Starting phenix.real_space_refine on Wed Mar 4 02:16:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kcq_22817/03_2026/7kcq_22817.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcq_22817/03_2026/7kcq_22817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kcq_22817/03_2026/7kcq_22817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcq_22817/03_2026/7kcq_22817.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kcq_22817/03_2026/7kcq_22817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcq_22817/03_2026/7kcq_22817.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 56 5.16 5 C 6548 2.51 5 N 1752 2.21 5 O 1968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10332 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 340 SG CYS A 43 37.825 61.223 54.909 1.00 31.48 S ATOM 1158 SG CYS A 153 39.178 57.419 53.592 1.00 13.86 S ATOM 747 SG CYS A 97 32.010 49.823 34.145 1.00 27.69 S ATOM 766 SG CYS A 100 35.538 49.934 34.447 1.00 18.56 S ATOM 793 SG CYS A 103 35.046 48.598 37.374 1.00 17.29 S ATOM 851 SG CYS A 111 33.725 51.995 36.289 1.00 24.14 S Restraints were copied for chains: B, C, D Time building chain proxies: 1.78, per 1000 atoms: 0.17 Number of scatterers: 10332 At special positions: 0 Unit cell: (114.45, 85.05, 80.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 56 16.00 O 1968 8.00 N 1752 7.00 C 6548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS D 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 672.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 66 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 153 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 103 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 111 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 100 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 66 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 153 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 97 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 103 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 111 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 100 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 66 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 153 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 111 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 100 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 66 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 153 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 103 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 111 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 100 " Number of angles added : 24 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 34.6% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.740A pdb=" N LEU A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.555A pdb=" N ASN A 110 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.945A pdb=" N VAL A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.696A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.667A pdb=" N THR A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.795A pdb=" N LYS A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.740A pdb=" N LEU B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.555A pdb=" N ASN B 110 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.945A pdb=" N VAL B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 165 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.696A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.667A pdb=" N THR B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 297 through 309 Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.795A pdb=" N LYS B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.740A pdb=" N LEU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.555A pdb=" N ASN C 110 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.945A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 165 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.696A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.667A pdb=" N THR C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.795A pdb=" N LYS C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 52 removed outlier: 3.740A pdb=" N LEU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.555A pdb=" N ASN D 110 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.945A pdb=" N VAL D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 165 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.696A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.667A pdb=" N THR D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 287 Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.795A pdb=" N LYS D 334 " --> pdb=" O GLU D 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU A 67 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A 40 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA A 69 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A 34 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET A 75 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU A 32 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU A 67 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A 40 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA A 69 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A 34 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET A 75 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU A 32 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR A 341 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.792A pdb=" N VAL A 197 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 219 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A 199 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 