Starting phenix.real_space_refine on Sun Aug 9 19:56:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bvj_16265/08_2026/8bvj_16265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvj_16265/08_2026/8bvj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2026/8bvj_16265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2026/8bvj_16265.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2026/8bvj_16265.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2026/8bvj_16265.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2026/8bvj_16265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvj_16265/08_2026/8bvj_16265.cif" } 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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 9.15, per 1000 atoms: 0.24 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: 3.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 6.26 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: 10.25 Time building geometry restraints manager: 5.05 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=" C3' A B 82 " pdb=" O3' A B 82 " ideal model delta sigma weight residual 1.415 1.434 -0.019 2.00e-02 2.50e+03 9.00e-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 ... (remaining 38723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 66165 1.07 - 2.14: 3245 2.14 - 3.20: 391 3.20 - 4.27: 168 4.27 - 5.34: 38 Bond angle restraints: 70007 Sorted by residual: angle pdb=" C3' A B 56 " pdb=" C2' A B 56 " pdb=" O2' A B 56 " ideal model delta sigma weight residual 109.80 114.77 -4.97 2.00e+00 2.50e-01 6.19e+00 angle pdb=" C3' A B 63 " pdb=" C2' A B 63 " pdb=" O2' A B 63 " ideal model delta sigma weight residual 109.80 114.74 -4.94 2.00e+00 2.50e-01 6.10e+00 angle pdb=" C3' A B 91 " pdb=" C2' A B 91 " pdb=" O2' A B 91 " ideal model delta sigma weight residual 109.80 114.74 -4.94 2.00e+00 2.50e-01 6.09e+00 angle pdb=" C3' A B 88 " pdb=" C2' A B 88 " pdb=" O2' A B 88 " ideal model delta sigma weight residual 109.80 114.73 -4.93 2.00e+00 2.50e-01 6.08e+00 angle pdb=" C3' A B 61 " pdb=" C2' A B 61 " pdb=" O2' A B 61 " ideal model delta sigma weight residual 109.80 114.73 -4.93 2.00e+00 2.50e-01 6.07e+00 ... (remaining 70002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 17460 34.30 - 68.59: 499 68.59 - 102.89: 58 102.89 - 137.19: 7 137.19 - 171.48: 7 Dihedral angle restraints: 18031 sinusoidal: 10276 harmonic: 7755 Sorted by residual: dihedral pdb=" C4' G B 20 " pdb=" C3' G B 20 " pdb=" C2' G B 20 " pdb=" C1' G B 20 " ideal model delta sinusoidal sigma weight residual 36.34 -36.75 73.09 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' G B 75 " pdb=" C3' G B 75 " pdb=" C2' G B 75 " pdb=" C1' G B 75 " ideal model delta sinusoidal sigma weight residual 36.34 -36.52 72.86 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' C B 66 " pdb=" C3' C B 66 " pdb=" C2' C B 66 " pdb=" C1' C B 66 " ideal model delta sinusoidal sigma weight residual 36.35 -36.25 72.60 1 3.10e+00 1.04e-01 7.00e+02 ... (remaining 18028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2517 0.057 - 0.114: 363 0.114 - 0.171: 65 0.171 - 0.228: 36 0.228 - 0.285: 82 Chirality restraints: 3063 Sorted by residual: chirality pdb=" P G B 83 " pdb=" OP1 G B 83 " pdb=" OP2 G B 83 " pdb=" O5' G B 83 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' A B 56 " pdb=" C3' A B 56 " pdb=" O2' A B 56 " pdb=" C1' A B 56 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' U B 86 " pdb=" C3' U B 86 " pdb=" O2' U B 86 " pdb=" C1' U B 86 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (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: 1.730 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 45.180 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 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= 0.121 Angle : 0.581 5.341 27142 Z= 0.309 Chirality : 0.063 0.285 3063 Planarity : 0.002 0.032 3283 Dihedral : 15.858 166.167 7619 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 are 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/Z covalent geometry : bond 0.00216 / 0.12 (19827) covalent geometry : angle 0.58151 / 0.31 (27140) SS BOND : bond 0.00349 / 0.22 ( 1) SS BOND : angle 0.24132 / 0.11 ( 2) hydrogen bonds : bond 0.22868 / 15.60 ( 700) hydrogen bonds : angle 9.06017 / 6.22 ( 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 : 1.135 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: 0.8021 (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: 0.7805 (p) cc_final: 0.7308 (p) REVERT: C 143 TYR cc_start: 0.7327 (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: 0.4252 time to fit residues: 380.0202 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 : 1.102 ------------------------------------------------------------------------------- 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... ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 HIS ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4041 r_free = 0.4041 target = 0.091296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061694 restraints weight = 402835.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.064800 restraints weight = 165960.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.066846 restraints weight = 91811.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.068200 restraints weight = 60914.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.068842 restraints weight = 46198.301| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 19828 Z= 0.273 Angle : 0.973 19.604 27142 Z= 0.447 Chirality : 0.070 0.735 3063 Planarity : 0.005 0.098 3283 Dihedral : 13.618 166.831 3122 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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 are not related in a simple way. whole: -1.74 (0.18), residues: 2198 helix: 0.10 (0.22), residues: 544 sheet: -2.39 (0.19), residues: 618 loop : -0.87 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 137 TYR 0.021 0.002 TYR D 11 PHE 0.015 0.001 PHE C 125 TRP 0.015 0.002 TRP G 203 HIS 0.009 0.001 HIS K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.27 (19827) covalent geometry : angle 0.97231 / 0.45 (27140) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 2.77229 / 1.19 ( 2) hydrogen bonds : bond 0.05553 / 3.81 ( 700) hydrogen bonds : angle 6.69917 / 4.57 ( 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 : 1.132 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: T 53 MET cc_start: -0.5121 (tpp) cc_final: -0.5740 (ttm) REVERT: N 53 MET cc_start: -0.5829 (tpp) cc_final: -0.6936 (ttt) REVERT: N 66 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8773 (ttt180) REVERT: P 53 MET cc_start: -0.2466 (tpp) cc_final: -0.3113 (tpt) REVERT: X 48 ASN cc_start: 0.8592 (t0) cc_final: 0.8154 (m-40) REVERT: Y 37 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8782 (tm-30) REVERT: V 9 ASP cc_start: 0.9313 (t70) cc_final: 0.8991 (t0) REVERT: V 35 GLN cc_start: 0.9048 (mt0) cc_final: 0.8832 (pm20) REVERT: K 60 SER cc_start: 0.7748 (m) cc_final: 0.7442 (p) REVERT: E 45 LEU cc_start: 0.9003 (tp) cc_final: 0.8787 (tp) REVERT: E 48 ASN cc_start: 0.7996 (p0) cc_final: 0.5773 (p0) REVERT: E 52 GLN cc_start: 0.9282 (mt0) cc_final: 0.8764 (mt0) REVERT: I 53 MET cc_start: 0.7792 (ttm) cc_final: 0.6968 (tmm) REVERT: Q 107 LEU cc_start: 0.9228 (tp) cc_final: 0.8874 (tt) REVERT: Q 139 LYS cc_start: 0.8899 (mptt) cc_final: 0.8388 (mttm) REVERT: Q 167 MET cc_start: 0.8987 (mtp) cc_final: 0.8710 (mtp) REVERT: Q 187 TYR cc_start: 0.9247 (m-80) cc_final: 0.8243 (m-80) REVERT: Q 230 ARG cc_start: 0.9136 (ptm-80) cc_final: 0.8904 (ptm-80) REVERT: G 167 MET cc_start: 0.8053 (mtt) cc_final: 0.7794 (mtp) REVERT: G 180 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9127 (tp30) REVERT: G 193 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8224 (tm-30) REVERT: G 222 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8996 (mm-40) REVERT: G 224 LEU cc_start: 0.9352 (pt) cc_final: 0.9089 (pt) REVERT: G 232 VAL cc_start: 0.9331 (m) cc_final: 0.8826 (m) REVERT: C 146 CYS cc_start: 0.9048 (t) cc_final: 0.8752 (t) outliers start: 2 outliers final: 1 residues processed: 430 average time/residue: 0.4374 time to fit residues: 270.5924 Evaluate side-chains 361 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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: 7.9990 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 205 optimal weight: 30.0000 chunk 93 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 GLN P 57 HIS V 8 GLN F 48 ASN ** I 52 GLN ** 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 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 = 0.4049 r_free = 0.4049 target = 0.091834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.062040 restraints weight = 427441.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.065145 restraints weight = 173526.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.067152 restraints weight = 94671.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.068599 restraints weight = 62881.