Starting phenix.real_space_refine on Sun Aug 24 00:21:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amw_15527/08_2025/8amw_15527.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amw_15527/08_2025/8amw_15527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8amw_15527/08_2025/8amw_15527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amw_15527/08_2025/8amw_15527.map" model { file = "/net/cci-nas-00/data/ceres_data/8amw_15527/08_2025/8amw_15527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amw_15527/08_2025/8amw_15527.cif" } resolution = 3.0 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= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 10454 2.51 5 N 2553 2.21 5 O 2681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15792 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1965 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Conformer: "B" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} bond proxies already assigned to first conformer: 2003 Chain: "B" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "D" Number of atoms: 1974 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Conformer: "B" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} bond proxies already assigned to first conformer: 2020 Chain: "E" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1978 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Conformer: "B" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} bond proxies already assigned to first conformer: 2016 Chain: "G" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "H" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 30 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 15 Chain: "D" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "C" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'GOL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AGLN A 145 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 145 " occ=0.50 residue: pdb=" N AALA D 23 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 23 " occ=0.50 residue: pdb=" N AGLN F 145 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN F 145 " occ=0.50 residue: pdb=" C1 AGOL C 402 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL C 402 " occ=0.50 residue: pdb=" C1 AGOL D 401 " occ=0.38 ... (10 atoms not shown) pdb=" O3 CGOL D 401 " occ=0.62 residue: pdb=" C1 AGOL E 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL E 401 " occ=0.50 residue: pdb=" C1 AGOL F 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL F 401 " occ=0.50 residue: pdb=" C1 AGOL H 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL H 401 " occ=0.50 Time building chain proxies: 5.36, per 1000 atoms: 0.34 Number of scatterers: 15792 At special positions: 0 Unit cell: (93.104, 100.722, 121.035, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2681 8.00 N 2553 7.00 C 10454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 935.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3574 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 27 through 30 Processing helix chain 'A' and resid 31 through 61 removed outlier: 3.561A pdb=" N PHE A 37 " --> pdb=" O MET A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.806A pdb=" N VAL A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.640A pdb=" N PHE A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 190 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.939A pdb=" N VAL A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Proline residue: A 232 - end of helix removed outlier: 3.536A pdb=" N GLY A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.712A pdb=" N VAL A 246 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 276 Proline residue: A 261 - end of helix Processing helix chain 'B' and resid 27 through 30 Processing helix chain 'B' and resid 31 through 61 Processing helix chain 'B' and resid 66 through 86 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.560A pdb=" N ILE B 157 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 158' Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.925A pdb=" N LEU B 173 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 218 removed outlier: 3.872A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.566A pdb=" N ASP B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Proline residue: B 232 - end of helix removed outlier: 3.508A pdb=" N GLY B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.958A pdb=" N VAL