173 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 200 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 175 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP A 172 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 243 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA A 174 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 239 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 262 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY A 241 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR A 264 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE A 243 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 266 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 10 Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU B 67 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B 40 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 69 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 34 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET B 75 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU B 32 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU B 67 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B 40 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 69 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 34 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET B 75 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU B 32 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR B 341 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 93 through 95 Processing sheet with id=AB1, first strand: chain 'B' and resid 217 through 220 removed outlier: 6.792A pdb=" N VAL B 197 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE B 219 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY B 199 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 173 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B 200 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 175 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP B 172 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 243 " --> pdb=" O TRP B 172 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA B 174 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 239 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 262 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY B 241 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 264 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE B 243 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 266 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 10 Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU C 67 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER C 40 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA C 69 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU C 34 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET C 75 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU C 32 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU C 67 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER C 40 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA C 69 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU C 34 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET C 75 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU C 32 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR C 341 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB6, first strand: chain 'C' and resid 217 through 220 removed outlier: 6.792A pdb=" N VAL C 197 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE C 219 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY C 199 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 173 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE C 200 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 175 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP C 172 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE C 243 " --> pdb=" O TRP C 172 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA C 174 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C 239 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 262 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY C 241 " --> pdb=" O ASN C 262 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR C 264 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE C 243 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 266 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 10 Processing sheet with id=AB8, first strand: chain 'D' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU D 67 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER D 40 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA D 69 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU D 34 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET D 75 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU D 32 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU D 67 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER D 40 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA D 69 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU D 34 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET D 75 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU D 32 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 341 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 95 Processing sheet with id=AC2, first strand: chain 'D' and resid 217 through 220 removed outlier: 6.792A pdb=" N VAL D 197 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE D 219 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY D 199 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 173 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE D 200 