds : angle 4.56371 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 254 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 123 MET cc_start: 0.6467 (ppp) cc_final: 0.4816 (tpp) REVERT: f 119 CYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7935 (p) REVERT: f 134 VAL cc_start: 0.7482 (m) cc_final: 0.7235 (p) REVERT: g 70 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6719 (mtmm) REVERT: g 86 GLN cc_start: 0.7339 (mm-40) cc_final: 0.7136 (mm110) REVERT: g 111 ASN cc_start: 0.5265 (p0) cc_final: 0.4998 (p0) REVERT: g 114 THR cc_start: 0.7348 (p) cc_final: 0.7035 (t) REVERT: g 115 ILE cc_start: 0.7811 (mt) cc_final: 0.7398 (tp) REVERT: n 266 TYR cc_start: 0.8537 (m-80) cc_final: 0.8302 (m-80) REVERT: P 144 MET cc_start: 0.3797 (mtm) cc_final: 0.3491 (mtt) REVERT: P 154 TYR cc_start: 0.7290 (p90) cc_final: 0.7076 (p90) REVERT: A 32 CYS cc_start: 0.7522 (p) cc_final: 0.7015 (t) REVERT: G 70 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6722 (mtmm) REVERT: N 265 MET cc_start: 0.7631 (tmm) cc_final: 0.7063 (tmm) REVERT: N 266 TYR cc_start: 0.8612 (m-80) cc_final: 0.8097 (m-80) REVERT: R 154 TYR cc_start: 0.7304 (p90) cc_final: 0.7086 (p90) outliers start: 80 outliers final: 70 residues processed: 311 average time/residue: 0.1108 time to fit residues: 53.4738 Evaluate side-chains 321 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 248 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 119 CYS Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain m residue 270 ARG Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 81 MET Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 34 TYR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 151 ILE Chi-restraints excluded: chain Q residue 160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.215416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.176582 restraints weight = 26064.710| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 3.17 r_work: 0.3705 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15990 Z= 0.161 Angle : 0.713 10.484 21712 Z= 0.357 Chirality : 0.044 0.238 2506 Planarity : 0.003 0.047 2690 Dihedral : 5.847 59.204 2160 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 4.16 % Allowed : 22.86 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1946 helix: 2.17 (0.22), residues: 476 sheet: -0.13 (0.21), residues: 626 loop : -1.19 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 82 TYR 0.028 0.002 TYR n 264 PHE 0.023 0.001 PHE O 136 TRP 0.013 0.001 TRP P 163 HIS 0.005 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00366 (15968) covalent geometry : angle 0.71215 (21668) SS BOND : bond 0.00562 ( 22) SS BOND : angle 1.16728 ( 44) hydrogen bonds : bond 0.03319 ( 759) hydrogen bonds : angle 4.50934 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 255 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 134 VAL cc_start: 0.7437 (m) cc_final: 0.7181 (p) REVERT: g 70 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6607 (mtmm) REVERT: g 86 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7064 (mm110) REVERT: g 105 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7718 (pp30) REVERT: P 144 MET cc_start: 0.3580 (mtm) cc_final: 0.3331 (mtt) REVERT: P 154 TYR cc_start: 0.7300 (p90) cc_final: 0.7044 (p90) REVERT: A 32 CYS cc_start: 0.7612 (p) cc_final: 0.7095 (t) REVERT: E 123 MET cc_start: 0.6575 (ppp) cc_final: 0.5110 (tpt) REVERT: F 134 VAL cc_start: 0.7499 (m) cc_final: 0.7252 (p) REVERT: G 70 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6608 (mtmm) REVERT: G 86 GLN cc_start: 0.7310 (mm-40) cc_final: 0.7040 (mm110) REVERT: N 265 MET cc_start: 0.7694 (tmm) cc_final: 0.7108 (tmm) REVERT: N 266 TYR cc_start: 0.8498 (m-80) cc_final: 0.7981 (m-80) REVERT: R 154 TYR cc_start: 0.7294 (p90) cc_final: 0.7039 (p90) outliers start: 73 outliers final: 68 residues processed: 306 average time/residue: 0.1123 time to fit residues: 54.3157 Evaluate side-chains 319 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 249 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 268 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 81 MET Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain R residue 205 ASN Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 68 optimal weight: 0.0010 chunk 14 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 175 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.215943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.187636 restraints weight = 25828.988| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.27 r_work: 0.3908 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15990 Z= 0.148 Angle : 0.729 10.764 21712 Z= 0.363 Chirality : 0.044 0.244 2506 Planarity : 0.003 0.047 2690 Dihedral : 5.750 59.904 2160 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 4.22 % Allowed : 23.26 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1946 helix: 2.19 (0.22), residues: 476 sheet: -0.07 (0.21), residues: 626 loop : -1.14 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 270 TYR 0.023 0.001 TYR n 264 PHE 0.020 0.001 PHE O 136 TRP 0.015 0.001 TRP P 163 HIS 0.005 0.001 HIS e 61 Details of bonding type rmsd covalent geometry : bond 0.00331 (15968) covalent geometry : angle 0.72756 (21668) SS BOND : bond 0.00501 ( 22) SS BOND : angle 1.33439 ( 44) hydrogen bonds : bond 0.03310 ( 759) hydrogen bonds : angle 4.44418 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 