B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 255 through 276 Proline residue: B 261 - end of helix Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 32 through 61 removed outlier: 3.562A pdb=" N PHE C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 86 removed outlier: 4.347A pdb=" N VAL C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.572A pdb=" N PHE C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 190 removed outlier: 3.508A pdb=" N THR C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.811A pdb=" N VAL C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.747A pdb=" N VAL C 246 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 255 through 276 Proline residue: C 261 - end of helix Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 31 through 61 Processing helix chain 'D' and resid 66 through 90 removed outlier: 4.183A pdb=" N VAL D 78 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG D 87 " --> pdb=" O HIS D 83 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 88 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 134 removed outlier: 3.557A pdb=" N TYR D 115 " --> pdb=" O LYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.643A pdb=" N PHE D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 190 removed outlier: 3.513A pdb=" N GLY D 171 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.889A pdb=" N VAL D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.941A pdb=" N VAL D 246 " --> pdb=" O GLY D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 255 through 276 Proline residue: D 261 - end of helix Processing helix chain 'E' and resid 31 through 61 removed outlier: 3.559A pdb=" N PHE E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 86 Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 111 through 134 removed outlier: 3.523A pdb=" N TYR E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 154 through 158 removed outlier: 3.618A pdb=" N PHE E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 191 removed outlier: 3.509A pdb=" N THR E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 217 removed outlier: 3.736A pdb=" N VAL E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 240 removed outlier: 3.662A pdb=" N ASP E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Proline residue: E 232 - end of helix Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.991A pdb=" N VAL E 246 " --> pdb=" O GLY E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 255 through 276 Proline residue: E 261 - end of helix Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 31 through 61 removed outlier: 3.796A pdb=" N ARG F 35 " --> pdb=" O ARG F 31 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU F 36 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 86 removed outlier: 3.635A pdb=" N MET F 80 " --> pdb=" O PHE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.555A pdb=" N ILE F 157 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 158' Processing helix chain 'F' and resid 167 through 190 removed outlier: 3.511A pdb=" N THR F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 217 removed outlier: 3.875A pdb=" N VAL F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 241 Proline residue: F 232 - end of helix removed outlier: 3.578A pdb=" N GLY F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.744A pdb=" N SER F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 254 No H-bonds generated for 'chain 'F' and resid 252 through 254' Processing helix chain 'F' and resid 255 through 276 Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 31 through 61 Processing helix chain 'G' and resid 66 through 86 Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.573A pdb=" N PHE G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 190 Processing helix chain 'G' and resid 201 through 218 removed outlier: 3.764A pdb=" N VAL G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 240 Proline residue: G 232 - end of helix Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.839A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 254 No H-bonds generated for 'chain 'G' and resid 252 through 254' Processing helix chain 'G' and resid 255 through 276 Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 31 through 61 Processing helix chain 'H' and resid 66 through 86 removed outlier: 4.028A pdb=" N VAL H 78 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.602A pdb=" N ILE H 157 " --> pdb=" O