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.069288 restraints weight = 47372.025| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19828 Z= 0.145 Angle : 0.689 10.215 27142 Z= 0.329 Chirality : 0.055 0.512 3063 Planarity : 0.004 0.067 3283 Dihedral : 14.252 179.456 3122 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.05 % Allowed : 1.19 % 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 are not related in a simple way. whole: -1.23 (0.18), residues: 2198 helix: 0.46 (0.23), residues: 533 sheet: -2.13 (0.20), residues: 604 loop : -0.49 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 16 TYR 0.013 0.001 TYR G 253 PHE 0.015 0.001 PHE Y 42 TRP 0.012 0.001 TRP C 177 HIS 0.009 0.001 HIS Q 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (19827) covalent geometry : angle 0.68840 / 0.33 (27140) SS BOND : bond 0.00288 / 0.18 ( 1) SS BOND : angle 2.08968 / 0.85 ( 2) hydrogen bonds : bond 0.04562 / 3.10 ( 700) hydrogen bonds : angle 6.15652 / 4.21 ( 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 421 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 1.178 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: T 53 MET cc_start: -0.5079 (tpp) cc_final: -0.5739 (ttm) REVERT: N 53 MET cc_start: -0.5637 (tpp) cc_final: -0.6793 (ttt) REVERT: N 66 ARG cc_start: 0.9177 (ttp80) cc_final: 0.8832 (ttt180) REVERT: P 53 MET cc_start: -0.2877 (tpp) cc_final: -0.3284 (tpt) REVERT: X 32 LEU cc_start: 0.9704 (tt) cc_final: 0.9501 (tt) REVERT: X 37 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8937 (tm-30) REVERT: X 48 ASN cc_start: 0.8649 (t0) cc_final: 0.8141 (m-40) REVERT: Y 36 ILE cc_start: 0.9077 (mp) cc_final: 0.8505 (tt) REVERT: Y 37 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8724 (tm-30) REVERT: S 31 LYS cc_start: 0.8721 (ptpt) cc_final: 0.8496 (pttm) REVERT: U 55 TYR cc_start: 0.8838 (m-80) cc_final: 0.8163 (m-80) REVERT: U 59 ILE cc_start: 0.9107 (mt) cc_final: 0.8785 (mt) REVERT: V 9 ASP cc_start: 0.9196 (t70) cc_final: 0.8972 (t0) REVERT: V 23 SER cc_start: 0.8862 (p) cc_final: 0.8591 (t) REVERT: V 46 LEU cc_start: 0.7672 (tp) cc_final: 0.7312 (tp) REVERT: V 48 ASN cc_start: 0.8957 (p0) cc_final: 0.8734 (p0) REVERT: V 52 GLN cc_start: 0.8972 (mt0) cc_final: 0.8722 (mp10) REVERT: V 59 ILE cc_start: 0.9323 (mt) cc_final: 0.9122 (mt) REVERT: W 53 MET cc_start: 0.8528 (ttp) cc_final: 0.8215 (ttt) REVERT: K 60 SER cc_start: 0.7566 (m) cc_final: 0.7329 (p) REVERT: E 45 LEU cc_start: 0.8893 (tp) cc_final: 0.8620 (tp) REVERT: E 48 ASN cc_start: 0.8011 (p0) cc_final: 0.5855 (p0) REVERT: E 52 GLN cc_start: 0.9259 (mt0) cc_final: 0.8701 (mt0) REVERT: F 46 LEU cc_start: 0.9522 (mp) cc_final: 0.9256 (tp) REVERT: I 53 MET cc_start: 0.7695 (ttm) cc_final: 0.6781 (tmm) REVERT: Q 98 ASP cc_start: 0.8056 (m-30) cc_final: 0.7782 (m-30) REVERT: Q 167 MET cc_start: 0.8948 (mtp) cc_final: 0.8605 (mtp) REVERT: G 143 TYR cc_start: 0.7851 (m-80) cc_final: 0.7586 (m-80) REVERT: G 180 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9140 (tp30) REVERT: G 193 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8145 (tm-30) REVERT: G 220 ASP cc_start: 0.8900 (m-30) cc_final: 0.8487 (m-30) REVERT: G 222 GLN cc_start: 0.9384 (mm-40) cc_final: 0.9165 (mm-40) REVERT: G 232 VAL cc_start: 0.9269 (m) cc_final: 0.8915 (m) REVERT: G 242 ARG cc_start: 0.5641 (mmp80) cc_final: 0.5365 (mmp80) REVERT: C 56 TYR cc_start: 0.8606 (m-80) cc_final: 0.8038 (m-80) REVERT: C 146 CYS cc_start: 0.8977 (t) cc_final: 0.8661 (t) REVERT: C 167 MET cc_start: 0.7761 (mmm) cc_final: 0.7560 (mmm) outliers start: 1 outliers final: 1 residues processed: 421 average time/residue: 0.4233 time to fit residues: 257.9927 Evaluate side-chains 362 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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: 5.9990 chunk 29 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 10 optimal weight: 50.0000 chunk 213 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS V 8 GLN D 41 GLN E 35 GLN F 8 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 131 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.086267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.057121 restraints weight = 402163.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.059741 restraints weight = 171074.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061581 restraints weight = 97033.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062565 restraints weight = 66107.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.063423 restraints weight = 52044.823| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 19828 Z= 0.299 Angle : 0.797 10.511 27142 Z= 0.400 Chirality : 0.052 0.335 3063 Planarity : 0.005 0.044 3283 Dihedral : 14.945 178.815 3122 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.18), residues: 2198 helix: -0.25 (0.22), residues: 535 sheet: -2.05 (0.21), residues: 568 loop : -0.71 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 19 TYR 0.028 0.002 TYR F 25 PHE 0.048 0.002 PHE A 125 TRP 0.020 0.002 TRP G 177 HIS 0.010 0.002 HIS K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.30 (19827) covalent geometry : angle 0.79698 / 0.40 (27140) SS BOND : bond 0.00181 / 0.11 ( 1) SS BOND : angle 1.80975 / 0.69 ( 2) hydrogen bonds : bond 0.05069 / 3.53 ( 700) hydrogen bonds : angle 