Starting phenix.real_space_refine on Mon Jul 6 18:16:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bvj_16265/07_2026/8bvj_16265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvj_16265/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8bvj_16265/07_2026/8bvj_16265.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bvj_16265/07_2026/8bvj_16265.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bvj_16265/07_2026/8bvj_16265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvj_16265/07_2026/8bvj_16265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bvj_16265/07_2026/8bvj_16265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvj_16265/07_2026/8bvj_16265.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 54 5.16 5 C 12131 2.51 5 N 3409 2.21 5 O 3633 1.98 5 H 18901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: {'RNA': 55} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 7, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 31, 'rna3p': 23} Chain breaks: 3 Chain: "G" Number of atoms: 4162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 4148 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Conformer: "B" Number of residues, atoms: 260, 4148 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} bond proxies already assigned to first conformer: 4186 Chain: "C" Number of atoms: 4184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Conformer: "B" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} bond proxies already assigned to first conformer: 4209 Chain: "A" Number of atoms: 4184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Conformer: "B" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} bond proxies already assigned to first conformer: 4209 Time building chain proxies: 8.03, per 1000 atoms: 0.21 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: 3.38 Conformation dependent library (CDL) restraints added in 1.1 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: 5.67 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: 7.92 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18887 1.03 - 1.23: 19 1.23 - 1.42: 8442 1.42 - 1.62: 11288 1.62 - 1.81: 92 Bond restraints: 38728 Sorted by residual: bond pdb=" N ALA G 0 " pdb=" CA ALA G 0 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N ALA G 0 " pdb=" H ALA G 0 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C HIS X 57 " pdb=" N ALA X 58 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.17e-02 7.31e+03 9.63e-01 bond pdb=" CA LEU C 70 " pdb=" C LEU C 70 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.99e-01 bond pdb=" CA MET G 1 " pdb=" CB MET G 1 " ideal model delta sigma weight residual 1.530 1.516 0.015 1.69e-02 3.50e+03 7.53e-01 ... (remaining 38723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 65721 0.99 - 1.98: 3872 1.98 - 2.98: 275 2.98 - 3.97: 124 3.97 - 4.96: 15 Bond angle restraints: 70007 Sorted by residual: angle pdb=" N PHE A 99 " pdb=" CA PHE A 99 " pdb=" C PHE A 99 " ideal model delta sigma weight residual 110.80 105.84 4.96 2.13e+00 2.20e-01 5.42e+00 angle pdb=" N ARG A 196 " pdb=" CA ARG A 196 " pdb=" C ARG A 196 " ideal model delta sigma weight residual 112.57 110.01 2.56 1.13e+00 7.83e-01 5.15e+00 angle pdb=" N LEU P 7 " pdb=" CA LEU P 7 " pdb=" C LEU P 7 " ideal model delta sigma weight residual 114.56 111.69 2.87 1.27e+00 6.20e-01 5.10e+00 angle pdb=" C VAL G 8 " pdb=" CA VAL G 8 " pdb=" CB VAL G 8 " ideal model delta sigma weight residual 112.16 108.66 3.50 1.55e+00 4.16e-01 5.09e+00 angle pdb=" C PHE A 99 " pdb=" CA PHE A 99 " pdb=" CB PHE A 99 " ideal model delta sigma weight residual 110.42 114.87 -4.45 1.99e+00 2.53e-01 5.00e+00 ... (remaining 70002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 17613 34.30 - 68.59: 367 68.59 - 102.89: 33 102.89 - 137.19: 10 137.19 - 171.48: 8 Dihedral angle restraints: 18031 sinusoidal: 10276 harmonic: 7755 Sorted by residual: dihedral pdb=" O4' C B 57 " pdb=" C1' C B 57 " pdb=" N1 C B 57 " pdb=" C2 C B 57 " ideal model delta sinusoidal sigma weight residual -128.00 25.02 -153.02 1 1.70e+01 3.46e-03 6.28e+01 dihedral pdb=" CB CYS Q 32 " pdb=" SG CYS Q 32 " pdb=" SG CYS Q 146 " pdb=" CB CYS Q 146 " ideal model delta sinusoidal sigma weight residual 93.00 31.71 61.29 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" O4' A B 77 " pdb=" C1' A B 77 " pdb=" N9 A B 77 " pdb=" C4 A B 77 " ideal model delta sinusoidal sigma weight residual -106.00 -170.10 64.10 1 1.70e+01 3.46e-03 1.87e+01 ... (remaining 18028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2053 0.030 - 0.059: 624 0.059 - 0.089: 117 0.089 - 0.118: 224 0.118 - 0.148: 45 Chirality restraints: 3063 Sorted by residual: chirality pdb=" C3' A B 82 " pdb=" C4' A B 82 " pdb=" O3' A B 82 " pdb=" C2' A B 82 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE G 144 " pdb=" N ILE G 144 " pdb=" C ILE G 144 " pdb=" CB ILE G 144 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA VAL P 20 " pdb=" N VAL P 20 " pdb=" C VAL P 20 " pdb=" CB VAL P 20 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 3060 not shown) Planarity restraints: 5428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 