THR H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 190 Processing helix chain 'H' and resid 201 through 218 removed outlier: 3.754A pdb=" N VAL H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 241 Proline residue: H 232 - end of helix removed outlier: 3.591A pdb=" N GLY H 241 " --> pdb=" O THR H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 249 removed outlier: 3.741A pdb=" N SER H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 255 through 276 Proline residue: H 261 - end of helix 1057 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4763 1.34 - 1.46: 3124 1.46 - 1.57: 8146 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 16225 Sorted by residual: bond pdb=" C1 AGOL E 401 " pdb=" C2 AGOL E 401 " ideal model delta sigma weight residual 1.514 1.549 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C2 GOL G 401 " pdb=" O2 GOL G 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C2 AGOL E 401 " pdb=" O2 AGOL E 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C2 BGOL H 401 " pdb=" O2 BGOL H 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C2 GOL B 401 " pdb=" O2 GOL B 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 16220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 21077 1.20 - 2.39: 720 2.39 - 3.59: 166 3.59 - 4.78: 62 4.78 - 5.98: 40 Bond angle restraints: 22065 Sorted by residual: angle pdb=" N VAL H 258 " pdb=" CA VAL H 258 " pdb=" C VAL H 258 " ideal model delta sigma weight residual 112.96 109.54 3.42 1.00e+00 1.00e+00 1.17e+01 angle pdb=" CA TYR A 223 " pdb=" CB TYR A 223 " pdb=" CG TYR A 223 " ideal model delta sigma weight residual 113.90 118.69 -4.79 1.80e+00 3.09e-01 7.07e+00 angle pdb=" CA TYR D 223 " pdb=" CB TYR D 223 " pdb=" CG TYR D 223 " ideal model delta sigma weight residual 113.90 118.67 -4.77 1.80e+00 3.09e-01 7.02e+00 angle pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " pdb=" CG TYR C 223 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.99e+00 angle pdb=" CA TYR G 223 " pdb=" CB TYR G 223 " pdb=" CG TYR G 223 " ideal model delta sigma weight residual 113.90 118.61 -4.71 1.80e+00 3.09e-01 6.85e+00 ... (remaining 22060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8573 17.89 - 35.78: 435 35.78 - 53.66: 81 53.66 - 71.55: 3 71.55 - 89.44: 4 Dihedral angle restraints: 9096 sinusoidal: 3412 harmonic: 5684 Sorted by residual: dihedral pdb=" CA PHE A 76 " pdb=" C PHE A 76 " pdb=" N GLY A 77 " pdb=" CA GLY A 77 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE F 76 " pdb=" C PHE F 76 " pdb=" N GLY F 77 " pdb=" CA GLY F 77 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE C 76 " pdb=" C PHE C 76 " pdb=" N GLY C 77 " pdb=" CA GLY C 77 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1317 0.030 - 0.060: 805 0.060 - 0.090: 255 0.090 - 0.120: 62 0.120 - 0.150: 22 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CA TYR C 223 " pdb=" N TYR C 223 " pdb=" C TYR C 223 " pdb=" CB TYR C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA TYR A 223 " pdb=" N TYR A 223 " pdb=" C TYR A 223 " pdb=" CB TYR A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA TYR H 223 " pdb=" N TYR H 223 " pdb=" C TYR H 223 " pdb=" CB TYR H 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2458 not shown) Planarity restraints: 2728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 226 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO E 227 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 227 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 227 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 162 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO D 163 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 231 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO G 232 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 232 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 232 " -0.022 5.00e-02 4.00e+02 ... (remaining 2725 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3421 2.78 - 3.31: 14371 3.31 - 3.84: 26054 3.84 - 4.37: 30116 4.37 - 4.90: 55260 Nonbonded interactions: 129222 Sorted by model distance: nonbonded pdb=" OD1 ASN C 101 " pdb=" O2 GOL C 403 " model vdw 2.245 3.040 nonbonded pdb=" OG SER F 142 " pdb=" O AGLN F 145 " model vdw 2.257 3.040 nonbonded pdb=" O3 GOL G 401 " pdb=" O1 GOL G 402 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR A 160 " pdb=" OD1 ASP A 230 " model vdw 2.279 3.040 nonbonded pdb=" O1 GOL C 401 " pdb=" O1 BGOL