6.23274 / 4.30 ( 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 366 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.139 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: R 53 MET cc_start: -0.2543 (ttm) cc_final: -0.3486 (tpp) REVERT: T 53 MET cc_start: -0.4589 (tpp) cc_final: -0.5133 (ttm) REVERT: N 53 MET cc_start: -0.5203 (tpp) cc_final: -0.6330 (ttt) REVERT: P 53 MET cc_start: -0.2881 (tpp) cc_final: -0.3324 (tpt) REVERT: X 48 ASN cc_start: 0.8670 (t0) cc_final: 0.8284 (m-40) REVERT: Y 36 ILE cc_start: 0.9225 (mp) cc_final: 0.8806 (tt) REVERT: Y 37 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8884 (tm-30) REVERT: U 55 TYR cc_start: 0.9068 (m-80) cc_final: 0.8403 (m-80) REVERT: U 59 ILE cc_start: 0.9100 (mt) cc_final: 0.8883 (mt) REVERT: V 23 SER cc_start: 0.8767 (p) cc_final: 0.8539 (t) REVERT: V 37 GLU cc_start: 0.9159 (tp30) cc_final: 0.8686 (tp30) REVERT: V 48 ASN cc_start: 0.9000 (p0) cc_final: 0.8636 (p0) REVERT: V 52 GLN cc_start: 0.9034 (mt0) cc_final: 0.8706 (mp10) REVERT: E 45 LEU cc_start: 0.8988 (tp) cc_final: 0.8684 (tp) REVERT: E 48 ASN cc_start: 0.8008 (p0) cc_final: 0.5799 (p0) REVERT: E 52 GLN cc_start: 0.9150 (mt0) cc_final: 0.8530 (mt0) REVERT: I 53 MET cc_start: 0.7914 (ttm) cc_final: 0.6950 (tmm) REVERT: Q 167 MET cc_start: 0.8867 (mtp) cc_final: 0.8486 (mtp) REVERT: Q 187 TYR cc_start: 0.9321 (m-80) cc_final: 0.8396 (m-80) REVERT: G 5 SER cc_start: 0.8933 (t) cc_final: 0.8685 (t) REVERT: G 236 LYS cc_start: 0.9565 (mtmm) cc_final: 0.9282 (mtmm) REVERT: G 242 ARG cc_start: 0.6086 (mmp80) cc_final: 0.5807 (mmp80) REVERT: C 72 SER cc_start: 0.9113 (m) cc_final: 0.8744 (t) REVERT: C 144 ILE cc_start: 0.9534 (mm) cc_final: 0.9328 (mp) REVERT: C 146 CYS cc_start: 0.9011 (t) cc_final: 0.8739 (t) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.4249 time to fit residues: 224.4495 Evaluate side-chains 308 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 209 optimal weight: 30.0000 chunk 174 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 35 GLN J 52 GLN N 52 GLN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS W 5 HIS ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3983 r_free = 0.3983 target = 0.088434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.059198 restraints weight = 388977.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.061851 restraints weight = 164018.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.063748 restraints weight = 92165.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.064841 restraints weight = 62019.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.065577 restraints weight = 48339.338| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19828 Z= 0.156 Angle : 0.648 9.421 27142 Z= 0.317 Chirality : 0.050 0.254 3063 Planarity : 0.004 0.081 3283 Dihedral : 14.858 179.966 3122 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.18), residues: 2198 helix: 0.24 (0.22), residues: 534 sheet: -1.99 (0.21), residues: 572 loop : -0.49 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 141 TYR 0.013 0.001 TYR M 25 PHE 0.030 0.001 PHE A 129 TRP 0.015 0.001 TRP A 177 HIS 0.004 0.001 HIS G 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (19827) covalent geometry : angle 0.64828 / 0.32 (27140) SS BOND : bond 0.00560 / 0.35 ( 1) SS BOND : angle 1.79992 / 0.72 ( 2) hydrogen bonds : bond 0.04161 / 2.83 ( 700) hydrogen bonds : angle 5.90712 / 4.06 ( 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 369 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.115 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: T 53 MET cc_start: -0.4671 (tpp) cc_final: -0.5193 (ttm) REVERT: N 53 MET cc_start: -0.5161 (tpp) cc_final: -0.6537 (ttt) REVERT: P 53 MET cc_start: -0.3171 (tpp) cc_final: -0.3546 (tpt) REVERT: X 37 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8757 (tm-30) REVERT: Y 36 ILE cc_start: 0.9251 (mp) cc_final: 0.8857 (tt) REVERT: Y 37 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8883 (tm-30) REVERT: U 55 TYR cc_start: 0.8987 (m-80) cc_final: 0.8274 (m-80) REVERT: U 59 ILE cc_start: 0.9098 (mt) cc_final: 0.8882 (mt) REVERT: V 12 LEU cc_start: 0.9601 (mm) cc_final: 0.9378 (tp) REVERT: V 23 SER cc_start: 0.9012 (p) cc_final: 0.8640 (t) REVERT: V 48 ASN cc_start: 0.9048 (p0) cc_final: 0.8689 (p0) REVERT: V 52 GLN cc_start: 0.9071 (mt0) cc_final: 0.8769 (mp10) REVERT: K 30 ILE cc_start: 0.9252 (pt) cc_final: 0.8603 (pt) REVERT: E 45 LEU cc_start: 0.9033 (tp) cc_final: 0.8747 (tp) REVERT: E 48 ASN cc_start: 0.8017 (p0) cc_final: 0.5835 (p0) REVERT: E 52 GLN cc_start: 0.9146 (mt0) cc_final: 0.8466 (mt0) REVERT: I 53 MET cc_start: 0.7835 (ttm) cc_final: 0.6923 (tmm) REVERT: Q 56 TYR cc_start: 0.8519 (m-10) cc_final: 0.8162 (m-10) REVERT: Q 167 MET cc_start: 