9 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO I 10 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 10 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 10 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 172 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO A 173 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP P 9 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO P 10 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO P 10 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO P 10 " -0.016 5.00e-02 4.00e+02 ... (remaining 5425 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1374 2.16 - 2.77: 74204 2.77 - 3.38: 106777 3.38 - 3.99: 140006 3.99 - 4.60: 215726 Nonbonded interactions: 538087 Sorted by model distance: nonbonded pdb=" O HIS G 131 " pdb=" HG SER G 134 " model vdw 1.546 2.450 nonbonded pdb=" O GLY G 115 " pdb=" HG SER G 118 " model vdw 1.581 2.450 nonbonded pdb=" H LYS F 31 " pdb=" OP2 A B 58 " model vdw 1.636 2.450 nonbonded pdb=" OE1 GLU G 174 " pdb=" H GLU G 174 " model vdw 1.638 2.450 nonbonded pdb=" O GLY C 115 " pdb=" HG SER C 118 " model vdw 1.639 2.450 ... (remaining 538082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 258)) selection = (chain 'C' and (resid 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 258)) selection = (chain 'G' and (resid 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 245 or (resid 246 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 247 through 258)) selection = (chain 'Q' and (resid 0 through 11 or resid 13 through 258)) } ncs_group { reference = (chain 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'E' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'I' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'J' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'L' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'M' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'N' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'P' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'R' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'S' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'T' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'U' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3 or name HD22)) or resid 49 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB or name CG or name ND1 or name CD \ 2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ D2 or name HE1)) or resid 58 through 66)) selection = (chain 'V' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'W' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'X' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'Y' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD2 or name HE1)) or resid 58 through 66)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 39.420 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- 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= 0.112 Angle : 0.472 4.959 27142 Z= 0.272 Chirality : 0.041 0.148 3063 Planarity : 0.002 0.032 3283 Dihedral : 13.738 166.167 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 0.00195 / 0.11 (19827) covalent geometry : angle 0.47229 / 0.27 (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 : 0.984 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: 0.3464 time to fit residues: 308.4809 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 : 1.025 ------------------------------------------------------------------------------- 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** P 57 HIS V 8 GLN K 35 GLN E 13 ASN F 52 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN G 153 HIS 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.090288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.060338 restraints weight = 404905.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.063224 restraints weight = 169026.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.065255 restraints weight = 94881.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.066526 restraints weight = 63855.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.067192 restraints weight = 48837.932| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 19828 Z= 0.257 Angle : 0.661 8.200 27142 Z= 0.351 Chirality : 0.044 0.257 3063 Planarity : 0.005 0.100 3283 Dihedral : 11.011 163.254 3122 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.10 % Allowed : 1.69 % 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: -1.67 (0.18), residues: 2198 helix: 0.20 (0.23), residues: 533 sheet: -2.36 (0.19), residues: 608 loop : -0.85 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.001 ARG J 16 TYR 0.019 0.002 TYR S 25 PHE 0.023 0.002 PHE C 125 TRP 0.016 0.002 TRP G 203 HIS 0.011 0.001 HIS K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.26 (19827) covalent geometry : angle 0.66019 / 0.35 (27140) SS BOND : bond 0.00486 / 0.30 ( 1) SS BOND : angle 3.36586 / 1.45 ( 2) hydrogen bonds : bond 0.05600 / 3.88 ( 700) hydrogen bonds : angle 6.61742 / 4.52 ( 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 427 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 425 time to evaluate : 1.053 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: T 53 MET cc_start: -0.4962 (tpp) cc_final: -0.5196 (tpp) REVERT: N 53 MET cc_start: -0.5710 (tpp) cc_final: -0.6873 (ttt) REVERT: P 53 MET cc_start: -0.2494 (tpp) cc_final: -0.3135 (tpt) REVERT: P 54 VAL cc_start: 0.8859 (p) cc_final: 0.8657 (p) REVERT: X 48 ASN cc_start: 0.8630 (t0) cc_final: 0.8148 (m-40) REVERT: Y 37 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8790 (tm-30) REVERT: V 9 ASP cc_start: 0.9342 (t70) cc_final: 0.9025 (t0) REVERT: V 35 GLN cc_start: 0.9049 (mt0) cc_final: 0.8838 (pm20) REVERT: K 60 SER cc_start: 0.7767 (m) cc_final: 0.7435 (p) REVERT: E 45 LEU cc_start: 0.9053 (tp) cc_final: 0.8843 (tp) REVERT: E 48 ASN cc_start: 0.7903 (p0) cc_final: 0.5666 (p0) REVERT: E 52 GLN cc_start: 0.9315 (mt0) cc_final: 0.8766 (mt0) REVERT: I 53 MET cc_start: 0.7851 (ttm) cc_final: 0.6963 (tmm) REVERT: Q 107 LEU cc_start: 0.9256 (tp) cc_final: 0.8896 (tt) REVERT: Q 167 MET cc_start: 0.8987 (mtp) cc_final: 0.8675 (mtp) REVERT: Q 187 TYR cc_start: 0.9288 (m-80) cc_final: 0.8264 (m-80) REVERT: Q 230 ARG cc_start: 0.9161 (ptm-80) cc_final: 0.8920 (ptm-80) REVERT: G 167 MET cc_start: 0.8029 (mtt) cc_final: 0.7775 (mtp) REVERT: G 193 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8306 (tm-30) REVERT: G 222 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8995 (mm-40) REVERT: G 224 LEU cc_start: 0.9353 (pt) cc_final: 0.9084 (pt) REVERT: G 232 VAL cc_start: 0.9342 (m) cc_final: 0.8890 (m) REVERT: G 242 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7776 (mmp80) REVERT: C 146 CYS cc_start: 0.9109 (t) cc_final: 0.8802 (t) outliers start: 2 outliers final: 1 residues processed: 426 average time/residue: 0.3546 time to fit residues: 217.2381 Evaluate side-chains 355 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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: 10.0000 chunk 65 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 chunk 205 optimal weight: 40.0000 chunk 93 optimal weight: 9.9990 chunk 129 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 193 optimal weight: 30.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN W 5 HIS F 48 ASN F 52 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 GLN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.091328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.061207 restraints weight = 421939.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.064170 restraints weight = 170251.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.066257 restraints weight = 94161.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.067360 restraints weight = 62490.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.068155 restraints weight = 48418.446| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19828 Z= 0.134 Angle : 0.542 5.127 27142 Z= 0.283 Chirality : 0.043 0.170 3063 Planarity : 0.004 0.064 3283 Dihedral : 10.928 164.255 3122 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % 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: -1.26 (0.18), residues: 2198 helix: 0.43 (0.23), residues: 533 sheet: -2.11 (0.20), residues: 600 loop : -0.54 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 16 TYR 0.012 0.001 TYR U 55 PHE 0.012 0.001 PHE Y 42 TRP 0.012 0.001 TRP G 203 HIS 0.010 0.001 HIS Q 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19827) covalent geometry : angle 0.54204 / 0.28 (27140) SS BOND : bond 0.00431 / 0.27 ( 1) SS BOND : angle 2.11222 / 0.88 ( 2) hydrogen bonds : bond 0.04643 / 3.15 ( 700) hydrogen bonds : angle 6.21146 / 4.25 ( 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 416 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.5010 (tpp) cc_final: -0.5651 (ttm) REVERT: N 53 MET cc_start: -0.5628 (tpp) cc_final: -0.6779 (ttt) REVERT: N 66 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8856 (ttt180) REVERT: P 53 MET cc_start: -0.2845 (tpp) cc_final: -0.3255 (tpt) REVERT: X 37 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8893 (tm-30) REVERT: X 48 ASN cc_start: 0.8643 (t0) cc_final: 0.8281 (m-40) REVERT: Y 36 ILE cc_start: 0.9098 (mp) cc_final: 0.8521 (tt) REVERT: Y 37 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8748 (tm-30) REVERT: U 52 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8340 (mp-120) REVERT: U 55 TYR cc_start: 0.8807 (m-80) cc_final: 0.8152 (m-80) REVERT: U 59 ILE cc_start: 0.9116 (mt) cc_final: 0.8848 (mt) REVERT: V 30 ILE cc_start: 0.9267 (mm) cc_final: 0.9050 (mt) REVERT: V 48 ASN cc_start: 0.8973 (p0) cc_final: 0.8770 (p0) REVERT: V 52 GLN cc_start: 0.8959 (mt0) cc_final: 0.8729 (mp10) REVERT: W 28 ASN cc_start: 0.8517 (p0) cc_final: 0.8242 (p0) REVERT: W 53 MET cc_start: 0.8527 (ttp) cc_final: 0.8189 (ttt) REVERT: K 60 SER cc_start: 0.7629 (m) cc_final: 0.7376 (p) REVERT: E 45 LEU cc_start: 0.8834 (tp) cc_final: 0.8548 (tp) REVERT: E 48 ASN cc_start: 0.7995 (p0) cc_final: 0.5806 (p0) REVERT: E 52 GLN cc_start: 0.9252 (mt0) cc_final: 0.8681 (mt0) REVERT: F 46 LEU cc_start: 0.9515 (mp) cc_final: 0.9288 (tp) REVERT: I 53 MET cc_start: 0.7717 (ttm) cc_final: 0.6790 (tmm) REVERT: Q 98 ASP cc_start: 0.7630 (m-30) cc_final: 