257 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: e 123 MET cc_start: 0.5526 (ppp) cc_final: 0.3991 (tpt) REVERT: f 134 VAL cc_start: 0.7271 (m) cc_final: 0.7055 (p) REVERT: g 70 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6274 (mtmm) REVERT: g 115 ILE cc_start: 0.7479 (mt) cc_final: 0.7253 (tp) REVERT: P 144 MET cc_start: 0.4210 (mtm) cc_final: 0.3880 (mtt) REVERT: E 123 MET cc_start: 0.5592 (ppp) cc_final: 0.4295 (tpp) REVERT: F 134 VAL cc_start: 0.7339 (m) cc_final: 0.7105 (p) REVERT: G 70 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6240 (mtmm) REVERT: G 115 ILE cc_start: 0.7423 (mt) cc_final: 0.7189 (tp) REVERT: N 265 MET cc_start: 0.7052 (tmm) cc_final: 0.6721 (tmm) outliers start: 74 outliers final: 63 residues processed: 309 average time/residue: 0.1081 time to fit residues: 52.1030 Evaluate side-chains 312 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 247 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 81 MET Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 151 ILE Chi-restraints excluded: chain Q residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 164 optimal weight: 0.0020 chunk 29 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 ASN ** P 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 205 ASN ** R 208 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 = 0.4692 r_free = 0.4692 target = 0.218733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.182285 restraints weight = 25548.389| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 3.03 r_work: 0.3728 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15990 Z= 0.170 Angle : 0.747 10.465 21712 Z= 0.375 Chirality : 0.044 0.239 2506 Planarity : 0.004 0.043 2690 Dihedral : 5.655 59.188 2158 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.52 % Favored : 95.43 % Rotamer: Outliers : 3.88 % Allowed : 23.83 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1946 helix: 2.16 (0.22), residues: 476 sheet: -0.06 (0.21), residues: 626 loop : -1.20 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 102 TYR 0.041 0.002 TYR n 266 PHE 0.024 0.001 PHE b 50 TRP 0.014 0.002 TRP P 163 HIS 0.005 0.001 HIS e 61 Details of bonding type rmsd covalent geometry : bond 0.00388 (15968) covalent geometry : angle 0.74555 (21668) SS BOND : bond 0.00674 ( 22) SS BOND : angle 1.33940 ( 44) hydrogen bonds : bond 0.03407 ( 759) hydrogen bonds : angle 4.47253 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 248 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: e 123 MET cc_start: 0.6185 (ppp) cc_final: 0.4420 (tpt) REVERT: f 134 VAL cc_start: 0.7377 (m) cc_final: 0.7150 (p) REVERT: g 70 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6499 (mtmm) REVERT: P 144 MET cc_start: 0.4002 (mtm) cc_final: 0.3698 (mtt) REVERT: E 123 MET cc_start: 0.6375 (ppp) cc_final: 0.4880 (tpp) REVERT: F 134 VAL cc_start: 0.7463 (m) cc_final: 0.7225 (p) REVERT: G 70 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6493 (mtmm) REVERT: N 265 MET cc_start: 0.7535 (tmm) cc_final: 0.7060 (tmm) REVERT: N 266 TYR cc_start: 0.8302 (m-80) cc_final: 0.7688 (m-80) outliers start: 68 outliers final: 64 residues processed: 298 average time/residue: 0.1091 time to fit residues: 50.3919 Evaluate side-chains 309 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 243 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 33 TYR Chi-restraints excluded: chain b residue 42 TYR Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 57 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 81 MET Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 145 ILE Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 92 GLN Chi-restraints excluded: chain F residue 122 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain M residue 283 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 268 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 121 PHE Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 145 ILE Chi-restraints excluded: chain Q residue 151 ILE Chi-restraints excluded: chain Q residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 139 optimal weight: 0.0060 chunk 21 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 101 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.6756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.215666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.179197 restraints weight = 25657.660| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 3.03 r_work: 0.3754 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15990 Z= 0.154 Angle : 0.744 10.456 21712 Z= 0.374 Chirality : 0.045 0.239 2506 Planarity : 0.003 0.049 2690 Dihedral : 5.636 59.790 2158 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 3.93 % Allowed : 23.95 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1946 helix: 2.04 (0.22), residues: 476 sheet: -0.03 (0.21), residues: 626 loop : -1.15 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 270 TYR 0.028 0.001 TYR n 264 PHE 0.026 0.001 PHE b 50 TRP 0.028 0.002 TRP P 163 HIS 0.006 0.001 HIS e 61 Details of bonding type rmsd covalent geometry : bond 0.00348 (15968) covalent geometry : angle 0.74224 (21668) SS BOND : bond 0.00445 ( 22) SS BOND : angle 1.33240 ( 44) hydrogen bonds : bond 0.03366 ( 759) hydrogen bonds : angle 4.43211 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4852.47 seconds wall clock time: 83 minutes 57.07 seconds (5037.07 seconds total)