0.8842 (mtp) cc_final: 0.8499 (mtp) REVERT: G 143 TYR cc_start: 0.7956 (m-80) cc_final: 0.7688 (m-80) REVERT: G 193 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8331 (tm-30) REVERT: G 236 LYS cc_start: 0.9573 (mtmm) cc_final: 0.9265 (mtmm) REVERT: C 72 SER cc_start: 0.9125 (m) cc_final: 0.8750 (t) REVERT: C 144 ILE cc_start: 0.9532 (mm) cc_final: 0.9324 (mp) REVERT: C 146 CYS cc_start: 0.8990 (t) cc_final: 0.8688 (t) REVERT: C 249 LEU cc_start: 0.9338 (tt) cc_final: 0.8906 (mp) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.4172 time to fit residues: 223.1585 Evaluate side-chains 308 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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: 30.0000 chunk 8 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 19 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS W 5 HIS ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** E 28 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** G 153 HIS C 12 GLN B Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.086393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057112 restraints weight = 417048.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.059740 restraints weight = 173546.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.061573 restraints weight = 97266.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.062615 restraints weight = 65837.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.063373 restraints weight = 51625.938| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19828 Z= 0.214 Angle : 0.685 9.847 27142 Z= 0.341 Chirality : 0.049 0.235 3063 Planarity : 0.005 0.081 3283 Dihedral : 15.040 179.437 3122 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.05 % Allowed : 0.84 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2198 helix: 0.22 (0.23), residues: 529 sheet: -2.00 (0.20), residues: 597 loop : -0.47 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 19 TYR 0.018 0.002 TYR D 25 PHE 0.025 0.002 PHE A 129 TRP 0.021 0.002 TRP Q 177 HIS 0.006 0.001 HIS K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 (19827) covalent geometry : angle 0.68488 / 0.34 (27140) SS BOND : bond 0.00364 / 0.23 ( 1) SS BOND : angle 1.76358 / 0.68 ( 2) hydrogen bonds : bond 0.04341 / 2.99 ( 700) hydrogen bonds : angle 5.85940 / 4.03 ( 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 341 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.423 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: T 53 MET cc_start: -0.4455 (tpp) cc_final: -0.5176 (ttm) REVERT: N 53 MET cc_start: -0.4319 (tpp) cc_final: -0.5916 (ttp) REVERT: P 53 MET cc_start: -0.3370 (tpp) cc_final: -0.3769 (tpt) REVERT: Y 31 LYS cc_start: 0.9123 (mttt) cc_final: 0.8518 (mtpp) REVERT: Y 37 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8889 (tm-30) REVERT: U 55 TYR cc_start: 0.9093 (m-80) cc_final: 0.8360 (m-80) REVERT: U 59 ILE cc_start: 0.9120 (mt) cc_final: 0.8893 (mt) REVERT: V 5 HIS cc_start: 0.8731 (p90) cc_final: 0.8376 (p90) REVERT: V 48 ASN cc_start: 0.9058 (p0) cc_final: 0.8662 (p0) REVERT: V 52 GLN cc_start: 0.9067 (mt0) cc_final: 0.8740 (mp10) REVERT: K 30 ILE cc_start: 0.9297 (pt) cc_final: 0.8621 (pt) REVERT: E 45 LEU cc_start: 0.9034 (tp) cc_final: 0.8749 (tp) REVERT: E 48 ASN cc_start: 0.8142 (p0) cc_final: 0.6095 (p0) REVERT: E 52 GLN cc_start: 0.9127 (mt0) cc_final: 0.8488 (mt0) REVERT: I 53 MET cc_start: 0.7951 (ttm) cc_final: 0.6915 (tmm) REVERT: Q 56 TYR cc_start: 0.8494 (m-10) cc_final: 0.8140 (m-10) REVERT: Q 167 MET cc_start: 0.8818 (mtp) cc_final: 0.8466 (mtp) REVERT: G 177 TRP cc_start: 0.9595 (t60) cc_final: 0.9366 (t60) REVERT: G 236 LYS cc_start: 0.9559 (mtmm) cc_final: 0.9241 (mtmm) REVERT: C 72 SER cc_start: 0.9187 (m) cc_final: 0.8777 (t) REVERT: C 144 ILE cc_start: 0.9473 (mm) cc_final: 0.9267 (mp) REVERT: C 146 CYS cc_start: 0.9033 (t) cc_final: 0.8803 (t) REVERT: C 167 MET cc_start: 0.8063 (mmm) cc_final: 0.7819 (mmm) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.4174 time to fit residues: 206.9152 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 : 1.012 ------------------------------------------------------------------------------- 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: 0.7980 chunk 144 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 192 optimal weight: 50.0000 chunk 89 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS W 5 HIS D 28 ASN E 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.087101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.057592 restraints weight = 431681.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.060255 restraints weight = 174734.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062155 restraints weight = 96823.