C 402 " model vdw 2.283 3.040 ... (remaining 129217 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 25 through 144 or resid 146 through 277)) selection = (chain 'B' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'C' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'D' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'E' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'F' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'G' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'H' and (resid 25 through 144 or resid 146 through 277)) } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.005 0.040 16225 Z= 0.209 Angle : 0.610 5.978 22065 Z= 0.317 Chirality : 0.042 0.150 2461 Planarity : 0.005 0.050 2728 Dihedral : 11.059 89.440 5522 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.44 % Allowed : 5.56 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.19), residues: 2024 helix: 1.92 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -1.18 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 106 TYR 0.021 0.002 TYR C 223 PHE 0.012 0.002 PHE F 134 TRP 0.012 0.001 TRP G 169 HIS 0.003 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00486 (16225) covalent geometry : angle 0.60969 (22065) hydrogen bonds : bond 0.14706 ( 1057) hydrogen bonds : angle 4.92564 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.594 Fit side-chains REVERT: A 63 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8431 (ptmm) REVERT: A 74 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7527 (t80) REVERT: A 193 GLU cc_start: 0.8288 (mp0) cc_final: 0.8066 (mp0) REVERT: A 270 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 28 ILE cc_start: 0.7382 (tt) cc_final: 0.6863 (mm) REVERT: B 63 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8034 (pttm) REVERT: C 63 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8121 (pttm) REVERT: C 74 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7777 (t80) REVERT: E 245 GLN cc_start: 0.8459 (mt0) cc_final: 0.8211 (mt0) REVERT: F 33 MET cc_start: 0.6828 (mmm) cc_final: 0.6511 (ptm) REVERT: G 244 LYS cc_start: 0.8266 (pttp) cc_final: 0.7748 (tptp) REVERT: H 74 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7561 (t80) outliers start: 6 outliers final: 2 residues processed: 193 average time/residue: 0.7316 time to fit residues: 153.8710 Evaluate side-chains 170 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 74 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.0370 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 94 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS F 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.096896 restraints weight = 38335.973| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.59 r_work: 0.2919 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16225 Z= 0.114 Angle : 0.512 5.950 22065 Z= 0.274 Chirality : 0.039 0.133 2461 Planarity : 0.005 0.047 2728 Dihedral : 5.612 57.674 2228 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.75 % Allowed : 9.56 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 2024 helix: 2.46 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.018 0.001 TYR D 223 PHE 0.010 0.001 PHE D 41 TRP 0.011 0.001 TRP F 169 HIS 0.009 0.001 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00231 (16225) covalent geometry : angle 0.51191 (22065) hydrogen bonds : bond 0.05037 ( 1057) hydrogen bonds : angle 3.92864 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.595 Fit side-chains REVERT: A 63 LYS cc_start: 0.8774 (ptpt) cc_final: 0.8452 (ptmm) REVERT: A 74 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7724 (t80) REVERT: A 270 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 28 ILE cc_start: 0.6930 (tt) cc_final: 0.6425 (mm) REVERT: B 63 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8061 (pttm) REVERT: C 63 LYS cc_start: 0.8537 (ptpt) cc_final: 0.8221 (pttm) REVERT: C 74 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7548 (t80) REVERT: E 47 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8439 (ptm) REVERT: E 244 LYS cc_start: 0.8469 (pttt) cc_final: 0.8024 (pmtt) REVERT: E 245 GLN cc_start: 0.8581 (mt0) cc_final: 0.8346 (mt0) REVERT: G 87 ARG cc_start: 0.8017 (tmm-80) cc_final: 0.7786 (tmm-80) REVERT: G 244 LYS cc_start: 0.8416 (pttp) cc_final: 0.7710 (tptp) REVERT: H 74 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7739 (t80) outliers start: 27 outliers final: 5 residues processed: 184 