0.7228 (m-30) REVERT: Q 167 MET cc_start: 0.8931 (mtp) cc_final: 0.8581 (mtp) REVERT: G 193 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8211 (tm-30) REVERT: G 220 ASP cc_start: 0.8894 (m-30) cc_final: 0.8491 (m-30) REVERT: G 222 GLN cc_start: 0.9369 (mm-40) cc_final: 0.9157 (mm-40) REVERT: G 232 VAL cc_start: 0.9308 (m) cc_final: 0.8987 (m) REVERT: G 242 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7774 (mmp80) REVERT: C 56 TYR cc_start: 0.8674 (m-80) cc_final: 0.8114 (m-80) REVERT: C 146 CYS cc_start: 0.8976 (t) cc_final: 0.8659 (t) REVERT: A 211 GLU cc_start: 0.4290 (mm-30) cc_final: 0.4085 (mm-30) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3587 time to fit residues: 214.7676 Evaluate side-chains 357 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 30.0000 chunk 34 optimal weight: 40.0000 chunk 148 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 157 optimal weight: 10.0000 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 ** P 35 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** ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.086042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056363 restraints weight = 397328.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058841 restraints weight = 171773.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.060634 restraints weight = 98592.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.061788 restraints weight = 67700.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062347 restraints weight = 52741.525| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19828 Z= 0.297 Angle : 0.692 8.215 27142 Z= 0.372 Chirality : 0.044 0.192 3063 Planarity : 0.005 0.044 3283 Dihedral : 11.426 164.869 3122 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 2198 helix: -0.28 (0.22), residues: 535 sheet: -2.18 (0.20), residues: 580 loop : -0.73 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 138 TYR 0.026 0.002 TYR G 132 PHE 0.044 0.002 PHE A 125 TRP 0.016 0.002 TRP G 22 HIS 0.010 0.002 HIS K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.30 (19827) covalent geometry : angle 0.69210 / 0.37 (27140) SS BOND : bond 0.00655 / 0.41 ( 1) SS BOND : angle 1.91917 / 0.74 ( 2) hydrogen bonds : bond 0.05110 / 3.56 ( 700) hydrogen bonds : angle 6.23251 / 4.29 ( 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 368 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4561 (tpp) cc_final: -0.5117 (ttm) REVERT: N 53 MET cc_start: -0.5185 (tpp) cc_final: -0.6308 (ttt) REVERT: P 53 MET cc_start: -0.2824 (tpp) cc_final: -0.3276 (tpt) REVERT: X 48 ASN cc_start: 0.8706 (t0) cc_final: 0.8344 (m-40) REVERT: Y 36 ILE cc_start: 0.9215 (mp) cc_final: 0.8822 (tt) REVERT: Y 37 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8863 (tm-30) REVERT: U 55 TYR cc_start: 0.9069 (m-80) cc_final: 0.8350 (m-80) REVERT: V 5 HIS cc_start: 0.8814 (p90) cc_final: 0.8613 (p90) REVERT: V 9 ASP cc_start: 0.9322 (t70) cc_final: 0.9120 (t0) REVERT: V 23 SER cc_start: 0.9083 (p) cc_final: 0.8823 (p) REVERT: V 37 GLU cc_start: 0.9139 (tp30) cc_final: 0.8660 (tp30) REVERT: V 46 LEU cc_start: 0.7813 (tp) cc_final: 0.7537 (tp) REVERT: V 48 ASN cc_start: 0.9003 (p0) cc_final: 0.8657 (p0) REVERT: V 52 GLN cc_start: 0.9052 (mt0) cc_final: 0.8734 (mp10) REVERT: E 45 LEU cc_start: 0.8996 (tp) cc_final: 0.8692 (tp) REVERT: E 48 ASN cc_start: 0.8026 (p0) cc_final: 0.5867 (p0) REVERT: E 52 GLN cc_start: 0.9173 (mt0) cc_final: 0.8560 (mt0) REVERT: I 53 MET cc_start: 0.7905 (ttm) cc_final: 0.6955 (tmm) REVERT: Q 167 MET cc_start: 0.8849 (mtp) cc_final: 0.8469 (mtp) REVERT: Q 187 TYR cc_start: 0.9337 (m-80) cc_final: 0.8427 (m-80) REVERT: G 1 MET cc_start: 0.8427 (tpp) cc_final: 0.7835 (tpp) REVERT: G 5 SER cc_start: 0.8925 (t) cc_final: 0.8660 (t) REVERT: G 236 LYS cc_start: 0.9554 (mtmm) cc_final: 0.9277 (mtmm) REVERT: G 253 TYR cc_start: 0.9547 (m-10) cc_final: 0.9296 (m-10) REVERT: C 72 SER cc_start: 0.9084 (m) cc_final: 0.8718 (t) REVERT: C 144 ILE cc_start: 0.9534 (mm) cc_final: 0.9319 (mp) REVERT: C 146 CYS cc_start: 0.8962 (t) cc_final: 0.8678 (t) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.3750 time to fit residues: 198.0400 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 : 0.768 ------------------------------------------------------------------------------- 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: 20.0000 chunk 107 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 35 GLN J 52 GLN N 52 GLN P 35 GLN Y 57 HIS W 5 HIS ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.088224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058071 restraints weight = 383584.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.060812 restraints weight = 161426.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.062668 restraints weight = 91075.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.063711 restraints weight = 61826.