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.063232 restraints weight = 64854.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063974 restraints weight = 50427.424| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- 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 = 0.31 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 = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19828 Z= 0.157 Angle : 0.645 8.734 27142 Z= 0.319 Chirality : 0.050 0.236 3063 Planarity : 0.004 0.059 3283 Dihedral : 14.985 178.689 3122 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.05 % Allowed : 0.74 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 2198 helix: 0.31 (0.23), residues: 529 sheet: -1.94 (0.20), residues: 596 loop : -0.38 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 19 TYR 0.017 0.002 TYR D 25 PHE 0.038 0.002 PHE G 85 TRP 0.037 0.002 TRP A 177 HIS 0.011 0.001 HIS Q 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (19827) covalent geometry : angle 0.64529 / 0.32 (27140) SS BOND : bond 0.00444 / 0.28 ( 1) SS BOND : angle 1.98675 / 0.79 ( 2) hydrogen bonds : bond 0.04119 / 2.85 ( 700) hydrogen bonds : angle 5.81589 / 4.00 ( 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 345 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.087 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: T 53 MET cc_start: -0.4414 (tpp) cc_final: -0.5133 (ttm) REVERT: N 53 MET cc_start: -0.4678 (tpp) cc_final: -0.5838 (ttt) REVERT: P 53 MET cc_start: -0.3538 (tpp) cc_final: -0.3900 (tpt) REVERT: X 37 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8697 (tm-30) REVERT: Y 31 LYS cc_start: 0.9121 (mttt) cc_final: 0.8525 (mtpp) REVERT: Y 37 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8917 (tm-30) REVERT: U 55 TYR cc_start: 0.9072 (m-80) cc_final: 0.8324 (m-80) REVERT: U 59 ILE cc_start: 0.9144 (mt) cc_final: 0.8909 (mt) REVERT: V 48 ASN cc_start: 0.9055 (p0) cc_final: 0.8770 (p0) REVERT: V 52 GLN cc_start: 0.9069 (mt0) cc_final: 0.8770 (mp10) REVERT: K 30 ILE cc_start: 0.9289 (pt) cc_final: 0.8773 (pt) REVERT: E 45 LEU cc_start: 0.9059 (tp) cc_final: 0.8780 (tp) REVERT: E 48 ASN cc_start: 0.8094 (p0) cc_final: 0.6013 (p0) REVERT: E 52 GLN cc_start: 0.9147 (mt0) cc_final: 0.8503 (mt0) REVERT: I 53 MET cc_start: 0.7947 (ttm) cc_final: 0.6883 (tmm) REVERT: Q 56 TYR cc_start: 0.8512 (m-10) cc_final: 0.8137 (m-10) REVERT: Q 167 MET cc_start: 0.8796 (mtp) cc_final: 0.8437 (mtp) REVERT: G 1 MET cc_start: 0.8834 (tpp) cc_final: 0.8124 (tpp) REVERT: G 135 LYS cc_start: 0.9048 (tppp) cc_final: 0.8774 (ttpt) REVERT: G 177 TRP cc_start: 0.9622 (t60) cc_final: 0.9411 (t60) REVERT: G 236 LYS cc_start: 0.9576 (mtmm) cc_final: 0.9263 (mtmm) REVERT: C 72 SER cc_start: 0.9201 (m) cc_final: 0.8780 (t) REVERT: C 146 CYS cc_start: 0.9076 (t) cc_final: 0.8861 (t) REVERT: C 167 MET cc_start: 0.8052 (mmm) cc_final: 0.7811 (mmm) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.4170 time to fit residues: 208.9880 Evaluate side-chains 297 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 0.0060 chunk 105 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 201 optimal weight: 50.0000 overall best weight: 2.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS W 5 HIS ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN D 28 ASN ** I 52 GLN ** 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 = 0.3962 r_free = 0.3962 target = 0.086887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056568 restraints weight = 458595.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.059657 restraints weight = 186730.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.061559 restraints weight = 103670.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.062711 restraints weight = 68864.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.063496 restraints weight = 53185.289| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19828 Z= 0.144 Angle : 0.626 8.442 27142 Z= 0.306 Chirality : 0.049 0.233 3063 Planarity : 0.004 0.045 3283 Dihedral : 14.923 178.393 3122 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % 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 are not related in a simple way. whole: -1.04 (0.19), residues: 2198 helix: 0.36 (0.22), residues: 547 sheet: -1.89 (0.21), residues: 597 loop : -0.33 (0.21), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 140 TYR 0.017 0.001 TYR D 25 PHE 0.022 0.001 PHE G 85 TRP 0.026 0.001 TRP A 177 HIS 0.004 0.001 HIS G 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (19827) covalent geometry : angle 0.62568 / 0.31 (27140) SS BOND : bond 0.00436 / 0.27 ( 1) SS BOND : angle 1.99469 / 0.79 ( 2) hydrogen bonds : bond 0.03853 / 2.66 ( 700) hydrogen bonds : angle 5.67980 / 3.91 ( 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 349 