average time/residue: 0.7398 time to fit residues: 148.8272 Evaluate side-chains 170 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 74 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 3.9990 chunk 33 optimal weight: 0.0000 chunk 59 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.088190 restraints weight = 47769.406| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.83 r_work: 0.2778 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16225 Z= 0.229 Angle : 0.626 6.811 22065 Z= 0.335 Chirality : 0.044 0.151 2461 Planarity : 0.005 0.051 2728 Dihedral : 5.909 54.453 2226 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.56 % Allowed : 12.25 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.19), residues: 2024 helix: 2.12 (0.14), residues: 1412 sheet: None (None), residues: 0 loop : -1.37 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 110 TYR 0.024 0.002 TYR C 223 PHE 0.011 0.002 PHE A 236 TRP 0.012 0.001 TRP G 169 HIS 0.013 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00572 (16225) covalent geometry : angle 0.62595 (22065) hydrogen bonds : bond 0.08048 ( 1057) hydrogen bonds : angle 4.02966 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.628 Fit side-chains REVERT: A 63 LYS cc_start: 0.8800 (ptpt) cc_final: 0.8302 (ptmm) REVERT: A 74 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7777 (t80) REVERT: A 270 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8186 (tp) REVERT: B 28 ILE cc_start: 0.7336 (tt) cc_final: 0.6844 (mm) REVERT: B 63 LYS cc_start: 0.8563 (ptpt) cc_final: 0.8098 (pttm) REVERT: C 63 LYS cc_start: 0.8625 (ptpt) cc_final: 0.8254 (pttm) REVERT: C 74 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7916 (t80) REVERT: E 245 GLN cc_start: 0.8690 (mt0) cc_final: 0.8397 (mt0) REVERT: F 33 MET cc_start: 0.7498 (mmt) cc_final: 0.6475 (ptm) REVERT: G 87 ARG cc_start: 0.8119 (tmm-80) cc_final: 0.7853 (tmm-80) REVERT: G 244 LYS cc_start: 0.8408 (pttp) cc_final: 0.7739 (tptp) REVERT: H 74 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7840 (t80) outliers start: 24 outliers final: 6 residues processed: 180 average time/residue: 0.7978 time to fit residues: 155.8542 Evaluate side-chains 170 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 248 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094230 restraints weight = 39663.292| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.63 r_work: 0.2876 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16225 Z= 0.123 Angle : 0.520 6.113 22065 Z= 0.279 Chirality : 0.039 0.136 2461 Planarity : 0.005 0.045 2728 Dihedral : 5.675 57.558 2226 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.62 % Allowed : 12.81 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.19), residues: 2024 helix: 2.43 (0.14), residues: 1418 sheet: None (None), residues: 0 loop : -1.18 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 110 TYR 0.018 0.001 TYR C 223 PHE 0.010 0.001 PHE A 37 TRP 0.011 0.001 TRP E 169 HIS 0.012 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00269 (16225) covalent geometry : angle 0.52023 (22065) hydrogen bonds : bond 0.05620 ( 1057) hydrogen bonds : angle 3.84047 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.436 Fit side-chains REVERT: A 63 LYS cc_start: 0.8750 (ptpt) cc_final: 0.8261 (ptmm) REVERT: A 74 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 270 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 28 ILE cc_start: 0.7116 (tt) cc_final: 0.6609 (mm) REVERT: B 63 LYS cc_start: 0.8479 (ptpt) cc_final: 0.8027 (pttm) REVERT: C 63 LYS cc_start: 0.8554 (ptpt) cc_final: 0.8179 (pttm) REVERT: C 74 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7632 (t80) REVERT: E 47 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8352 (ttm) REVERT: E 245 GLN cc_start: 0.8594 (mt0) cc_final: 0.8291 (mt0) REVERT: F 142 SER cc_start: 0.8690 (t) cc_final: 0.8472 (p) REVERT: G 87 ARG cc_start: 0.8043 (tmm-80) cc_final: 0.7712 (ttt90) REVERT: G 244 LYS cc_start: 0.8378 (pttp) cc_final: 0.7687 (tptp) REVERT: H 74 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7765 (t80) outliers start: 25 outliers final: 7 residues processed: 178 average time/residue: 0.7343 time to fit residues: 142.2027 Evaluate side-chains 173 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 0.0270 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN H 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.093018 restraints weight = 