Starting phenix.real_space_refine on Tue Aug 26 14:42:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bvj_16265/08_2025/8bvj_16265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvj_16265/08_2025/8bvj_16265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2025/8bvj_16265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2025/8bvj_16265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2025/8bvj_16265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2025/8bvj_16265.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 54 5.16 5 C 12131 2.51 5 N 3409 2.21 5 O 3633 1.98 5 H 18901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38183 Number of models: 1 Model: "" Number of chains: 23 Chain: "R" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1085 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "T" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "J" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1111 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "L" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1025 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "N" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1107 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "P" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "X" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1021 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "Y" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1103 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "S" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1111 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "U" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1008 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "V" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1084 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "W" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1126 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "K" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1119 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "M" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "D" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1112 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "E" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1141 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "F" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "I" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1097 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "Q" Number of atoms: 4163 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 261, 4149 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 248} Conformer: "B" Number of residues, atoms: 261, 4149 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 248} bond proxies already assigned to first conformer: 4188 Chain: "B" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1788 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 7, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 31, 'rna3p': 23} Chain breaks: 3 Chain: "G" Number of atoms: 4162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 4148 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Conformer: "B" Number of residues, atoms: 260, 4148 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} bond proxies already assigned to first conformer: 4186 Chain: "C" Number of atoms: 4184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Conformer: "B" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} bond proxies already assigned to first conformer: 4209 Chain: "A" Number of atoms: 4184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Conformer: "B" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} bond proxies already assigned to first conformer: 4209 Time building chain proxies: 8.59, per 1000 atoms: 0.22 Number of scatterers: 38183 At special positions: 0 Unit cell: (99.6, 146.91, 152.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 55 15.00 O 3633 8.00 N 3409 7.00 C 12131 6.00 H 18901 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Q 32 " - pdb=" SG CYS Q 146 " 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: 3.27 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 19 sheets defined 27.7% alpha, 25.0% beta 5 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'R' and resid 7 through 18 Processing helix chain 'T' and resid 7 through 19 Processing helix chain 'J' and resid 7 through 19 Processing helix chain 'L' and resid 7 through 18 removed outlier: 3.640A pdb=" N TYR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'P' and resid 7 through 18 removed outlier: 3.645A pdb=" N GLU P 18 " --> pdb=" O THR P 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 19 Processing helix chain 'Y' and resid 7 through 18 Processing helix chain 'S' and resid 7 through 19 Processing helix chain 'U' and resid 9 through 18 Processing helix chain 'V' and resid 7 through 19 Processing helix chain 'W' and resid 7 through 18 removed outlier: 3.503A pdb=" N TYR W 11 " --> pdb=" O LEU W 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 19 removed outlier: 3.665A pdb=" N TYR K 11 " --> pdb=" O LEU K 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 18 Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'E' and resid 7 through 18 Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'I' and resid 7 through 19 Processing helix chain 'Q' and resid 10 through 18 removed outlier: 3.540A pdb=" N ALA Q 14 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 26 Processing helix chain 'Q' and resid 39 through 44 Processing helix chain 'Q' and resid 85 through 90 Processing helix chain 'Q' and resid 115 through 137 Processing helix chain 'Q' and resid 154 through 158 Processing helix chain 'Q' and resid 160 through 165 Processing helix chain 'Q' and resid 171 through 183 Processing helix chain 'Q' and resid 190 through 195 Processing helix chain 'Q' and resid 207 through 214 removed outlier: 3.751A pdb=" N GLU Q 211 " --> pdb=" O SER Q 207 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 230 removed outlier: 3.924A pdb=" N ARG Q 230 " --> pdb=" O GLY Q 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 227 through 230' Processing helix chain 'G' and resid 10 through 17 Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 85 through 90 Processing helix chain 'G' and resid 115 through 135 Processing helix chain 'G' and resid 154 through 158 Processing helix chain 'G' and resid 160 through 165 removed outlier: 3.527A pdb=" N CYS G 164 " --> pdb=" O ASN G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 183 Processing helix chain 'G' and resid 190 through 195 Processing helix chain 'G' and resid 207 through 214 Processing helix chain 'G' and resid 228 through 230 No H-bonds generated for 'chain 'G' and resid 228 through 230' Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.555A pdb=" N GLY C 66 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 115 through 137 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 160 through 165 removed outlier: 3.562A pdb=" N CYS C 164 " --> pdb=" O ASN C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.935A pdb=" N ARG C 230 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.761A pdb=" N TRP A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.547A pdb=" N LEU A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.784A