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.080 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: R 53 MET cc_start: -0.2317 (ttm) cc_final: -0.2665 (tpp) REVERT: T 53 MET cc_start: -0.4383 (tpp) cc_final: -0.5026 (ttm) REVERT: N 53 MET cc_start: -0.4714 (tpp) cc_final: -0.5876 (ttt) REVERT: P 53 MET cc_start: -0.3489 (tpp) cc_final: -0.3856 (tpt) REVERT: X 37 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8649 (tm-30) REVERT: Y 23 SER cc_start: 0.8155 (m) cc_final: 0.7912 (t) REVERT: Y 36 ILE cc_start: 0.9293 (mp) cc_final: 0.8934 (tt) REVERT: Y 37 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8894 (tm-30) REVERT: U 55 TYR cc_start: 0.9046 (m-80) cc_final: 0.8472 (m-80) REVERT: V 48 ASN cc_start: 0.9073 (p0) cc_final: 0.8802 (p0) REVERT: V 52 GLN cc_start: 0.9076 (mt0) cc_final: 0.8765 (mp10) REVERT: K 30 ILE cc_start: 0.9299 (pt) cc_final: 0.8786 (pt) REVERT: E 45 LEU cc_start: 0.9011 (tp) cc_final: 0.8715 (tp) REVERT: E 48 ASN cc_start: 0.8114 (p0) cc_final: 0.7724 (p0) REVERT: I 53 MET cc_start: 0.7951 (ttm) cc_final: 0.6918 (tmm) REVERT: Q 56 TYR cc_start: 0.8427 (m-10) cc_final: 0.8067 (m-10) REVERT: Q 167 MET cc_start: 0.8780 (mtp) cc_final: 0.8410 (mtp) REVERT: G 177 TRP cc_start: 0.9609 (t60) cc_final: 0.9377 (t60) REVERT: G 236 LYS cc_start: 0.9539 (mtmm) cc_final: 0.9232 (mtmm) REVERT: C 72 SER cc_start: 0.9171 (m) cc_final: 0.8742 (t) REVERT: C 167 MET cc_start: 0.7979 (mmm) cc_final: 0.7730 (mmm) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.4077 time to fit residues: 206.5314 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 : 1.096 ------------------------------------------------------------------------------- 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: 10.0000 chunk 25 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 208 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS W 5 HIS M 28 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.088071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.058297 restraints weight = 432165.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.061000 restraints weight = 174284.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.062958 restraints weight = 96474.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.064270 restraints weight = 64778.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.064932 restraints weight = 49333.820| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19828 Z= 0.110 Angle : 0.602 7.920 27142 Z= 0.292 Chirality : 0.050 0.235 3063 Planarity : 0.004 0.047 3283 Dihedral : 14.760 177.866 3122 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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 are not related in a simple way. whole: -0.86 (0.19), residues: 2198 helix: 0.59 (0.23), residues: 547 sheet: -1.83 (0.20), residues: 621 loop : -0.18 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 19 TYR 0.014 0.001 TYR D 25 PHE 0.018 0.001 PHE G 85 TRP 0.049 0.001 TRP A 177 HIS 0.005 0.001 HIS E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (19827) covalent geometry : angle 0.60170 / 0.29 (27140) SS BOND : bond 0.00406 / 0.25 ( 1) SS BOND : angle 2.19410 / 0.87 ( 2) hydrogen bonds : bond 0.03633 / 2.50 ( 700) hydrogen bonds : angle 5.48548 / 3.77 ( 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 350 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.038 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: -0.4471 (tpp) cc_final: -0.5114 (ttm) REVERT: N 53 MET cc_start: -0.4941 (tpp) cc_final: -0.6054 (ttt) REVERT: P 53 MET cc_start: -0.3600 (tpp) cc_final: -0.3941 (tpt) REVERT: X 37 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8592 (tm-30) REVERT: Y 36 ILE cc_start: 0.9252 (mp) cc_final: 0.8781 (tt) REVERT: Y 37 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8854 (tm-30) REVERT: V 46 LEU cc_start: 0.8245 (tp) cc_final: 0.7899 (tp) REVERT: V 48 ASN cc_start: 0.9113 (p0) cc_final: 0.8830 (p0) REVERT: V 52 GLN cc_start: 0.9099 (mt0) cc_final: 0.8772 (mp10) REVERT: K 30 ILE cc_start: 0.9247 (pt) cc_final: 0.8504 (pt) REVERT: E 45 LEU cc_start: 0.9016 (tp) cc_final: 0.8725 (tp) REVERT: E 48 ASN cc_start: 0.8211 (p0) cc_final: 0.7832 (p0) REVERT: I 53 MET cc_start: 0.7954 (ttm) cc_final: 0.6949 (tmm) REVERT: Q 56 TYR cc_start: 0.8329 (m-10) cc_final: 0.7863 (m-80) REVERT: Q 167 MET cc_start: 0.8793 (mtp) cc_final: 0.8417 (mtp) REVERT: Q 224 LEU cc_start: 0.9254 (mm) cc_final: 0.8880 (mm) REVERT: G 177 TRP cc_start: 0.9610 (t60) cc_final: 0.9401 (t60) REVERT: G 228 LEU cc_start: 0.9261 (mm) cc_final: 0.8895 (tp) REVERT: C 72 SER cc_start: 0.9099 (m) cc_final: 0.8716 (t) REVERT: C 167 MET cc_start: 0.7922 (mmm) cc_final: 0.7636 (mmm) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.3530 time to fit residues: 180.2010 Evaluate side-chains 308 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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: 50.0000 chunk 190 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 185 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS M 28 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.088535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.058478 restraints weight = 438170.