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.064507 restraints weight = 48826.011| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 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 = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19828 Z= 0.129 Angle : 0.548 5.615 27142 Z= 0.288 Chirality : 0.044 0.165 3063 Planarity : 0.004 0.047 3283 Dihedral : 11.181 164.094 3122 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.30 % 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: 0.21 (0.22), residues: 542 sheet: -1.98 (0.21), residues: 567 loop : -0.53 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 16 TYR 0.013 0.001 TYR C 132 PHE 0.030 0.001 PHE A 129 TRP 0.044 0.001 TRP A 177 HIS 0.004 0.001 HIS G 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (19827) covalent geometry : angle 0.54795 / 0.29 (27140) SS BOND : bond 0.00645 / 0.40 ( 1) SS BOND : angle 1.76461 / 0.70 ( 2) hydrogen bonds : bond 0.04105 / 2.78 ( 700) hydrogen bonds : angle 5.88218 / 4.04 ( 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 371 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.984 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: T 53 MET cc_start: -0.4683 (tpp) cc_final: -0.5228 (ttm) REVERT: N 53 MET cc_start: -0.5043 (tpp) cc_final: -0.6390 (ttt) REVERT: P 53 MET cc_start: -0.3134 (tpp) cc_final: -0.3530 (tpt) REVERT: X 37 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8761 (tm-30) REVERT: X 48 ASN cc_start: 0.8647 (t0) cc_final: 0.8315 (m-40) REVERT: Y 36 ILE cc_start: 0.9239 (mp) cc_final: 0.8857 (tt) REVERT: Y 37 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8834 (tm-30) REVERT: U 25 TYR cc_start: 0.9216 (m-80) cc_final: 0.8784 (m-80) REVERT: U 55 TYR cc_start: 0.8986 (m-80) cc_final: 0.8268 (m-80) REVERT: V 5 HIS cc_start: 0.8748 (p90) cc_final: 0.8532 (p90) REVERT: V 23 SER cc_start: 0.9152 (p) cc_final: 0.8910 (p) REVERT: V 46 LEU cc_start: 0.7963 (tp) cc_final: 0.7698 (tp) REVERT: V 48 ASN cc_start: 0.9077 (p0) cc_final: 0.8768 (p0) REVERT: V 52 GLN cc_start: 0.9014 (mt0) cc_final: 0.8806 (mp10) REVERT: E 45 LEU cc_start: 0.9016 (tp) cc_final: 0.8720 (tp) REVERT: E 48 ASN cc_start: 0.8054 (p0) cc_final: 0.5924 (p0) REVERT: E 52 GLN cc_start: 0.9158 (mt0) cc_final: 0.8488 (mt0) REVERT: I 53 MET cc_start: 0.7817 (ttm) cc_final: 0.6933 (tmm) REVERT: Q 56 TYR cc_start: 0.8628 (m-10) cc_final: 0.8322 (m-10) REVERT: Q 167 MET cc_start: 0.8827 (mtp) cc_final: 0.8485 (mtp) REVERT: G 143 TYR cc_start: 0.7692 (m-80) cc_final: 0.7481 (m-10) REVERT: G 193 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8371 (tm-30) REVERT: G 236 LYS cc_start: 0.9568 (mtmm) cc_final: 0.9360 (mtmm) REVERT: C 72 SER cc_start: 0.9133 (m) cc_final: 0.8769 (t) REVERT: C 146 CYS cc_start: 0.9006 (t) cc_final: 0.8684 (t) REVERT: C 249 LEU cc_start: 0.9332 (tt) cc_final: 0.8913 (mp) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.3837 time to fit residues: 205.1011 Evaluate side-chains 317 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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: 0.9990 chunk 81 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 GLN Y 57 HIS E 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.087208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057262 restraints weight = 415270.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.059863 restraints weight = 171709.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.061786 restraints weight = 95971.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062888 restraints weight = 64705.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.063729 restraints weight = 50562.611| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- 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 = 0.35 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 = 0.26 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: 0.7192 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19828 Z= 0.172 Angle : 0.557 6.106 27142 Z= 0.296 Chirality : 0.043 0.170 3063 Planarity : 0.004 0.078 3283 Dihedral : 11.210 164.949 3122 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % 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: -1.17 (0.18), residues: 2198 helix: 0.29 (0.22), residues: 536 sheet: -1.89 (0.21), residues: 577 loop : -0.53 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 19 TYR 0.012 0.001 TYR G 91 PHE 0.023 0.001 PHE A 129 TRP 0.051 0.002 TRP A 177 HIS 0.005 0.001 HIS K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (19827) covalent geometry : angle 0.55714 / 0.30 (27140) SS BOND : bond 0.00430 / 0.27 ( 1) SS BOND : angle 1.82029 / 0.71 ( 2) hydrogen bonds : bond 0.04101 / 2.81 ( 700) hydrogen bonds : angle 5.77895 / 3.98 ( 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 353 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.018 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: -0.4530 (tpp) cc_final: -0.5072 (ttm) REVERT: N 53 MET cc_start: -0.4422 (tpp) cc_final: -0.5982 (ttp) REVERT: P 53 MET cc_start: -0.3408 (tpp) cc_final: -0.3789 (tpt) REVERT: Y 36 ILE cc_start: 0.9255 (mp) cc_final: 0.8895 (tt) REVERT: Y 37 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8909 (tm-30) REVERT: S 31 LYS cc_start: 0.8380 (ptmt) cc_final: 0.8068 (pttm) REVERT: V 23 SER cc_start: 0.9144 (p) cc_final: 0.8891 (p) REVERT: V 48 ASN cc_start: 0.9051 (p0) cc_final: 