pdb=" N CYS A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.733A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing sheet with id=AA1, first strand: chain 'R' and resid 22 through 26 removed outlier: 3.565A pdb=" N THR R 61 " --> pdb=" O TYR R 25 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER R 60 " --> pdb=" O TYR P 55 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL P 43 " --> pdb=" O PHE P 39 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE P 39 " --> pdb=" O VAL P 43 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU P 45 " --> pdb=" O GLU P 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 36 through 39 removed outlier: 3.647A pdb=" N SER R 38 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER T 60 " --> pdb=" O TYR R 55 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR T 61 " --> pdb=" O TYR T 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR T 25 " --> pdb=" O THR T 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'T' and resid 35 through 40 removed outlier: 6.517A pdb=" N LEU T 45 " --> pdb=" O GLU T 37 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE T 39 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL T 43 " --> pdb=" O PHE T 39 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR J 61 " --> pdb=" O TYR J 25 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL J 63 " --> pdb=" O SER J 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 35 through 39 removed outlier: 7.245A pdb=" N LEU J 45 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE J 39 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL J 43 " --> pdb=" O PHE J 39 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER J 51 " --> pdb=" O PRO L 64 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER L 60 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR L 61 " --> pdb=" O TYR L 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN L 35 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU L 45 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE L 39 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL L 43 " --> pdb=" O PHE L 39 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN L 52 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER L 51 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET L 53 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER N 60 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL N 63 " --> pdb=" O SER N 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 35 through 39 removed outlier: 7.147A pdb=" N LEU N 45 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE N 39 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL N 43 " --> pdb=" O PHE N 39 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER P 60 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR P 25 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL P 62 " --> pdb=" O SER P 23 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER P 23 " --> pdb=" O VAL P 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 31 through 34 removed outlier: 3.616A pdb=" N VAL X 22 " --> pdb=" O GLY X 34 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR X 61 " --> pdb=" O TYR X 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 36 through 39 removed outlier: 6.894A pdb=" N SER Y 60 " --> pdb=" O TYR X 55 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR Y 25 " --> pdb=" O THR Y 61 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL Y 63 " --> pdb=" O SER Y 23 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU Y 45 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE Y 39 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL Y 43 " --> pdb=" O PHE Y 39 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR S 61 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER S 51 " --> pdb=" O PRO U 64 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER U 60 " --> pdb=" O TYR S 55 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE U 36 " --> pdb=" O LYS U 47 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS U 47 " --> pdb=" O ILE U 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER U 38 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL U 43 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER U 51 " --> pdb=" O PRO V 64 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET U 53 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU V 45 " --> pdb=" O GLU V 37 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE V 39 " --> pdb=" O VAL V 43 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL V 43 " --> pdb=" O PHE V 39 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER W 60 " --> pdb=" O TYR V 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 36 through 39 removed outlier: 6.551A pdb=" N LEU W 45 " --> pdb=" O GLU W 37 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE W 39 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL W 43 " --> pdb=" O PHE W 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL W 54 " --> pdb=" O ILE W 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 22 through 26 removed outlier: 3.523A pdb=" N THR M 61 " --> pdb=" O TYR M 25 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER M 60 " --> pdb=" O TYR K 55 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER K 38 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL K 22 " --> pdb=" O GLY K 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER K 23 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL K 62 " --> pdb=" O SER K 23 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR K 25 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER K 60 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER I 51 " --> pdb=" O PRO K 64 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN I 52 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER I 38 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LYS I 47 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE I 36 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER I 23 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL I 62 " --> pdb=" O SER I 23 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR I 25 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER I 60 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE F 39 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU F 45 " --> pdb=" O GLU F 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.666A pdb=" N LEU M 45 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE M 39 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL M 43 " --> pdb=" O PHE M 39 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR M 55 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N SER D 60 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR D 25 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL D 62 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER D 23 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.755A pdb=" N LEU D 45 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE D 39 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 43 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER D 51 " --> pdb=" O PRO E 64 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER E 60 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR E 25 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL E 62 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER E 23 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU E 45 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE E 39 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER E 51 " --> pdb=" O PRO F 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER F 60 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR F 25 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL F 62 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER F 23 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 56 through 58 removed outlier: 3.716A pdb=" N VAL Q 68 " --> pdb=" O CYS Q 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA Q 69 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU Q 33 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE Q 31 " --> pdb=" O TYR Q 71 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG Q 2 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N CYS Q 32 " --> pdb=" O ARG Q 2 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE Q 4 " --> pdb=" O CYS Q 32 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN Q 34 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL Q 6 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE Q 250 " --> pdb=" O LYS Q 236 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 78 through 80 removed outlier: 3.801A pdb=" N ALA Q 78 " --> pdb=" O ASP Q 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE Q 104 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 56 through 58 removed outlier: 3.605A pdb=" N LEU G 33 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG G 2 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N CYS G 32 " --> pdb=" O ARG G 2 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE G 4 " --> pdb=" O CYS G 32 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE G 250 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA G 235 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP G 252 " --> pdb=" O ARG G 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 78 through 81 removed outlier: 3.540A pdb=" N ILE G 144 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU G 224 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 188 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.577A pdb=" N TYR C 56 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 81 removed outlier: 6.558A pdb=" N SER C 103 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS C 146 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA C 105 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER C 148 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 107 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 223 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY C 147 " --> pdb=" O TYR C 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 54 through 58 removed outlier: 3.601A pdb=" N TYR A 56 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG A 2 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS A 32 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 4 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A 34 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 6 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 250 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 234 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.651A pdb=" N VAL A 223 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 147 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 221 " --> pdb=" O GLY A 147 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 8.98 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18887 1.03 - 1.23: 19 1.23 - 1.42: 8442 1.42 - 1.62: 11288 1.62 - 1.81: 92 Bond restraints: 38728 Sorted by residual: bond pdb=" N ALA G 0 " pdb=" CA ALA G 0 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N ALA G 0 " pdb=" H ALA G 0 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C HIS X 57 " pdb=" N ALA X 58 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.17e-02 7.31e+03 9.63e-01 bond pdb=" CA LEU C 70 " pdb=" C LEU C 70 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.99e-01 bond pdb=" CA MET G 1 " pdb=" CB MET G 1 " ideal model delta sigma weight residual 1.530 1.516 0.015 1.69e-02 3.50e+03 7.53e-01 ... (remaining 38723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 65721 0.99 - 1.98: 3872 1.98 - 2.98: 275 2.98 - 3.97: 124 3.97 - 4.96: 15 Bond angle restraints: 70007 Sorted by residual: angle pdb=" N PHE A 99 " pdb=" CA PHE A 99 " pdb=" C PHE A 99 " ideal model delta sigma weight residual 110.80 105.84 4.96 2.13e+00 2.20e-01 5.42e+00 angle pdb=" N ARG A 196 " pdb=" CA ARG A 196 " pdb=" C ARG A 196 " ideal model delta sigma weight residual 112.57 110.01 2.56 1.13e+00 7.83e-01 5.15e+00 angle pdb=" N LEU P 7 " pdb=" CA LEU P 7 " pdb=" C LEU P 7 " ideal model delta sigma weight residual 114.56 111.69 2.87 1.27e+00 6.20e-01 5.10e+00 angle pdb=" C VAL G 8 " pdb=" CA VAL G 8 " pdb=" CB VAL G 8 " ideal model delta sigma weight residual 112.16 108.66 3.50 1.55e+00 4.16e-01 5.09e+00 angle pdb=" C PHE A 99 " pdb=" CA PHE A 99 " pdb=" CB PHE A 99 " ideal model delta sigma weight residual 110.42 114.87 -4.45 1.99e+00 2.53e-01 5.00e+00 ... (remaining 70002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 17697 34.30 - 68.59: 450 68.59 - 102.89: 46 102.89 - 137.19: 10 137.19 - 171.48: 8 Dihedral angle restraints: 18211 sinusoidal: 10456 harmonic: 7755 Sorted by residual: dihedral pdb=" O4' C B 57 " pdb=" C1' C B 57 " pdb=" N1 C B 57 " pdb=" C2 C B 57 " ideal model delta sinusoidal sigma weight residual -128.00 25.02 -153.02 1 1.70e+01 3.46e-03 6.28e+01 dihedral pdb=" CB CYS Q 32 " pdb=" SG CYS Q 32 " pdb=" SG CYS Q 146 " pdb=" CB CYS Q 146 " ideal model delta sinusoidal sigma weight residual 93.00 31.71 61.29 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" O4' A B 77 " pdb=" C1' A B 77 " pdb=" N9 A B 77 " pdb=" C4 A B 77 " ideal model delta sinusoidal sigma weight residual -106.00 -170.10 64.10 1 1.70e+01 3.46e-03 1.87e+01 ... (remaining 18208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2053 0.030 - 0.059: 624 0.059 - 0.089: 117 0.089 - 0.118: 224 0.118 - 0.148: 45 Chirality restraints: 3063 Sorted by residual: chirality pdb=" C3' A B 82 " pdb=" C4' A B 82 " pdb=" O3' A B 82 " pdb=" C2' A B 82 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE G 144 " pdb=" N ILE G 144 " pdb=" C ILE G 144 " pdb=" CB ILE G 144 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA VAL P 20 " pdb=" N VAL P 20 " pdb=" C VAL P 20 " pdb=" CB VAL P 20 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 3060 not shown) Planarity restraints: 5428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 9 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO I 10 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 10 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 10 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 172 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO A 173 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP P 9 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO P 10 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO P 10 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO P 10 " -0.016 5.00e-02 4.00e+02 ... (remaining 5425 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1374 2.16 - 2.77: 74204 2.77 - 3.38: 106777 3.38 - 3.99: 140006 3.99 - 4.60: 215726 Nonbonded interactions: 538087 Sorted by model distance: nonbonded pdb=" O HIS G 131 " pdb=" HG SER G 134 " model vdw 1.546 2.450 nonbonded pdb=" O GLY G 115 " pdb=" HG SER G 118 " model vdw 1.581 2.450 nonbonded pdb=" H LYS F 31 " pdb=" OP2 A B 58 " model vdw 1.636 2.450 nonbonded pdb=" OE1 GLU G 174 " pdb=" H GLU G 174 " model vdw 1.638 2.450 nonbonded pdb=" O GLY C 115 " pdb=" HG SER C 118 " model vdw 1.639 2.450 ... (remaining 538082 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 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 258)) selection = (chain 'C' and (resid 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 258)) selection = (chain 'G' and (resid 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 245 or (resid 246 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 247 through 258)) selection = (chain 'Q' and (resid 0 through 11 or resid 13 through 258)) } ncs_group { reference = (chain 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'E' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'I' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'J' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'L' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'M' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'N' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'P' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'R' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'S' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'T' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'U' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3 or name HD22)) or resid 49 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB or name CG or name ND1 or name CD \ 2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ D2 or name HE1)) or resid 58 through 66)) selection = (chain 'V' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'W' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'X' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'Y' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD2 or name HE1)) or resid 58 through 66)) } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.220 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 40.780 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19828 Z= 0.112 Angle : 0.472 4.959 27142 Z= 0.272 Chirality : 0.041 0.148 3063 Planarity : 0.002 0.032 3283 Dihedral : 15.009 166.167 7781 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.17), residues: 2198 helix: -0.52 (0.21), residues: 517 sheet: -2.80 (0.17), residues: 713 loop : -1.24 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 218 TYR 0.009 0.000 TYR X 11 PHE 0.012 0.001 PHE A 99 TRP 0.006 0.001 TRP G 217 HIS 0.002 0.000 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00195 (19827) covalent geometry : angle 0.47229 (27140) SS BOND : bond 0.00349 ( 1) SS BOND : angle 0.24132 ( 2) hydrogen bonds : bond 0.22868 ( 700) hydrogen bonds : angle 9.06017 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4949 (tpp) cc_final: -0.5646 (ttm) REVERT: N 53 MET cc_start: -0.6499 (tpp) cc_final: -0.7469 (ttt) REVERT: P 32 LEU cc_start: 0.9195 (mp) cc_final: 0.8948 (mm) REVERT: Y 55 TYR cc_start: 0.9097 (m-80) cc_final: 0.8885 (m-10) REVERT: S 55 TYR cc_start: 0.8225 (m-80) cc_final: 0.7978 (m-80) REVERT: U 59 ILE cc_start: 0.9177 (mt) cc_final: 0.8967 (mt) REVERT: V 23 SER cc_start: 0.8887 (p) cc_final: 0.7908 (p) REVERT: V 35 GLN cc_start: 0.9118 (mt0) cc_final: 0.8766 (pm20) REVERT: V 38 SER cc_start: 0.9209 (m) cc_final: 0.9004 (p) REVERT: V 53 MET cc_start: 0.7440 (ttp) cc_final: 0.6918 (tmm) REVERT: V 55 TYR cc_start: 0.8404 (m-80) cc_final: 0.8065 (m-10) REVERT: W 59 ILE cc_start: 0.9462 (mt) cc_final: 0.9155 (mt) REVERT: K 60 SER cc_start: 0.7782 (m) cc_final: 0.7363 (t) REVERT: E 25 TYR cc_start: 0.8906 (m-80) cc_final: 0.8693 (m-10) REVERT: I 53 MET cc_start: 0.6858 (ttm) cc_final: 0.6475 (tmm) REVERT: Q 80 ILE cc_start: 0.9269 (pt) cc_final: 0.8938 (pt) REVERT: Q 107 LEU cc_start: 0.9036 (tp) cc_final: 0.8699 (tt) REVERT: Q 177 TRP cc_start: 0.8595 (t60) cc_final: 0.8009 (t60) REVERT: Q 187 TYR cc_start: 0.9082 (m-80) cc_final: 0.8075 (m-80) REVERT: G 5 SER cc_start: 0.8810 (t) cc_final: 0.8535 (t) REVERT: G 180 GLU cc_start: 0.9266 (tm-30) cc_final: 0.9038 (tp30) REVERT: G 193 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8020 (tm-30) REVERT: G 220 ASP cc_start: 0.8330 (m-30) cc_final: 0.7884 (t0) REVERT: G 222 GLN cc_start: 0.8989 (mm110) cc_final: 0.8592 (mm-40) REVERT: C 56 TYR cc_start: 0.8739 (m-80) cc_final: 0.8531 (m-80) REVERT: C 106 THR cc_start: 0.7806 (p) cc_final: 0.7309 (p) REVERT: C 143 TYR cc_start: 0.7326 (m-80) cc_final: 0.6428 (m-80) REVERT: A 212 MET cc_start: 0.9361 (tpt) cc_final: 0.9125 (tpt) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.3464 time to fit residues: 304.6007 Evaluate side-chains 418 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 50.0000 chunk 212 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 HIS V 8 GLN K 35 GLN E 13 ASN F 52 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 245 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.090992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.061049 restraints weight = 403573.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.064121 restraints weight = 168839.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066165 restraints weight = 93709.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.067290 restraints weight = 62901.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.068077 restraints weight = 48936.803| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19828 Z= 0.249 Angle : 0.643 7.429 27142 Z= 0.342 Chirality : 0.043 0.163 3063 Planarity : 0.005 0.093 3283 Dihedral : 14.264 163.846 3284 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.10 % Allowed : 1.44 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.18), residues: 2198 helix: 0.17 (0.22), residues: 538 sheet: -2.43 (0.19), residues: 623 loop : -0.83 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG J 16 TYR 0.019 0.002 TYR D 11 PHE 0.014 0.001 PHE A 129 TRP 0.015 0.002 TRP G 203 HIS 0.009 0.001 HIS K 57 Details of bonding type rmsd covalent geometry : bond 0.00495 (19827) covalent geometry : angle 0.64214 (27140) SS BOND : bond 0.00560 ( 1) SS BOND : angle 3.49978 ( 2) hydrogen bonds : bond 0.05837 ( 700) hydrogen bonds : angle 6.68474 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 429 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.5100 (tpp) cc_final: -0.5343 (tpp) REVERT: N 53 MET cc_start: -0.5806 (tpp) cc_final: -0.6931 (ttt) REVERT: N 66 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8807 (ttt180) REVERT: P 53 MET cc_start: -0.2475 (tpp) cc_final: -0.3114 (tpt) REVERT: X 48 ASN cc_start: 0.8600 (t0) cc_final: 0.8157 (m-40) REVERT: Y 37 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8808 (tm-30) REVERT: V 9 ASP cc_start: 0.9316 (t70) cc_final: 0.8999 (t0) REVERT: V 35 GLN cc_start: 0.9054 (mt0) cc_final: 0.8843 (pm20) REVERT: K 60 SER cc_start: 0.7758 (m) cc_final: 0.7460 (p) REVERT: E 45 LEU cc_start: 0.9002 (tp) cc_final: 0.8790 (tp) REVERT: E 48 ASN cc_start: 0.7979 (p0) cc_final: 0.5744 (p0) REVERT: E 52 GLN cc_start: 0.9281 (mt0) cc_final: 0.8754 (mt0) REVERT: I 53 MET cc_start: 0.7776 (ttm) cc_final: 0.6935 (tmm) REVERT: Q 107 LEU cc_start: 0.9233 (tp) cc_final: 0.8874 (tt) REVERT: Q 167 MET cc_start: 0.8983 (mtp) cc_final: 0.8671 (mtp) REVERT: Q 187 TYR cc_start: 0.9261 (m-80) cc_final: 0.8240 (m-80) REVERT: Q 230 ARG cc_start: 0.9144 (ptm-80) cc_final: 0.8914 (ptm-80) REVERT: G 167 MET cc_start: 0.8004 (mtt) cc_final: 0.7746 (mtp) REVERT: G 180 GLU cc_start: 0.9413 (tm-30) cc_final: 0.9127 (tp30) REVERT: G 193 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8264 (tm-30) REVERT: G 222 GLN cc_start: 0.9261 (mm-40) cc_final: 0.9018 (mm-40) REVERT: G 224 LEU cc_start: 0.9326 (pt) cc_final: 0.9069 (pt) REVERT: G 232 VAL cc_start: 0.9323 (m) cc_final: 0.8833 (m) REVERT: G 242 ARG cc_start: 0.7941 (mtm180) cc_final: 0.7740 (mmp80) REVERT: C 146 CYS cc_start: 0.9065 (t) cc_final: 0.8755 (t) outliers start: 2 outliers final: 1 residues processed: 430 average time/residue: 0.3711 time to fit residues: 226.6499 Evaluate side-chains 358 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 137 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 153 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 205 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 193 optimal weight: 40.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN D 41 GLN F 48 ASN F 52 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.091199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.061006 restraints weight = 423858.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.064072 restraints weight = 172893.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.066113 restraints weight = 95135.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.067409 restraints weight = 63437.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.068101 restraints weight = 48160.069| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19828 Z= 0.146 Angle : 0.547 5.316 27142 Z= 0.287 Chirality : 0.043 0.164 3063 Planarity : 0.004 0.064 3283 Dihedral : 14.293 164.634 3284 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.18), residues: 2198 helix: 0.44 (0.23), residues: 533 sheet: -2.13 (0.20), residues: 600 loop : -0.56 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 16 TYR 0.015 0.001 TYR U 55 PHE 0.012 0.001 PHE G 99 TRP 0.013 0.001 TRP G 203 HIS 0.010 0.001 HIS Q 153 Details of bonding type rmsd covalent geometry : bond 0.00298 (19827) covalent geometry : angle 0.54696 (27140) SS BOND : bond 0.00438 ( 1) SS BOND : angle 2.13820 ( 2) hydrogen bonds : bond 0.04693 ( 700) hydrogen bonds : angle 6.28254 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.5069 (tpp) cc_final: -0.5666 (ttm) REVERT: N 53 MET cc_start: -0.5659 (tpp) cc_final: -0.6823 (ttt) REVERT: N 66 ARG cc_start: 0.9187 (ttp80) cc_final: 0.8841 (ttt180) REVERT: P 53 MET cc_start: -0.2930 (tpp) cc_final: -0.3338 (tpt) REVERT: X 32 LEU cc_start: 0.9714 (tt) cc_final: 0.9512 (tt) REVERT: X 37 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8938 (tm-30) REVERT: X 48 ASN cc_start: 0.8637 (t0) cc_final: 0.8136 (m-40) REVERT: Y 37 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8751 (tm-30) REVERT: U 52 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8364 (mp-120) REVERT: U 55 TYR cc_start: 0.8784 (m-80) cc_final: 0.8083 (m-80) REVERT: U 59 ILE cc_start: 0.9114 (mt) cc_final: 0.8829 (mt) REVERT: V 46 LEU cc_start: 0.7604 (tp) cc_final: 0.7234 (tp) REVERT: V 48 ASN cc_start: 0.8963 (p0) cc_final: 0.8729 (p0) REVERT: V 52 GLN cc_start: 0.8977 (mt0) cc_final: 0.8723 (mp10) REVERT: V 59 ILE cc_start: 0.9300 (mt) cc_final: 0.9088 (mt) REVERT: W 53 MET cc_start: 0.8512 (ttp) cc_final: 0.8148 (ttt) REVERT: K 60 SER cc_start: 0.7660 (m) cc_final: 0.7396 (p) REVERT: E 45 LEU cc_start: 0.8996 (tp) cc_final: 0.8735 (tp) REVERT: E 48 ASN cc_start: 0.8006 (p0) cc_final: 0.5825 (p0) REVERT: E 52 GLN cc_start: 0.9241 (mt0) cc_final: 0.8674 (mt0) REVERT: F 46 LEU cc_start: 0.9501 (mp) cc_final: 0.9264 (tp) REVERT: I 53 MET cc_start: 0.7740 (ttm) cc_final: 0.6788 (tmm) REVERT: Q 98 ASP cc_start: 0.7626 (m-30) cc_final: 0.7275 (m-30) REVERT: Q 167 MET cc_start: 0.8940 (mtp) cc_final: 0.8640 (mtp) REVERT: Q 231 PHE cc_start: 0.9637 (m-80) cc_final: 0.9265 (m-80) REVERT: G 167 MET cc_start: 0.8017 (mtt) cc_final: 0.7766 (mtp) REVERT: G 180 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9110 (tp30) REVERT: G 193 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8190 (tm-30) REVERT: G 220 ASP cc_start: 0.8908 (m-30) cc_final: 0.8513 (m-30) REVERT: G 232 VAL cc_start: 0.9319 (m) cc_final: 0.8834 (m) REVERT: G 242 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7782 (mmp80) REVERT: C 146 CYS cc_start: 0.8987 (t) cc_final: 0.8679 (t) REVERT: C 167 MET cc_start: 0.7768 (mmm) cc_final: 0.7558 (mmm) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.3589 time to fit residues: 212.6834 Evaluate side-chains 350 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 59 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 34 optimal weight: 0.2980 chunk 148 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 213 optimal weight: 30.0000 overall best weight: 5.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 5 HIS ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 HIS P 5 HIS ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS E 35 GLN F 8 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN B C 96 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.087317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.057321 restraints weight = 384454.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.060058 restraints weight = 164139.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.061995 restraints weight = 93535.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.063062 restraints weight = 63472.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063803 restraints weight = 49675.589| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19828 Z= 0.236 Angle : 0.617 6.394 27142 Z= 0.330 Chirality : 0.043 0.197 3063 Planarity : 0.005 0.045 3283 Dihedral : 14.487 165.166 3284 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.05 % Allowed : 1.54 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.18), residues: 2198 helix: 0.09 (0.22), residues: 534 sheet: -2.18 (0.20), residues: 587 loop : -0.51 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 138 TYR 0.021 0.002 TYR G 143 PHE 0.054 0.002 PHE A 125 TRP 0.024 0.002 TRP G 177 HIS 0.008 0.002 HIS K 57 Details of bonding type rmsd covalent geometry : bond 0.00462 (19827) covalent geometry : angle 0.61675 (27140) SS BOND : bond 0.00559 ( 1) SS BOND : angle 1.70781 ( 2) hydrogen bonds : bond 0.04628 ( 700) hydrogen bonds : angle 6.07132 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4740 (tpp) cc_final: -0.5314 (ttm) REVERT: N 53 MET cc_start: -0.5195 (tpp) cc_final: -0.6353 (ttt) REVERT: P 53 MET cc_start: -0.2971 (tpp) cc_final: -0.3384 (tpt) REVERT: X 48 ASN cc_start: 0.8625 (t0) cc_final: 0.8254 (m-40) REVERT: Y 36 ILE cc_start: 0.9166 (mp) cc_final: 0.8670 (tt) REVERT: Y 37 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8839 (tm-30) REVERT: S 31 LYS cc_start: 0.8424 (ptmt) cc_final: 0.8130 (pttm) REVERT: U 55 TYR cc_start: 0.9049 (m-80) cc_final: 0.8306 (m-80) REVERT: V 23 SER cc_start: 0.8864 (t) cc_final: 0.8589 (t) REVERT: V 48 ASN cc_start: 0.9044 (p0) cc_final: 0.8693 (p0) REVERT: V 52 GLN cc_start: 0.9061 (mt0) cc_final: 