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE D 175 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP D 172 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE D 243 " --> pdb=" O TRP D 172 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA D 174 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA D 239 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN D 262 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY D 241 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR D 264 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE D 243 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 266 " --> pdb=" O ILE D 243 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1188 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: 1.93 Time building geometry restraints manager: 1.18 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: 3376 1.34 - 1.46: 2076 1.46 - 1.58: 5008 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 10540 Sorted by residual: bond pdb=" CA SER B 96 " pdb=" CB SER B 96 " ideal model delta sigma weight residual 1.534 1.478 0.056 1.45e-02 4.76e+03 1.51e+01 bond pdb=" CA SER A 96 " pdb=" CB SER A 96 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.45e-02 4.76e+03 1.45e+01 bond pdb=" CA SER D 96 " pdb=" CB SER D 96 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.45e-02 4.76e+03 1.44e+01 bond pdb=" CA SER C 96 " pdb=" CB SER C 96 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.45e-02 4.76e+03 1.44e+01 bond pdb=" N CYS C 100 " pdb=" CA CYS C 100 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.22e-02 6.72e+03 6.77e+00 ... (remaining 10535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 13369 1.49 - 2.97: 752 2.97 - 4.46: 127 4.46 - 5.94: 32 5.94 - 7.43: 8 Bond angle restraints: 14288 Sorted by residual: angle pdb=" N ALA B 99 " pdb=" CA ALA B 99 " pdb=" C ALA B 99 " ideal model delta sigma weight residual 114.64 107.21 7.43 1.52e+00 4.33e-01 2.39e+01 angle pdb=" N ALA C 99 " pdb=" CA ALA C 99 " pdb=" C ALA C 99 " ideal model delta sigma weight residual 114.64 107.22 7.42 1.52e+00 4.33e-01 2.39e+01 angle pdb=" N ALA D 99 " pdb=" CA ALA D 99 " pdb=" C ALA D 99 " ideal model delta sigma weight residual 114.64 107.22 7.42 1.52e+00 4.33e-01 2.39e+01 angle pdb=" N ALA A 99 " pdb=" CA ALA A 99 " pdb=" C ALA A 99 " ideal model delta sigma weight residual 114.64 107.22 7.42 1.52e+00 4.33e-01 2.38e+01 angle pdb=" CA CYS A 111 " pdb=" C CYS A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 118.87 122.80 -3.93 9.00e-01 1.23e+00 1.90e+01 ... (remaining 14283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5420 17.18 - 34.37: 554 34.37 - 51.55: 148 51.55 - 68.73: 40 68.73 - 85.91: 16 Dihedral angle restraints: 6178 sinusoidal: 2314 harmonic: 3864 Sorted by residual: dihedral pdb=" CA TYR B 294 " pdb=" C TYR B 294 " pdb=" N VAL B 295 " pdb=" CA VAL B 295 " ideal model delta harmonic sigma weight residual 180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR D 294 " pdb=" C TYR D 294 " pdb=" N VAL D 295 " pdb=" CA VAL D 295 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR A 294 " pdb=" C TYR A 294 " pdb=" N VAL A 295 " pdb=" CA VAL A 295 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1112 0.052 - 0.104: 352 0.104 - 0.156: 116 0.156 - 0.208: 8 0.208 - 0.260: 4 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CA MET D 168 " pdb=" N MET D 168 " pdb=" C MET D 168 " pdb=" CB MET D 168 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA MET A 168 " pdb=" N MET A 168 " pdb=" C MET A 168 " pdb=" CB MET A 168 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA MET C 168 " pdb=" N MET C 168 " pdb=" C MET C 168 " pdb=" CB MET C 168 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1589 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 325 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO D 326 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 326 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 326 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 325 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO C 326 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 326 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 326 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 325 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 326 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " 0.019 5.00e-02 4.00e+02 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 68 2.57 - 3.15: 8456 3.15 - 3.73: 15853 3.73 - 4.32: 24945 4.32 - 4.90: 42082 Nonbonded interactions: 91404 Sorted by model distance: nonbonded pdb=" OE2 GLU C 67 " pdb="ZN ZN C 401 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU A 67 " pdb="ZN ZN A 401 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU B 67 " pdb="ZN ZN B 401 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU D 67 " pdb="ZN ZN D 401 " model vdw 1.987 2.230 nonbonded pdb=" O CYS C 153 " pdb=" OG1 THR C 157 " model vdw 2.267 3.040 ... (remaining 91399 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.012 0.275 10570 Z= 0.522 Angle : 1.268 46.903 14316 Z= 0.522 Chirality : 0.056 0.260 1592 Planarity : 0.004 0.038 1844 Dihedral : 15.993 85.911 3748 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 7.09 % Allowed : 15.67 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.18), residues: 1380 helix: -2.41 (0.18), residues: 444 sheet: -2.99 (0.30), residues: 168 loop : -2.79 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 298 TYR 0.020 0.003 TYR B 258 PHE 0.008 0.002 PHE A 221 TRP 0.011 0.002 TRP A 50 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.01058 (10540) covalent geometry : angle 0.79862 (14288) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.24164 ( 