0.8689 (p0) REVERT: V 52 GLN cc_start: 0.8997 (mt0) cc_final: 0.8754 (mp10) REVERT: E 45 LEU cc_start: 0.9014 (tp) cc_final: 0.8727 (tp) REVERT: E 48 ASN cc_start: 0.8137 (p0) cc_final: 0.6067 (p0) REVERT: E 52 GLN cc_start: 0.9148 (mt0) cc_final: 0.8511 (mt0) REVERT: I 53 MET cc_start: 0.7881 (ttm) cc_final: 0.6884 (tmm) REVERT: Q 56 TYR cc_start: 0.8578 (m-10) cc_final: 0.8325 (m-10) REVERT: Q 167 MET cc_start: 0.8768 (mtp) cc_final: 0.8418 (mtp) REVERT: G 135 LYS cc_start: 0.8991 (tppp) cc_final: 0.8773 (tttm) REVERT: G 236 LYS cc_start: 0.9559 (mtmm) cc_final: 0.9236 (mtmm) REVERT: C 72 SER cc_start: 0.9122 (m) cc_final: 0.8738 (t) REVERT: C 167 MET cc_start: 0.8048 (mmm) cc_final: 0.7825 (mmm) REVERT: C 249 LEU cc_start: 0.9333 (tt) cc_final: 0.8920 (mp) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.3776 time to fit residues: 191.5620 Evaluate side-chains 294 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 8.9990 chunk 144 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 192 optimal weight: 50.0000 chunk 89 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 57 HIS ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN B Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.085592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.055555 restraints weight = 444239.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.058068 restraints weight = 180730.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.059906 restraints weight = 101713.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.061165 restraints weight = 68795.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.061787 restraints weight = 52745.688| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19828 Z= 0.212 Angle : 0.599 5.271 27142 Z= 0.319 Chirality : 0.044 0.151 3063 Planarity : 0.004 0.051 3283 Dihedral : 11.388 165.107 3122 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 0.05 % Allowed : 0.79 % 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: -1.33 (0.18), residues: 2198 helix: 0.15 (0.23), residues: 528 sheet: -2.06 (0.20), residues: 628 loop : -0.45 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 19 TYR 0.016 0.002 TYR G 132 PHE 0.023 0.002 PHE A 129 TRP 0.054 0.002 TRP A 177 HIS 0.010 0.001 HIS Q 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (19827) covalent geometry : angle 0.59861 / 0.32 (27140) SS BOND : bond 0.00362 / 0.23 ( 1) SS BOND : angle 1.93543 / 0.75 ( 2) hydrogen bonds : bond 0.04384 / 3.01 ( 700) hydrogen bonds : angle 5.92276 / 4.08 ( 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 340 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.786 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: T 53 MET cc_start: -0.4263 (tpp) cc_final: -0.4964 (ttm) REVERT: N 53 MET cc_start: -0.4627 (tpp) cc_final: -0.5798 (ttt) REVERT: P 53 MET cc_start: -0.3447 (tpp) cc_final: -0.3819 (tpt) REVERT: X 37 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8719 (tm-30) REVERT: Y 37 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8933 (tm-30) REVERT: S 31 LYS cc_start: 0.8425 (ptmt) cc_final: 0.8119 (pttm) REVERT: U 55 TYR cc_start: 0.9126 (m-80) cc_final: 0.8478 (m-80) REVERT: V 23 SER cc_start: 0.9102 (p) cc_final: 0.8847 (p) REVERT: V 30 ILE cc_start: 0.9361 (mm) cc_final: 0.9076 (mt) REVERT: V 48 ASN cc_start: 0.9070 (p0) cc_final: 0.8689 (p0) REVERT: V 52 GLN cc_start: 0.9054 (mt0) cc_final: 0.8772 (mp10) REVERT: E 45 LEU cc_start: 0.9045 (tp) cc_final: 0.8757 (tp) REVERT: E 48 ASN cc_start: 0.8118 (p0) cc_final: 0.6114 (p0) REVERT: E 52 GLN cc_start: 0.9128 (mt0) cc_final: 0.8485 (mt0) REVERT: I 53 MET cc_start: 0.8023 (ttm) cc_final: 0.6959 (tmm) REVERT: Q 56 TYR cc_start: 0.8535 (m-10) cc_final: 0.8177 (m-10) REVERT: Q 167 MET cc_start: 0.8792 (mtp) cc_final: 0.8414 (mtp) REVERT: C 167 MET cc_start: 0.8055 (mmm) cc_final: 0.7799 (mmm) REVERT: C 249 LEU cc_start: 0.9341 (tt) cc_final: 0.8922 (mp) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.3937 time to fit residues: 192.3257 Evaluate side-chains 296 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 140 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 201 optimal weight: 40.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3945 r_free = 0.3945 target = 0.086520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056028 restraints weight = 457078.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058757 restraints weight = 182496.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.060676 restraints weight = 100389.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.061789 restraints weight = 67311.