0.8746 (mp10) REVERT: E 45 LEU cc_start: 0.8986 (tp) cc_final: 0.8707 (tp) REVERT: E 48 ASN cc_start: 0.8037 (p0) cc_final: 0.5914 (p0) REVERT: E 52 GLN cc_start: 0.9195 (mt0) cc_final: 0.8539 (mt0) REVERT: F 46 LEU cc_start: 0.9552 (mp) cc_final: 0.9170 (tt) REVERT: I 53 MET cc_start: 0.7869 (ttm) cc_final: 0.6915 (tmm) REVERT: Q 167 MET cc_start: 0.8873 (mtp) cc_final: 0.8478 (mtp) REVERT: G 1 MET cc_start: 0.8515 (tpp) cc_final: 0.7747 (tpp) REVERT: G 135 LYS cc_start: 0.9024 (tppp) cc_final: 0.8781 (ttpt) REVERT: G 193 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8354 (tm-30) REVERT: G 222 GLN cc_start: 0.9485 (mm-40) cc_final: 0.9180 (mm-40) REVERT: G 232 VAL cc_start: 0.9470 (m) cc_final: 0.9144 (m) REVERT: G 236 LYS cc_start: 0.9573 (mtmm) cc_final: 0.9277 (mtmm) REVERT: G 242 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7885 (mmp80) REVERT: C 72 SER cc_start: 0.9085 (m) cc_final: 0.8752 (t) REVERT: C 144 ILE cc_start: 0.9525 (mm) cc_final: 0.9312 (mp) REVERT: C 146 CYS cc_start: 0.8972 (t) cc_final: 0.8664 (t) REVERT: C 167 MET cc_start: 0.7976 (mmm) cc_final: 0.7737 (mmm) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.3526 time to fit residues: 190.3408 Evaluate side-chains 328 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 209 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 GLN J 52 GLN N 52 GLN P 35 GLN Y 57 HIS V 8 GLN W 5 HIS E 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.087503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.057668 restraints weight = 388029.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.060315 restraints weight = 166442.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062206 restraints weight = 95457.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.063242 restraints weight = 65244.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063977 restraints weight = 51432.591| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19828 Z= 0.167 Angle : 0.555 5.373 27142 Z= 0.292 Chirality : 0.043 0.169 3063 Planarity : 0.004 0.044 3283 Dihedral : 14.387 164.711 3284 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.10 % Allowed : 1.14 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.18), residues: 2198 helix: 0.26 (0.23), residues: 534 sheet: -2.01 (0.20), residues: 594 loop : -0.43 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 141 TYR 0.019 0.002 TYR G 132 PHE 0.030 0.001 PHE A 129 TRP 0.022 0.001 TRP Q 177 HIS 0.004 0.001 HIS Y 57 Details of bonding type rmsd covalent geometry : bond 0.00336 (19827) covalent geometry : angle 0.55480 (27140) SS BOND : bond 0.00605 ( 1) SS BOND : angle 1.79270 ( 2) hydrogen bonds : bond 0.04139 ( 700) hydrogen bonds : angle 5.84457 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4716 (tpp) cc_final: -0.5239 (ttm) REVERT: N 53 MET cc_start: -0.5135 (tpp) cc_final: -0.6533 (ttt) REVERT: N 66 ARG cc_start: 0.9381 (tmm160) cc_final: 0.8864 (ttt180) REVERT: P 53 MET cc_start: -0.3115 (tpp) cc_final: -0.3513 (tpt) REVERT: X 37 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8774 (tm-30) REVERT: Y 36 ILE cc_start: 0.9246 (mp) cc_final: 0.8797 (tt) REVERT: Y 37 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8850 (tm-30) REVERT: U 55 TYR cc_start: 0.9049 (m-80) cc_final: 0.8322 (m-80) REVERT: V 23 SER cc_start: 0.8855 (t) cc_final: 0.8597 (t) REVERT: V 46 LEU cc_start: 0.8022 (tp) cc_final: 0.7707 (tp) REVERT: V 48 ASN cc_start: 0.9096 (p0) cc_final: 0.8732 (p0) REVERT: V 52 GLN cc_start: 0.9093 (mt0) cc_final: 0.8774 (mp10) REVERT: E 45 LEU cc_start: 0.8988 (tp) cc_final: 0.8685 (tp) REVERT: E 48 ASN cc_start: 0.8060 (p0) cc_final: 0.5979 (p0) REVERT: E 52 GLN cc_start: 0.9164 (mt0) cc_final: 0.8492 (mt0) REVERT: F 46 LEU cc_start: 0.9557 (mp) cc_final: 0.9144 (tt) REVERT: I 53 MET cc_start: 0.7837 (ttm) cc_final: 0.6928 (tmm) REVERT: Q 56 TYR cc_start: 0.8615 (m-10) cc_final: 0.8235 (m-10) REVERT: Q 167 MET cc_start: 0.8848 (mtp) cc_final: 0.8503 (mtp) REVERT: G 1 MET cc_start: 0.8529 (tpp) cc_final: 0.7792 (tpp) REVERT: G 193 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8345 (tm-30) REVERT: G 222 GLN cc_start: 0.9355 (mm-40) cc_final: 0.9151 (mm-40) REVERT: G 232 VAL cc_start: 0.9508 (m) cc_final: 0.9168 (m) REVERT: G 236 LYS cc_start: 0.9555 (mtmm) cc_final: 0.9253 (mtmm) REVERT: C 72 SER cc_start: 0.9150 (m) cc_final: 0.8795 (t) REVERT: C 146 CYS cc_start: 0.8955 (t) cc_final: 0.8644 (t) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.3463 time to fit residues: 184.0216 Evaluate side-chains 318 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 28 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 GLN Y 13 ASN Y 57 HIS ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 5 HIS E 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.084842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.055405 restraints weight = 426323.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.057803 restraints weight = 180913.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.059587 restraints weight = 103425.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.060627 restraints weight = 71022.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.061332 restraints weight = 55919.088| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19828 Z= 0.273 Angle : 0.656 6.627 27142 Z= 0.353 Chirality : 0.044 0.161 3063 Planarity : 0.005 0.048 3283 Dihedral : 14.580 165.503 3284 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.21 % Rotamer: Outliers : 0.05 % Allowed : 0.89 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.18), residues: 2198 helix: -0.13 (0.22), residues: 542 sheet: -2.10 (0.20), residues: 607 loop : -0.65 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 93 TYR 0.019 0.002 TYR C 132 PHE 0.025 0.002 PHE A 129 TRP 0.044 0.002 TRP A 177 HIS 0.008 0.002 HIS K 57 Details of bonding type rmsd covalent geometry : bond 0.00530 (19827) covalent geometry : angle 0.65587 (27140) SS BOND : bond 0.00451 ( 1) SS BOND : angle 1.72696 ( 2) hydrogen bonds : bond 0.04763 ( 700) hydrogen bonds : angle 6.05802 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4343 (tpp) cc_final: -0.5055 (ttm) REVERT: N 53 MET cc_start: -0.4274 (tpp) cc_final: -0.5811 (ttp) REVERT: N 66 ARG cc_start: 0.9430 (tmm160) cc_final: 0.8873 (ttt180) REVERT: P 53 MET cc_start: -0.3354 (tpp) cc_final: -0.3770 (tpt) REVERT: X 48 ASN cc_start: 0.8752 (t0) cc_final: 0.8525 (t0) REVERT: X 57 HIS cc_start: 0.9026 (m90) cc_final: 0.8797 (m90) REVERT: Y 37 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8883 (tm-30) REVERT: S 31 LYS cc_start: 0.8436 (ptmt) cc_final: 0.8130 (pttm) REVERT: U 55 TYR cc_start: 0.9148 (m-80) cc_final: 0.8490 (m-80) REVERT: V 23 SER cc_start: 0.8552 (t) cc_final: 0.8193 (t) REVERT: V 37 GLU cc_start: 0.9157 (tp30) cc_final: 0.8698 (tp30) REVERT: V 46 LEU cc_start: 0.8137 (tp) cc_final: 0.7765 (tp) REVERT: V 48 ASN cc_start: 0.9046 (p0) cc_final: 0.8637 (p0) REVERT: V 52 GLN cc_start: 0.9046 (mt0) cc_final: 0.8709 (mp10) REVERT: V 55 TYR cc_start: 0.8714 (m-80) cc_final: 0.8390 (m-10) REVERT: E 45 LEU cc_start: 0.9025 (tp) cc_final: 0.8742 (tp) REVERT: E 48 ASN cc_start: 0.8076 (p0) cc_final: 0.6075 (p0) REVERT: E 52 GLN cc_start: 0.9112 (mt0) cc_final: 0.8481 (mt0) REVERT: I 53 MET cc_start: 0.8017 (ttm) cc_final: 0.6972 (tmm) REVERT: Q 56 TYR cc_start: 0.8548 (m-10) cc_final: 0.8202 (m-10) REVERT: Q 167 MET cc_start: 0.8803 (mtp) cc_final: 0.8433 (mtp) REVERT: G 1 MET cc_start: 0.8560 (tpp) cc_final: 0.7882 (tpp) REVERT: G 5 SER cc_start: 0.8616 (t) cc_final: 0.8341 (t) REVERT: C 249 LEU cc_start: 0.9333 (tt) cc_final: 0.8940 (mp) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.3561 time to fit residues: 175.4003 Evaluate side-chains 298 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 121 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 192 optimal weight: 50.0000 chunk 89 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 57 HIS ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 5 HIS ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 GLN ** G 9 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 = 0.3938 r_free = 0.3938 target = 0.085828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055366 restraints weight = 438694.