4) hydrogen bonds : bond 0.15191 ( 380) hydrogen bonds : angle 7.52955 ( 1188) metal coordination : bond 0.11799 ( 28) metal coordination : angle 24.07529 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 96 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8756 (pp) REVERT: A 77 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: A 236 ASP cc_start: 0.7797 (t70) cc_final: 0.7375 (t0) REVERT: B 33 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8757 (pp) REVERT: B 77 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: B 236 ASP cc_start: 0.7791 (t70) cc_final: 0.7372 (t0) REVERT: C 33 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8765 (pp) REVERT: C 77 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 236 ASP cc_start: 0.7795 (t70) cc_final: 0.7374 (t0) REVERT: D 33 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8763 (pp) REVERT: D 77 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: D 236 ASP cc_start: 0.7791 (t70) cc_final: 0.7373 (t0) outliers start: 76 outliers final: 40 residues processed: 160 average time/residue: 0.0989 time to fit residues: 22.4482 Evaluate side-chains 132 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 84 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 HIS A 94 ASN A 262 ASN A 336 GLN B 44 HIS B 94 ASN B 262 ASN B 336 GLN C 44 HIS C 94 ASN C 262 ASN C 336 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS D 94 ASN D 262 ASN D 336 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.130580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.105505 restraints weight = 9526.493| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.14 r_work: 0.2834 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10570 Z= 0.102 Angle : 0.491 5.986 14316 Z= 0.246 Chirality : 0.043 0.137 1592 Planarity : 0.004 0.033 1844 Dihedral : 6.911 65.259 1552 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.99 % Allowed : 17.82 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.21), residues: 1380 helix: -0.23 (0.23), residues: 444 sheet: -2.52 (0.27), residues: 224 loop : -1.61 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.015 0.001 TYR B 258 PHE 0.018 0.001 PHE A 210 TRP 0.004 0.001 TRP C 50 HIS 0.002 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00230 (10540) covalent geometry : angle 0.46862 (14288) SS BOND : bond 0.00261 ( 2) SS BOND : angle 0.69292 ( 4) hydrogen bonds : bond 0.02806 ( 380) hydrogen bonds : angle 4.83318 ( 1188) metal coordination : bond 0.00526 ( 28) metal coordination : angle 3.61000 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.9020 (m-80) cc_final: 0.8289 (m-80) REVERT: A 44 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7646 (t-90) REVERT: A 86 ASP cc_start: 0.8259 (m-30) cc_final: 0.7923 (m-30) REVERT: A 193 MET cc_start: 0.9342 (mtp) cc_final: 0.9079 (mtp) REVERT: A 236 ASP cc_start: 0.8210 (t70) cc_final: 0.7601 (t0) REVERT: A 347 LYS cc_start: 0.8082 (mttm) cc_final: 0.7736 (mtmt) REVERT: B 39 TYR cc_start: 0.9021 (m-80) cc_final: 0.8290 (m-80) REVERT: B 44 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7637 (t-90) REVERT: B 86 ASP cc_start: 0.8264 (m-30) cc_final: 0.7931 (m-30) REVERT: B 193 MET cc_start: 0.9341 (mtp) cc_final: 0.9080 (mtp) REVERT: B 236 ASP cc_start: 0.8166 (t70) cc_final: 0.7561 (t0) REVERT: B 347 LYS cc_start: 0.8084 (mttm) cc_final: 0.7739 (mtmt) REVERT: C 39 TYR cc_start: 0.9029 (m-80) cc_final: 0.8306 (m-80) REVERT: C 44 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7629 (t-90) REVERT: C 86 ASP cc_start: 0.8266 (m-30) cc_final: 0.7936 (m-30) REVERT: C 193 MET cc_start: 0.9340 (mtp) cc_final: 0.9079 (mtp) REVERT: C 236 ASP cc_start: 0.8191 (t70) cc_final: 0.7586 (t0) REVERT: C 347 LYS cc_start: 0.8076 (mttm) cc_final: 0.7728 (mtmt) REVERT: D 39 TYR cc_start: 0.9027 (m-80) cc_final: 0.8303 (m-80) REVERT: D 44 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: D 86 ASP cc_start: 0.8270 (m-30) cc_final: 0.7936 (m-30) REVERT: D 193 MET cc_start: 0.9338 (mtp) cc_final: 0.9078 (mtp) REVERT: D 236 ASP cc_start: 0.8197 (t70) cc_final: 0.7592 (t0) REVERT: D 347 LYS cc_start: 0.8101 (mttm) cc_final: 0.7763 (mtmt) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.1000 time to fit residues: 20.4479 Evaluate side-chains 124 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 0.0050 chunk 124 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 44 HIS ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 44 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 44 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 44 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.130374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.102825 restraints weight = 9413.724| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.20 r_work: 0.2790 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10570 Z= 0.213 Angle : 0.531 6.316 14316 Z= 0.265 Chirality : 0.046 0.136 1592 Planarity : 0.004 0.027 1844 Dihedral : 5.766 35.291 1508 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.73 % Allowed : 19.68 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.22), residues: 1380 helix: 0.21 (0.23), residues: 460 sheet: -2.39 (0.27), residues: 224 loop : -1.38 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 211 TYR 0.017 0.002 TYR D 258 PHE 0.011 0.002 PHE D 210 TRP 0.005 0.001 TRP B 92 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00508 (10540) covalent geometry : angle 0.50897 (14288) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.82401 ( 4) hydrogen bonds : bond 0.03380 ( 380) hydrogen bonds : angle 4.94566 ( 1188) metal coordination : bond 0.00672 ( 28) metal coordination : angle 3.69944 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8346 (t-90) REVERT: A 33 