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061228 restraints weight = 176985.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.063159 restraints weight = 98187.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.064534 restraints weight = 66991.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.065170 restraints weight = 51718.880| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19828 Z= 0.107 Angle : 0.594 7.735 27142 Z= 0.288 Chirality : 0.049 0.227 3063 Planarity : 0.004 0.047 3283 Dihedral : 14.666 178.316 3122 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.05 % Allowed : 0.15 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 2198 helix: 0.75 (0.23), residues: 547 sheet: -1.87 (0.20), residues: 629 loop : -0.11 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 16 TYR 0.014 0.001 TYR D 25 PHE 0.018 0.001 PHE A 129 TRP 0.043 0.001 TRP A 177 HIS 0.003 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (19827) covalent geometry : angle 0.59367 / 0.29 (27140) SS BOND : bond 0.00398 / 0.25 ( 1) SS BOND : angle 2.01971 / 0.80 ( 2) hydrogen bonds : bond 0.03528 / 2.42 ( 700) hydrogen bonds : angle 5.40503 / 3.71 ( 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 352 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.101 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: T 53 MET cc_start: -0.4565 (tpp) cc_final: -0.5202 (ttm) REVERT: N 53 MET cc_start: -0.5005 (tpp) cc_final: -0.6081 (ttt) REVERT: P 53 MET cc_start: -0.3654 (tpp) cc_final: -0.3961 (tpt) REVERT: X 37 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8556 (tm-30) REVERT: Y 31 LYS cc_start: 0.9064 (mttt) cc_final: 0.8444 (mtpp) REVERT: Y 36 ILE cc_start: 0.9241 (mp) cc_final: 0.8756 (tt) REVERT: Y 37 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8848 (tm-30) REVERT: V 46 LEU cc_start: 0.8231 (tp) cc_final: 0.7889 (tp) REVERT: V 48 ASN cc_start: 0.9083 (p0) cc_final: 0.8832 (p0) REVERT: V 52 GLN cc_start: 0.8988 (mt0) cc_final: 0.8742 (mp10) REVERT: K 30 ILE cc_start: 0.9248 (pt) cc_final: 0.8521 (pt) REVERT: E 45 LEU cc_start: 0.9021 (tp) cc_final: 0.8735 (tp) REVERT: E 48 ASN cc_start: 0.8221 (p0) cc_final: 0.7844 (p0) REVERT: I 53 MET cc_start: 0.7937 (ttm) cc_final: 0.6933 (tmm) REVERT: Q 56 TYR cc_start: 0.8244 (m-10) cc_final: 0.7816 (m-10) REVERT: Q 167 MET cc_start: 0.8798 (mtp) cc_final: 0.8411 (mtp) REVERT: Q 224 LEU cc_start: 0.9257 (mm) cc_final: 0.8972 (mm) REVERT: G 177 TRP cc_start: 0.9611 (t60) cc_final: 0.9393 (t60) REVERT: C 72 SER cc_start: 0.9059 (m) cc_final: 0.8678 (t) REVERT: C 167 MET cc_start: 0.7846 (mmm) cc_final: 0.7619 (mmm) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.3709 time to fit residues: 190.8617 Evaluate side-chains 307 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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: 6.9990 chunk 139 optimal weight: 0.2980 chunk 134 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.087942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.058439 restraints weight = 438870.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.061207 restraints weight = 177414.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.063090 restraints weight = 98605.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.064366 restraints weight = 67023.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.064995 restraints weight = 52119.260| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19828 Z= 0.129 Angle : 0.595 8.342 27142 Z= 0.290 Chirality : 0.049 0.223 3063 Planarity : 0.004 0.044 3283 Dihedral : 14.702 179.249 3122 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.05 % Allowed : 0.15 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.19), residues: 2198 helix: 0.73 (0.23), residues: 549 sheet: -1.89 (0.20), residues: 639 loop : -0.10 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 16 TYR 0.016 0.001 TYR D 25 PHE 0.017 0.001 PHE A 129 TRP 0.043 0.001 TRP A 177 HIS 0.003 0.001 HIS K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (19827) covalent geometry : angle 0.59467 / 0.29 (27140) SS BOND : bond 0.00318 / 0.20 ( 1) SS BOND : angle 2.04235 / 0.81 ( 2) hydrogen bonds : bond 0.03613 / 2.49 ( 700) hydrogen bonds : angle 5.37936 / 3.67 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9072.14 seconds wall clock time: 155 minutes 7.73 seconds (9307.73 seconds total)