31662.625| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.34 r_work: 0.2863 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16225 Z= 0.156 Angle : 0.550 6.206 22065 Z= 0.295 Chirality : 0.041 0.143 2461 Planarity : 0.005 0.048 2728 Dihedral : 5.707 58.367 2226 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.69 % Allowed : 13.19 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.19), residues: 2024 helix: 2.44 (0.14), residues: 1398 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.021 0.002 TYR C 223 PHE 0.010 0.001 PHE A 37 TRP 0.010 0.001 TRP G 169 HIS 0.013 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00371 (16225) covalent geometry : angle 0.54975 (22065) hydrogen bonds : bond 0.06427 ( 1057) hydrogen bonds : angle 3.85430 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.591 Fit side-chains REVERT: A 63 LYS cc_start: 0.8735 (ptpt) cc_final: 0.8242 (ptmm) REVERT: A 74 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7811 (t80) REVERT: A 270 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8133 (tp) REVERT: B 28 ILE cc_start: 0.7258 (tt) cc_final: 0.6746 (mm) REVERT: B 63 LYS cc_start: 0.8501 (ptpt) cc_final: 0.7998 (pttm) REVERT: C 63 LYS cc_start: 0.8582 (ptpt) cc_final: 0.8189 (pttm) REVERT: C 74 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7732 (t80) REVERT: E 244 LYS cc_start: 0.8612 (ptmt) cc_final: 0.8131 (pttm) REVERT: E 245 GLN cc_start: 0.8660 (mt0) cc_final: 0.8287 (mt0) REVERT: F 63 LYS cc_start: 0.8676 (ptpt) cc_final: 0.8450 (ptmm) REVERT: F 195 ASN cc_start: 0.8592 (t0) cc_final: 0.8381 (t0) REVERT: G 87 ARG cc_start: 0.8141 (tmm-80) cc_final: 0.7800 (ttt90) REVERT: G 244 LYS cc_start: 0.8450 (pttp) cc_final: 0.7674 (tptp) REVERT: H 74 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.7861 (t80) outliers start: 26 outliers final: 10 residues processed: 183 average time/residue: 0.7865 time to fit residues: 156.2575 Evaluate side-chains 175 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 183 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096730 restraints weight = 29924.124| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.27 r_work: 0.2924 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16225 Z= 0.120 Angle : 0.510 6.187 22065 Z= 0.272 Chirality : 0.039 0.135 2461 Planarity : 0.005 0.044 2728 Dihedral : 5.545 58.472 2226 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.56 % Allowed : 13.56 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.19), residues: 2024 helix: 2.69 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.018 0.001 TYR D 223 PHE 0.010 0.001 PHE A 37 TRP 0.009 0.001 TRP E 169 HIS 0.012 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00265 (16225) covalent geometry : angle 0.51042 (22065) hydrogen bonds : bond 0.05195 ( 1057) hydrogen bonds : angle 3.76920 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.632 Fit side-chains REVERT: A 63 LYS cc_start: 0.8706 (ptpt) cc_final: 0.8198 (ptmm) REVERT: A 74 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.7830 (t80) REVERT: A 270 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8132 (tp) REVERT: B 28 ILE cc_start: 0.7203 (tt) cc_final: 0.6683 (mm) REVERT: B 63 LYS cc_start: 0.8478 (ptpt) cc_final: 0.7981 (pttm) REVERT: C 63 LYS cc_start: 0.8557 (ptpt) cc_final: 0.8155 (pttm) REVERT: C 74 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7597 (t80) REVERT: D 87 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7917 (ttp-170) REVERT: E 244 LYS cc_start: 0.8639 (ptmt) cc_final: 0.8148 (pttm) REVERT: E 245 GLN cc_start: 0.8621 (mt0) cc_final: 0.8270 (mt0) REVERT: F 63 LYS cc_start: 0.8635 (ptpt) cc_final: 0.8408 (ptmm) REVERT: F 142 SER cc_start: 0.8675 (t) cc_final: 0.8447 (p) REVERT: G 87 ARG cc_start: 0.8128 (tmm-80) cc_final: 0.7926 (tmm-80) REVERT: G 244 LYS cc_start: 0.8441 (pttp) cc_final: 0.7684 (tptp) REVERT: H 74 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7758 (t80) outliers start: 24 outliers final: 8 residues processed: 184 average time/residue: 0.7320 time to fit residues: 147.0226 Evaluate side-chains 175 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN H 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.094950 restraints weight = 37579.342| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.57 r_work: 0.2892 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16225 Z= 0.125 Angle : 0.518 6.646 22065 Z= 0.276 Chirality : 0.039 0.135 2461 Planarity : 0.005 0.045 2728 