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8810 (pp) REVERT: A 39 TYR cc_start: 0.9048 (m-80) cc_final: 0.8291 (m-80) REVERT: A 86 ASP cc_start: 0.8314 (m-30) cc_final: 0.7972 (m-30) REVERT: A 104 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 193 MET cc_start: 0.9350 (mtp) cc_final: 0.9041 (mtp) REVERT: A 219 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 236 ASP cc_start: 0.8466 (t70) cc_final: 0.7887 (t0) REVERT: A 347 LYS cc_start: 0.8149 (mttm) cc_final: 0.7824 (mtmt) REVERT: B 15 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8356 (t-90) REVERT: B 33 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8815 (pp) REVERT: B 39 TYR cc_start: 0.9050 (m-80) cc_final: 0.8288 (m-80) REVERT: B 86 ASP cc_start: 0.8318 (m-30) cc_final: 0.7981 (m-30) REVERT: B 104 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8255 (mt-10) REVERT: B 193 MET cc_start: 0.9350 (mtp) cc_final: 0.9043 (mtp) REVERT: B 219 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8390 (mp) REVERT: B 236 ASP cc_start: 0.8453 (t70) cc_final: 0.7874 (t0) REVERT: B 347 LYS cc_start: 0.8145 (mttm) cc_final: 0.7820 (mtmt) REVERT: C 15 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8345 (t-90) REVERT: C 33 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8812 (pp) REVERT: C 39 TYR cc_start: 0.9045 (m-80) cc_final: 0.8281 (m-80) REVERT: C 86 ASP cc_start: 0.8305 (m-30) cc_final: 0.7965 (m-30) REVERT: C 104 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8252 (mt-10) REVERT: C 193 MET cc_start: 0.9349 (mtp) cc_final: 0.9042 (mtp) REVERT: C 219 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 236 ASP cc_start: 0.8452 (t70) cc_final: 0.7877 (t0) REVERT: C 347 LYS cc_start: 0.8149 (mttm) cc_final: 0.7822 (mtmt) REVERT: D 15 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8343 (t-90) REVERT: D 33 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8814 (pp) REVERT: D 39 TYR cc_start: 0.9046 (m-80) cc_final: 0.8284 (m-80) REVERT: D 86 ASP cc_start: 0.8322 (m-30) cc_final: 0.7984 (m-30) REVERT: D 104 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 193 MET cc_start: 0.9351 (mtp) cc_final: 0.9045 (mtp) REVERT: D 219 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8374 (mp) REVERT: D 236 ASP cc_start: 0.8456 (t70) cc_final: 0.7882 (t0) REVERT: D 347 LYS cc_start: 0.8147 (mttm) cc_final: 0.7823 (mtmt) outliers start: 40 outliers final: 24 residues processed: 148 average time/residue: 0.0976 time to fit residues: 20.3980 Evaluate side-chains 144 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 15 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 96 optimal weight: 0.0470 chunk 121 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 127 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.0020 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.137725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.113263 restraints weight = 9394.809| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.11 r_work: 0.2938 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 10570 Z= 0.076 Angle : 0.437 4.910 14316 Z= 0.217 Chirality : 0.042 0.129 1592 Planarity : 0.003 0.024 1844 Dihedral : 4.901 35.559 1508 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.73 % Allowed : 19.40 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.23), residues: 1380 helix: 1.14 (0.24), residues: 460 sheet: -2.04 (0.29), residues: 232 loop : -0.92 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.014 0.001 TYR D 258 PHE 0.014 0.001 PHE D 210 TRP 0.002 0.000 TRP C 82 HIS 0.002 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00167 (10540) covalent geometry : angle 0.41841 (14288) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.57230 ( 4) hydrogen bonds : bond 0.02370 ( 380) hydrogen bonds : angle 4.19990 ( 1188) metal coordination : bond 0.00245 ( 28) metal coordination : angle 3.09292 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 104 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8154 (mt-10) REVERT: A 219 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 236 ASP cc_start: 0.8190 (t70) cc_final: 0.7542 (t0) REVERT: A 347 LYS cc_start: 0.8040 (mttm) cc_final: 0.7710 (mtmt) REVERT: B 33 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8684 (pp) REVERT: B 104 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8145 (mt-10) REVERT: B 219 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 236 ASP cc_start: 0.8212 (t70) cc_final: 0.7572 (t0) REVERT: B 347 LYS cc_start: 0.8047 (mttm) cc_final: 0.7719 (mtmt) REVERT: C 33 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (pp) REVERT: C 104 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8147 (mt-10) REVERT: C 219 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8209 (mp) REVERT: C 236 ASP cc_start: 0.8205 (t70) cc_final: 0.7572 (t0) REVERT: C 347 LYS cc_start: 0.8050 (mttm) cc_final: 0.7723 (mtmt) REVERT: D 33 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8684 (pp) REVERT: D 104 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8134 (mt-10) REVERT: D 219 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8206 (mp) REVERT: D 236 ASP cc_start: 0.8223 (t70) cc_final: 0.7581 (t0) REVERT: D 347 LYS cc_start: 0.8034 (mttm) cc_final: 0.7709 (mtmt) outliers start: 40 outliers final: 24 residues processed: 136 average time/residue: 0.1052 time to fit residues: 20.1776 Evaluate side-chains 120 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 62 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 29 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 9 optimal weight: 7.9990 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.135934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.108942 restraints weight = 