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062725 restraints weight = 52327.675| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19828 Z= 0.145 Angle : 0.544 5.703 27142 Z= 0.286 Chirality : 0.043 0.152 3063 Planarity : 0.004 0.045 3283 Dihedral : 11.287 165.003 3122 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer: Outliers : 0.05 % Allowed : 0.40 % Favored : 99.55 % 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: -1.18 (0.18), residues: 2198 helix: 0.25 (0.23), residues: 541 sheet: -1.91 (0.20), residues: 600 loop : -0.45 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 66 TYR 0.011 0.001 TYR C 132 PHE 0.021 0.001 PHE G 85 TRP 0.050 0.002 TRP A 177 HIS 0.005 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (19827) covalent geometry : angle 0.54384 / 0.29 (27140) SS BOND : bond 0.00354 / 0.22 ( 1) SS BOND : angle 2.10416 / 0.84 ( 2) hydrogen bonds : bond 0.03898 / 2.68 ( 700) hydrogen bonds : angle 5.73338 / 3.94 ( 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 344 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 1.121 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: T 53 MET cc_start: -0.4392 (tpp) cc_final: -0.5063 (ttm) REVERT: N 53 MET cc_start: -0.4576 (tpp) cc_final: -0.5758 (ttt) REVERT: P 53 MET cc_start: -0.3561 (tpp) cc_final: -0.3931 (tpt) REVERT: X 37 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8662 (tm-30) REVERT: Y 37 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8890 (tm-30) REVERT: S 31 LYS cc_start: 0.8407 (ptmt) cc_final: 0.8084 (pttm) REVERT: S 42 PHE cc_start: 0.9427 (m-80) cc_final: 0.9139 (m-80) REVERT: U 55 TYR cc_start: 0.9060 (m-80) cc_final: 0.8363 (m-80) REVERT: V 23 SER cc_start: 0.9164 (p) cc_final: 0.8932 (p) REVERT: V 30 ILE cc_start: 0.9373 (mm) cc_final: 0.9090 (mt) REVERT: V 48 ASN cc_start: 0.9044 (p0) cc_final: 0.8783 (p0) REVERT: V 52 GLN cc_start: 0.9032 (mt0) cc_final: 0.8792 (mp10) REVERT: E 45 LEU cc_start: 0.9027 (tp) cc_final: 0.8733 (tp) REVERT: E 48 ASN cc_start: 0.8110 (p0) cc_final: 0.7716 (p0) REVERT: I 53 MET cc_start: 0.7964 (ttm) cc_final: 0.6912 (tmm) REVERT: Q 56 TYR cc_start: 0.8433 (m-10) cc_final: 0.8093 (m-10) REVERT: Q 167 MET cc_start: 0.8763 (mtp) cc_final: 0.8379 (mtp) REVERT: G 236 LYS cc_start: 0.9528 (mtmm) cc_final: 0.9222 (mtmm) REVERT: C 72 SER cc_start: 0.9191 (m) cc_final: 0.8749 (t) REVERT: C 146 CYS cc_start: 0.8884 (t) cc_final: 0.8648 (t) REVERT: C 167 MET cc_start: 0.8000 (mmm) cc_final: 0.7706 (mmm) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.3689 time to fit residues: 183.7804 Evaluate side-chains 294 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 208 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 57 HIS ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3954 r_free = 0.3954 target = 0.086869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056198 restraints weight = 446360.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058806 restraints weight = 179452.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.060742 restraints weight = 99503.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.061819 restraints weight = 67064.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.062573 restraints weight = 52557.379| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6152 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= 0.127 Angle : 0.527 5.163 27142 Z= 0.275 Chirality : 0.043 0.149 3063 Planarity : 0.004 0.047 3283 Dihedral : 11.159 165.166 3122 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % 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: -1.03 (0.19), residues: 2198 helix: 0.39 (0.23), residues: 547 sheet: -1.85 (0.20), residues: 607 loop : -0.34 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 66 TYR 0.014 0.001 TYR G 71 PHE 0.018 0.001 PHE A 129 TRP 0.050 0.002 TRP A 177 HIS 0.003 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (19827) covalent geometry : angle 0.52680 / 0.28 (27140) SS BOND : bond 0.00604 / 0.38 ( 1) SS BOND : angle 2.12844 / 0.85 ( 2) hydrogen bonds : bond 0.03722 / 2.56 ( 700) hydrogen bonds : angle 5.57652 / 3.84 ( 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 343 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.904 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: -0.4449 (tpp) cc_final: -0.5091 (ttm) REVERT: N 53 MET cc_start: -0.4849 (tpp) cc_final: -0.5943 (ttt) REVERT: P 53 MET cc_start: -0.3607 (tpp) cc_final: -0.3959 (tpt) REVERT: X 37 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8589 (tm-30) REVERT: Y 23 SER cc_start: 0.8093 (m) cc_final: 0.7887 (t) REVERT: Y 36 ILE cc_start: 0.9254 (mp) cc_final: 0.8911 (tt) REVERT: Y 37 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8896 (tm-30) REVERT: S 31 LYS cc_start: 0.8416 (ptmt) cc_final: 0.8090 (pttm) REVERT: S 42 PHE cc_start: 0.9430 (m-80) cc_final: 0.9112 (m-80) REVERT: V 23 SER cc_start: 0.9183 (p) cc_final: 0.8959 (p) REVERT: V 30 ILE cc_start: 0.9390 (mm) cc_final: 0.9109 (mt) REVERT: V 46 LEU cc_start: 0.8326 (tp) cc_final: 0.7995 (tp) REVERT: V 48 ASN cc_start: 0.9091 (p0) cc_final: 0.8812 (p0) REVERT: V 52 GLN cc_start: 0.9014 (mt0) cc_final: 0.8739 (mp10) REVERT: W 36 ILE cc_start: 0.9268 (mp) cc_final: 0.9051 (tp) REVERT: E 45 LEU cc_start: 0.9037 (tp) cc_final: 0.8751 (tp) REVERT: E 48 ASN cc_start: 0.8135 (p0) cc_final: 0.7741 (p0) REVERT: I 53 MET cc_start: 0.7959 (ttm) cc_final: 0.6936 (tmm) REVERT: Q 56 TYR cc_start: 0.8410 (m-10) cc_final: 0.7976 (m-80) REVERT: Q 167 MET cc_start: 0.8756 (mtp) cc_final: 0.8386 (mtp) REVERT: G 236 LYS cc_start: 0.9541 (mtmm) cc_final: 0.9234 (mtmm) REVERT: C 72 SER cc_start: 0.9157 (m) cc_final: 0.8738 (t) REVERT: C 146 CYS cc_start: 0.8865 (t) cc_final: 0.8664 (t) REVERT: C 167 MET cc_start: 0.8029 (mmm) cc_final: 0.7770 (mmm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.3592 time to fit residues: 177.8063 Evaluate side-chains 299 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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: 9.9990 chunk 55 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 57 HIS M 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.087107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.056438 restraints weight = 449086.