Dihedral : 5.448 58.239 2226 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.56 % Allowed : 14.12 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.19), residues: 2024 helix: 2.70 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.019 0.001 TYR C 223 PHE 0.010 0.001 PHE A 37 TRP 0.009 0.001 TRP G 169 HIS 0.013 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00281 (16225) covalent geometry : angle 0.51808 (22065) hydrogen bonds : bond 0.05414 ( 1057) hydrogen bonds : angle 3.75634 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.404 Fit side-chains REVERT: A 63 LYS cc_start: 0.8702 (ptpt) cc_final: 0.8209 (ptmm) REVERT: A 74 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7770 (t80) REVERT: A 270 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8123 (tp) REVERT: B 28 ILE cc_start: 0.7167 (tt) cc_final: 0.6655 (mm) REVERT: B 63 LYS cc_start: 0.8444 (ptpt) cc_final: 0.7957 (pttm) REVERT: C 63 LYS cc_start: 0.8530 (ptpt) cc_final: 0.8131 (pttm) REVERT: C 74 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7563 (t80) REVERT: D 87 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7829 (ttp-170) REVERT: E 244 LYS cc_start: 0.8595 (ptmt) cc_final: 0.8101 (pttm) REVERT: E 245 GLN cc_start: 0.8529 (mt0) cc_final: 0.8176 (mt0) REVERT: F 63 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8451 (ptmm) REVERT: F 142 SER cc_start: 0.8659 (t) cc_final: 0.8414 (p) REVERT: G 87 ARG cc_start: 0.8044 (tmm-80) cc_final: 0.7828 (tmm-80) REVERT: G 244 LYS cc_start: 0.8378 (pttp) cc_final: 0.7667 (tptp) REVERT: H 74 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7741 (t80) outliers start: 24 outliers final: 11 residues processed: 179 average time/residue: 0.6942 time to fit residues: 135.4245 Evaluate side-chains 173 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 19 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098824 restraints weight = 39255.526| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.55 r_work: 0.2964 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16225 Z= 0.154 Angle : 0.552 7.757 22065 Z= 0.294 Chirality : 0.040 0.142 2461 Planarity : 0.005 0.048 2728 Dihedral : 5.561 56.860 2226 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.69 % Allowed : 14.00 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.19), residues: 2024 helix: 2.52 (0.14), residues: 1398 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 87 TYR 0.021 0.002 TYR C 223 PHE 0.010 0.001 PHE A 37 TRP 0.009 0.001 TRP G 169 HIS 0.013 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00364 (16225) covalent geometry : angle 0.55194 (22065) hydrogen bonds : bond 0.06284 ( 1057) hydrogen bonds : angle 3.80703 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.592 Fit side-chains REVERT: A 63 LYS cc_start: 0.8795 (ptpt) cc_final: 0.8353 (ptmm) REVERT: A 74 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.7875 (t80) REVERT: A 270 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 28 ILE cc_start: 0.7369 (tt) cc_final: 0.6864 (mm) REVERT: B 63 LYS cc_start: 0.8516 (ptpt) cc_final: 0.8062 (pttm) REVERT: C 63 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8227 (pttm) REVERT: C 74 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7803 (t80) REVERT: D 87 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7889 (ttp-170) REVERT: E 244 LYS cc_start: 0.8695 (ptmt) cc_final: 0.8219 (pttm) REVERT: E 245 GLN cc_start: 0.8591 (mt0) cc_final: 0.8242 (mt0) REVERT: G 87 ARG cc_start: 0.8066 (tmm-80) cc_final: 0.7837 (tmm-80) REVERT: G 244 LYS cc_start: 0.8430 (pttp) cc_final: 0.7809 (tptp) REVERT: H 74 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.7881 (t80) outliers start: 26 outliers final: 11 residues processed: 178 average time/residue: 0.7774 time to fit residues: 150.5257 Evaluate side-chains 174 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 51 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102497 restraints weight = 41250.727| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.60 r_work: 0.3024 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16225 Z= 0.115 Angle : 0.512 10.023 22065 Z= 0.271 Chirality : 0.038 0.131 2461 Planarity : 0.005 0.047 2728 Dihedral : 5.385 59.372 2226 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.88 % Allowed : 14.94 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.19), residues: 2024 helix: 2.69 (0.14), residues: 1406 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.017 