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.058269 restraints weight = 179795.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.060159 restraints weight = 100186.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.061206 restraints weight = 67430.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061953 restraints weight = 52682.413| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19828 Z= 0.177 Angle : 0.571 5.429 27142 Z= 0.303 Chirality : 0.044 0.159 3063 Planarity : 0.004 0.047 3283 Dihedral : 14.480 165.100 3284 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.44 % Rotamer: Outliers : 0.05 % Allowed : 0.70 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.18), residues: 2198 helix: 0.07 (0.22), residues: 541 sheet: -2.08 (0.20), residues: 626 loop : -0.45 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 19 TYR 0.016 0.002 TYR C 150 PHE 0.030 0.002 PHE G 85 TRP 0.056 0.002 TRP A 177 HIS 0.006 0.001 HIS Q 131 Details of bonding type rmsd covalent geometry : bond 0.00353 (19827) covalent geometry : angle 0.57066 (27140) SS BOND : bond 0.00423 ( 1) SS BOND : angle 1.98655 ( 2) hydrogen bonds : bond 0.04210 ( 700) hydrogen bonds : angle 5.87519 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4281 (tpp) cc_final: -0.4953 (ttm) REVERT: N 53 MET cc_start: -0.4639 (tpp) cc_final: -0.6059 (ttp) REVERT: N 66 ARG cc_start: 0.9445 (tmm160) cc_final: 0.8914 (ttt180) REVERT: P 53 MET cc_start: -0.3487 (tpp) cc_final: -0.3865 (tpt) REVERT: X 37 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8726 (tm-30) REVERT: X 57 HIS cc_start: 0.9064 (m90) cc_final: 0.8842 (m90) REVERT: Y 37 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8879 (tm-30) REVERT: S 31 LYS cc_start: 0.8417 (ptmt) cc_final: 0.8095 (pttm) REVERT: U 55 TYR cc_start: 0.9135 (m-80) cc_final: 0.8461 (m-80) REVERT: V 46 LEU cc_start: 0.8189 (tp) cc_final: 0.7868 (tp) REVERT: V 48 ASN cc_start: 0.9043 (p0) cc_final: 0.8757 (p0) REVERT: V 52 GLN cc_start: 0.9078 (mt0) cc_final: 0.8764 (mp10) REVERT: E 45 LEU cc_start: 0.9072 (tp) cc_final: 0.8793 (tp) REVERT: E 48 ASN cc_start: 0.8088 (p0) cc_final: 0.6119 (p0) REVERT: E 52 GLN cc_start: 0.9148 (mt0) cc_final: 0.8498 (mt0) REVERT: I 53 MET cc_start: 0.7976 (ttm) cc_final: 0.6921 (tmm) REVERT: Q 56 TYR cc_start: 0.8496 (m-10) cc_final: 0.8165 (m-10) REVERT: Q 167 MET cc_start: 0.8760 (mtp) cc_final: 0.8388 (mtp) REVERT: G 222 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8899 (mm-40) REVERT: G 236 LYS cc_start: 0.9558 (mtmm) cc_final: 0.9222 (mtmm) REVERT: C 167 MET cc_start: 0.8082 (mmm) cc_final: 0.7836 (mmm) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.3427 time to fit residues: 170.2518 Evaluate side-chains 292 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 140 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 201 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 5 HIS ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 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 = 0.3929 r_free = 0.3929 target = 0.085603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055491 restraints weight = 463849.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.058092 restraints weight = 185846.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.060008 restraints weight = 103276.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.061243 restraints weight = 69075.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.061892 restraints weight = 52577.998| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19828 Z= 0.175 Angle : 0.571 5.373 27142 Z= 0.301 Chirality : 0.044 0.168 3063 Planarity : 0.004 0.048 3283 Dihedral : 14.467 165.361 3284 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.20 % Favored : 92.71 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.18), residues: 2198 helix: 0.16 (0.23), residues: 540 sheet: -2.01 (0.20), residues: 636 loop : -0.42 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 140 TYR 0.014 0.001 TYR C 132 PHE 0.026 0.002 PHE G 85 TRP 0.051 0.002 TRP A 177 HIS 0.006 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00355 (19827) covalent geometry : angle 0.57030 (27140) SS BOND : bond 0.00474 ( 1) SS BOND : angle 2.03055 ( 2) hydrogen bonds : bond 0.04105 ( 700) hydrogen bonds : angle 5.85397 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 MET cc_start: -0.3431 (ttm) cc_final: -0.3648 (tpp) REVERT: T 53 MET cc_start: -0.4294 (tpp) cc_final: -0.4940 (ttm) REVERT: N 53 MET cc_start: -0.4562 (tpp) cc_final: -0.5719 (ttt) REVERT: N 66 ARG cc_start: 0.9384 (tmm160) cc_final: 0.8878 (ttt180) REVERT: P 53 MET cc_start: -0.3484 (tpp) cc_final: -0.3858 (tpt) REVERT: X 37 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8718 (tm-30) REVERT: Y 37 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8901 (tm-30) REVERT: S 31 LYS cc_start: 0.8389 (ptmt) cc_final: 0.8067 (pttm) REVERT: U 55 TYR cc_start: 0.9101 (m-80) cc_final: 0.8453 (m-80) REVERT: V 46 LEU cc_start: 0.8278 (tp) cc_final: 0.7968 (tp) REVERT: V 48 ASN cc_start: 0.9027 (p0) cc_final: 0.8751 (p0) REVERT: V 52 GLN cc_start: 0.9063 (mt0) cc_final: 0.8760 (mp10) REVERT: E 45 LEU cc_start: 0.9054 (tp) cc_final: 0.8770 (tp) REVERT: E 48 ASN cc_start: 0.8141 (p0) cc_final: 0.6182 (p0) REVERT: E 52 GLN cc_start: 0.9131 (mt0) cc_final: 0.8500 (mt0) REVERT: I 53 MET cc_start: 0.7986 (ttm) cc_final: 0.6935 (tmm) REVERT: Q 56 TYR cc_start: 0.8404 (m-10) cc_final: 0.8100 (m-10) REVERT: Q 167 MET cc_start: 0.8740 (mtp) cc_final: 0.8365 (mtp) REVERT: G 222 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8859 (mm-40) REVERT: G 236 LYS cc_start: 0.9529 (mtmm) cc_final: 0.9214 (mtmm) REVERT: C 167 MET cc_start: 0.8107 (mmm) cc_final: 0.7851 (mmm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.3509 time to fit residues: 170.8088 Evaluate side-chains 287 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 119 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 40 optimal weight: 0.0980 chunk 106 optimal weight: 7.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 57 HIS W 5 HIS M 28 ASN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 GLN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.086909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.056294 restraints weight = 445449.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.059002 restraints weight = 180566.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.060877 restraints weight = 100263.