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.059000 restraints weight = 182177.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.060895 restraints weight = 102032.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.061932 restraints weight = 69165.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.062694 restraints weight = 54553.931| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19828 Z= 0.120 Angle : 0.519 5.194 27142 Z= 0.270 Chirality : 0.043 0.154 3063 Planarity : 0.004 0.045 3283 Dihedral : 11.096 165.387 3122 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % 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: -0.96 (0.19), residues: 2198 helix: 0.53 (0.23), residues: 546 sheet: -1.85 (0.20), residues: 615 loop : -0.30 (0.21), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 138 TYR 0.010 0.001 TYR X 55 PHE 0.017 0.001 PHE A 129 TRP 0.047 0.002 TRP A 177 HIS 0.003 0.001 HIS G 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (19827) covalent geometry : angle 0.51844 / 0.27 (27140) SS BOND : bond 0.00408 / 0.26 ( 1) SS BOND : angle 1.95927 / 0.79 ( 2) hydrogen bonds : bond 0.03634 / 2.50 ( 700) hydrogen bonds : angle 5.50747 / 3.79 ( 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 343 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: -0.4528 (tpp) cc_final: -0.5172 (ttm) REVERT: N 53 MET cc_start: -0.4915 (tpp) cc_final: -0.5983 (ttt) REVERT: P 53 MET cc_start: -0.3629 (tpp) cc_final: -0.3984 (tpt) REVERT: X 37 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8539 (tm-30) REVERT: Y 36 ILE cc_start: 0.9190 (mp) cc_final: 0.8832 (tt) REVERT: Y 37 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8890 (tm-30) REVERT: S 31 LYS cc_start: 0.8411 (ptmt) cc_final: 0.8060 (pttm) REVERT: S 42 PHE cc_start: 0.9413 (m-80) cc_final: 0.9092 (m-80) REVERT: V 23 SER cc_start: 0.9148 (p) cc_final: 0.8910 (p) REVERT: V 46 LEU cc_start: 0.8364 (tp) cc_final: 0.8036 (tp) REVERT: V 48 ASN cc_start: 0.9082 (p0) cc_final: 0.8811 (p0) REVERT: V 52 GLN cc_start: 0.9075 (mt0) cc_final: 0.8729 (mp10) REVERT: W 36 ILE cc_start: 0.9243 (mp) cc_final: 0.9042 (tp) REVERT: E 45 LEU cc_start: 0.9018 (tp) cc_final: 0.8720 (tp) REVERT: E 48 ASN cc_start: 0.8165 (p0) cc_final: 0.7784 (p0) REVERT: I 53 MET cc_start: 0.7932 (ttm) cc_final: 0.6915 (tmm) REVERT: Q 56 TYR cc_start: 0.8425 (m-10) cc_final: 0.8102 (m-10) REVERT: Q 167 MET cc_start: 0.8757 (mtp) cc_final: 0.8371 (mtp) REVERT: G 236 LYS cc_start: 0.9544 (mtmm) cc_final: 0.9243 (mtmm) REVERT: C 72 SER cc_start: 0.9109 (m) cc_final: 0.8705 (t) REVERT: C 146 CYS cc_start: 0.8849 (t) cc_final: 0.8604 (t) REVERT: C 167 MET cc_start: 0.7908 (mmm) cc_final: 0.7666 (mmm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.3677 time to fit residues: 181.6233 Evaluate side-chains 302 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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: 7.9990 chunk 139 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 152 optimal weight: 0.4980 chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 57 HIS M 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 ASN ** C 7 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.087012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.056263 restraints weight = 446142.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058820 restraints weight = 179950.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.060736 restraints weight = 100944.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.061949 restraints weight = 69397.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.062511 restraints weight = 54347.554| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.6358 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= 0.121 Angle : 0.517 5.278 27142 Z= 0.269 Chirality : 0.043 0.179 3063 Planarity : 0.004 0.045 3283 Dihedral : 11.068 165.460 3122 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 2198 helix: 0.52 (0.23), residues: 552 sheet: -1.80 (0.21), residues: 605 loop : -0.30 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 138 TYR 0.010 0.001 TYR C 145 PHE 0.017 0.001 PHE A 129 TRP 0.047 0.002 TRP A 177 HIS 0.003 0.001 HIS G 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (19827) covalent geometry : angle 0.51710 / 0.27 (27140) SS BOND : bond 0.00326 / 0.20 ( 1) SS BOND : angle 2.02146 / 0.81 ( 2) hydrogen bonds : bond 0.03622 / 2.49 ( 700) hydrogen bonds : angle 5.52076 / 3.79 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8412.66 seconds wall clock time: 143 minutes 36.71 seconds (8616.71 seconds total)