0.001 TYR D 223 PHE 0.009 0.001 PHE A 37 TRP 0.010 0.001 TRP E 169 HIS 0.010 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00249 (16225) covalent geometry : angle 0.51171 (22065) hydrogen bonds : bond 0.04888 ( 1057) hydrogen bonds : angle 3.72449 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.613 Fit side-chains REVERT: A 63 LYS cc_start: 0.8765 (ptpt) cc_final: 0.8532 (ptmm) REVERT: A 74 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 270 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8265 (tp) REVERT: B 28 ILE cc_start: 0.7276 (tt) cc_final: 0.6760 (mm) REVERT: B 63 LYS cc_start: 0.8491 (ptpt) cc_final: 0.8024 (pttm) REVERT: C 63 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8190 (pttm) REVERT: C 74 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7575 (t80) REVERT: E 244 LYS cc_start: 0.8702 (ptmt) cc_final: 0.8201 (pttm) REVERT: G 87 ARG cc_start: 0.8047 (tmm-80) cc_final: 0.7824 (tmm-80) REVERT: G 244 LYS cc_start: 0.8374 (pttp) cc_final: 0.7767 (tptp) REVERT: H 74 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.7745 (t80) outliers start: 13 outliers final: 6 residues processed: 173 average time/residue: 0.7155 time to fit residues: 135.0506 Evaluate side-chains 167 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS C 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099583 restraints weight = 43768.594| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.68 r_work: 0.2978 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16225 Z= 0.138 Angle : 0.541 10.384 22065 Z= 0.286 Chirality : 0.040 0.138 2461 Planarity : 0.005 0.046 2728 Dihedral : 5.404 57.976 2226 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.19 % Allowed : 14.62 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.19), residues: 2024 helix: 2.58 (0.14), residues: 1406 sheet: None (None), residues: 0 loop : -1.49 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 110 TYR 0.020 0.001 TYR C 223 PHE 0.010 0.001 PHE A 37 TRP 0.009 0.001 TRP G 169 HIS 0.012 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00321 (16225) covalent geometry : angle 0.54086 (22065) hydrogen bonds : bond 0.05757 ( 1057) hydrogen bonds : angle 3.75509 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.546 Fit side-chains REVERT: A 63 LYS cc_start: 0.8765 (ptpt) cc_final: 0.8529 (ptmm) REVERT: A 74 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7890 (t80) REVERT: A 270 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8280 (tp) REVERT: B 28 ILE cc_start: 0.7397 (tt) cc_final: 0.6891 (mm) REVERT: B 63 LYS cc_start: 0.8481 (ptpt) cc_final: 0.8017 (pttm) REVERT: C 63 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8194 (pttm) REVERT: C 74 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7721 (t80) REVERT: E 244 LYS cc_start: 0.8716 (ptmt) cc_final: 0.8209 (pttm) REVERT: E 245 GLN cc_start: 0.8630 (mt0) cc_final: 0.8243 (mt0) REVERT: G 87 ARG cc_start: 0.8082 (tmm-80) cc_final: 0.7857 (tmm-80) REVERT: G 244 LYS cc_start: 0.8403 (pttp) cc_final: 0.7768 (tptp) REVERT: H 42 MET cc_start: 0.8106 (mmm) cc_final: 0.7836 (tpt) REVERT: H 74 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.7838 (t80) outliers start: 18 outliers final: 8 residues processed: 171 average time/residue: 0.6829 time to fit residues: 126.7250 Evaluate side-chains 169 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 0.0970 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 189 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103060 restraints weight = 38786.823| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.52 r_work: 0.3043 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16225 Z= 0.115 Angle : 0.513 11.411 22065 Z= 0.270 Chirality : 0.038 0.132 2461 Planarity : 0.005 0.044 2728 Dihedral : 5.262 59.487 2226 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.81 % Allowed : 15.19 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.20), residues: 2024 helix: 2.72 (0.14), residues: 1406 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 110 TYR 0.017 0.001 TYR D 223 PHE 0.010 0.001 PHE A 37 TRP 0.010 0.001 TRP G 169 HIS 0.012 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00250 (16225) covalent geometry : angle 0.51282 (22065) hydrogen bonds : bond 0.04845 ( 1057) hydrogen bonds : angle 3.70907 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4476.25 seconds wall clock time: 77 minutes 15.96 seconds (4635.96 seconds total)