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062183 restraints weight = 67788.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.062778 restraints weight = 52004.304| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19828 Z= 0.114 Angle : 0.526 5.922 27142 Z= 0.273 Chirality : 0.044 0.153 3063 Planarity : 0.004 0.049 3283 Dihedral : 14.269 165.309 3284 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.26 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.19), residues: 2198 helix: 0.43 (0.23), residues: 553 sheet: -1.89 (0.20), residues: 616 loop : -0.30 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 19 TYR 0.013 0.001 TYR Q 132 PHE 0.020 0.001 PHE G 85 TRP 0.052 0.001 TRP A 177 HIS 0.004 0.001 HIS Y 57 Details of bonding type rmsd covalent geometry : bond 0.00246 (19827) covalent geometry : angle 0.52524 (27140) SS BOND : bond 0.00390 ( 1) SS BOND : angle 2.26024 ( 2) hydrogen bonds : bond 0.03705 ( 700) hydrogen bonds : angle 5.57159 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4437 (tpp) cc_final: -0.5102 (ttm) REVERT: N 53 MET cc_start: -0.4880 (tpp) cc_final: -0.5944 (ttt) REVERT: N 66 ARG cc_start: 0.9394 (tmm160) cc_final: 0.8880 (ttt180) REVERT: P 53 MET cc_start: -0.3635 (tpp) cc_final: -0.3973 (tpt) REVERT: Y 36 ILE cc_start: 0.9250 (mp) cc_final: 0.8889 (tt) REVERT: Y 37 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8893 (tm-30) REVERT: S 31 LYS cc_start: 0.8411 (ptmt) cc_final: 0.8083 (pttm) REVERT: V 46 LEU cc_start: 0.8319 (tp) cc_final: 0.8001 (tp) REVERT: V 48 ASN cc_start: 0.9071 (p0) cc_final: 0.8827 (p0) REVERT: V 52 GLN cc_start: 0.9079 (mt0) cc_final: 0.8768 (mp10) REVERT: E 45 LEU cc_start: 0.9040 (tp) cc_final: 0.8754 (tp) REVERT: E 48 ASN cc_start: 0.8096 (p0) cc_final: 0.7706 (p0) REVERT: I 53 MET cc_start: 0.7918 (ttm) cc_final: 0.6921 (tmm) REVERT: Q 56 TYR cc_start: 0.8360 (m-10) cc_final: 0.8055 (m-10) REVERT: Q 167 MET cc_start: 0.8739 (mtp) cc_final: 0.8374 (mtp) REVERT: G 222 GLN cc_start: 0.9284 (mm-40) cc_final: 0.9021 (mm-40) REVERT: G 236 LYS cc_start: 0.9526 (mtmm) cc_final: 0.9226 (mtmm) REVERT: C 72 SER cc_start: 0.9186 (m) cc_final: 0.8767 (t) REVERT: C 146 CYS cc_start: 0.8886 (t) cc_final: 0.8679 (t) REVERT: C 167 MET cc_start: 0.8003 (mmm) cc_final: 0.7706 (mmm) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3713 time to fit residues: 183.1100 Evaluate side-chains 296 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 194 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 192 optimal weight: 40.0000 chunk 98 optimal weight: 0.3980 chunk 185 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 50 optimal weight: 0.0870 chunk 78 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 57 HIS M 28 ASN D 8 GLN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.087439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.057255 restraints weight = 439939.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.059838 restraints weight = 178478.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.061804 restraints weight = 100084.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.062862 restraints weight = 68046.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.063625 restraints weight = 53925.195| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19828 Z= 0.102 Angle : 0.513 5.706 27142 Z= 0.265 Chirality : 0.044 0.159 3063 Planarity : 0.004 0.050 3283 Dihedral : 14.119 165.817 3284 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.05 % Allowed : 0.05 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.19), residues: 2198 helix: 0.63 (0.23), residues: 553 sheet: -1.78 (0.21), residues: 617 loop : -0.28 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 138 TYR 0.011 0.001 TYR Q 132 PHE 0.018 0.001 PHE A 129 TRP 0.051 0.001 TRP A 177 HIS 0.003 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00225 (19827) covalent geometry : angle 0.51244 (27140) SS BOND : bond 0.00438 ( 1) SS BOND : angle 1.98463 ( 2) hydrogen bonds : bond 0.03562 ( 700) hydrogen bonds : angle 5.45620 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4525 (tpp) cc_final: -0.5179 (ttm) REVERT: N 53 MET cc_start: -0.4962 (tpp) cc_final: -0.6037 (ttt) REVERT: N 66 ARG cc_start: 0.9367 (tmm160) cc_final: 0.8853 (ttt180) REVERT: P 53 MET cc_start: -0.3658 (tpp) cc_final: -0.3992 (tpt) REVERT: X 37 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8570 (tm-30) REVERT: Y 23 SER cc_start: 0.8124 (m) cc_final: 0.7905 (t) REVERT: Y 36 ILE cc_start: 0.9219 (mp) cc_final: 0.8846 (tt) REVERT: Y 37 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8892 (tm-30) REVERT: S 31 LYS cc_start: 0.8401 (ptmt) cc_final: 0.8052 (pttm) REVERT: V 46 LEU cc_start: 0.8294 (tp) cc_final: 0.7974 (tp) REVERT: V 48 ASN cc_start: 0.9065 (p0) cc_final: 0.8853 (p0) REVERT: V 52 GLN cc_start: 0.9009 (mt0) cc_final: 0.8682 (mp10) REVERT: E 45 LEU cc_start: 0.9021 (tp) cc_final: 0.8732 (tp) REVERT: E 48 ASN cc_start: 0.8191 (p0) cc_final: 0.7793 (p0) REVERT: I 53 MET cc_start: 0.7909 (ttm) cc_final: 0.6914 (tmm) REVERT: Q 56 TYR cc_start: 0.8334 (m-10) cc_final: 0.8122 (m-10) REVERT: Q 167 MET cc_start: 0.8744 (mtp) cc_final: 0.8339 (mtp) REVERT: Q 224 LEU cc_start: 0.9262 (mm) cc_final: 0.8905 (mm) REVERT: G 222 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8983 (mm-40) REVERT: G 236 LYS cc_start: 0.9535 (mtmm) cc_final: 0.9318 (mtmm) REVERT: C 72 SER cc_start: 0.9145 (m) cc_final: 0.8764 (t) REVERT: C 146 CYS cc_start: 0.8895 (t) cc_final: 0.8658 (t) REVERT: C 167 MET cc_start: 0.7937 (mmm) cc_final: 0.7694 (mmm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.3826 time to fit residues: 192.2095 Evaluate side-chains 299 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 9 optimal weight: 40.0000 chunk 89 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 chunk 169 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 57 HIS ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 GLN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 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 = 0.3970 r_free = 0.3970 target = 0.088116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057939 restraints weight = 437783.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060617 restraints weight = 176383.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.062525 restraints weight = 98551.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.063802 restraints weight = 66838.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.064500 restraints weight = 51620.411| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19828 Z= 0.100 Angle : 0.508 5.585 27142 Z= 0.262 Chirality : 0.044 0.150 3063 Planarity : 0.004 0.049 3283 Dihedral : 14.038 166.144 3284 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.19), residues: 2198 helix: 0.74 (0.23), residues: 553 sheet: -1.75 (0.21), residues: 620 loop : -0.15 (0.21), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 138 TYR 0.011 0.001 TYR Q 132 PHE 0.017 0.001 PHE A 129 TRP 0.049 0.001 TRP A 177 HIS 0.003 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00220 (19827) covalent geometry : angle 0.50791 (27140) SS BOND : bond 0.00375 ( 1) SS BOND : angle 1.98220 ( 2) hydrogen bonds : bond 0.03525 ( 700) hydrogen bonds : angle 5.37974 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8329.21 seconds wall clock time: 142 minutes 7.15 seconds (8527.15 seconds total)