9384.411| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.19 r_work: 0.2870 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 10570 Z= 0.098 Angle : 0.445 4.978 14316 Z= 0.219 Chirality : 0.043 0.130 1592 Planarity : 0.003 0.023 1844 Dihedral : 4.879 34.752 1508 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.36 % Allowed : 19.78 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1380 helix: 1.36 (0.24), residues: 460 sheet: -1.74 (0.30), residues: 232 loop : -0.73 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 211 TYR 0.016 0.001 TYR C 258 PHE 0.011 0.001 PHE B 210 TRP 0.002 0.001 TRP C 172 HIS 0.002 0.000 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00227 (10540) covalent geometry : angle 0.42788 (14288) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.46831 ( 4) hydrogen bonds : bond 0.02441 ( 380) hydrogen bonds : angle 4.17961 ( 1188) metal coordination : bond 0.00332 ( 28) metal coordination : angle 2.97856 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8734 (pp) REVERT: A 104 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8232 (mt-10) REVERT: A 219 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 236 ASP cc_start: 0.8345 (t70) cc_final: 0.7715 (t0) REVERT: A 347 LYS cc_start: 0.8092 (mttm) cc_final: 0.7730 (mtmt) REVERT: B 33 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8728 (pp) REVERT: B 104 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8225 (mt-10) REVERT: B 219 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8294 (mp) REVERT: B 236 ASP cc_start: 0.8357 (t70) cc_final: 0.7730 (t0) REVERT: B 347 LYS cc_start: 0.8074 (mttm) cc_final: 0.7713 (mtmt) REVERT: C 33 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8727 (pp) REVERT: C 104 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8263 (mt-10) REVERT: C 219 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 236 ASP cc_start: 0.8327 (t70) cc_final: 0.7710 (t0) REVERT: C 347 LYS cc_start: 0.8083 (mttm) cc_final: 0.7720 (mtmt) REVERT: D 33 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8729 (pp) REVERT: D 104 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8253 (mt-10) REVERT: D 219 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8275 (mp) REVERT: D 236 ASP cc_start: 0.8376 (t70) cc_final: 0.7755 (t0) REVERT: D 347 LYS cc_start: 0.8087 (mttm) cc_final: 0.7723 (mtmt) outliers start: 36 outliers final: 24 residues processed: 136 average time/residue: 0.0942 time to fit residues: 18.2547 Evaluate side-chains 132 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 82 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.131610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.103813 restraints weight = 9456.244| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.21 r_work: 0.2798 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10570 Z= 0.204 Angle : 0.519 5.368 14316 Z= 0.257 Chirality : 0.046 0.134 1592 Planarity : 0.003 0.024 1844 Dihedral : 5.305 32.544 1504 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.10 % Allowed : 19.78 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1380 helix: 1.19 (0.24), residues: 460 sheet: -1.62 (0.32), residues: 224 loop : -0.77 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.016 0.002 TYR B 258 PHE 0.008 0.001 PHE C 210 TRP 0.005 0.001 TRP B 92 HIS 0.002 0.000 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00489 (10540) covalent geometry : angle 0.50276 (14288) SS BOND : bond 0.00060 ( 2) SS BOND : angle 0.61928 ( 4) hydrogen bonds : bond 0.03089 ( 380) hydrogen bonds : angle 4.59352 ( 1188) metal coordination : bond 0.00537 ( 28) metal coordination : angle 3.14438 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8786 (pp) REVERT: A 39 TYR cc_start: 0.9023 (m-80) cc_final: 0.8307 (m-80) REVERT: A 44 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7667 (t-90) REVERT: A 104 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8310 (mt-10) REVERT: A 219 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8345 (mp) REVERT: A 236 ASP cc_start: 0.8577 (t70) cc_final: 0.7998 (t0) REVERT: A 347 LYS cc_start: 0.8144 (mttm) cc_final: 0.7792 (mtmt) REVERT: B 33 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8785 (pp) REVERT: B 39 TYR cc_start: 0.9021 (m-80) cc_final: 0.8300 (m-80) REVERT: B 44 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7681 (t-90) REVERT: B 104 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8320 (mt-10) REVERT: B 219 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8343 (mp) REVERT: B 236 ASP cc_start: 0.8550 (t70) cc_final: 0.7975 (t0) REVERT: B 347 LYS cc_start: 0.8137 (mttm) cc_final: 0.7781 (mtmt) REVERT: C 33 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8784 (pp) REVERT: C 39 TYR cc_start: 0.9026 (m-80) cc_final: 0.8314 (m-80) REVERT: C 44 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7674 (t-90) REVERT: C 104 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8300 (mt-10) REVERT: C 219 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8327 (mp) REVERT: C 236 ASP cc_start: 0.8496 (t70) cc_final: 0.7927 (t0) REVERT: C 347 LYS cc_start: 0.8139 (mttm) cc_final: 0.7779 (mtmt) REVERT: D 33 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8787 (pp) REVERT: D 39 TYR cc_start: 0.9020 (m-80) cc_final: 0.8301 (m-80) REVERT: D 44 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7673 (t-90) REVERT: D 104 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8307 (mt-10) REVERT: D 219 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8323 (mp) REVERT: D 236 ASP cc_start: 0.8565 (t70) cc_final: 0.7993 (t0) REVERT: D 347 LYS cc_start: 0.8139 (mttm) cc_final: 0.7783 (mtmt) outliers start: 44 outliers final: 24 residues processed: 141 average time/residue: 0.1000 time to fit residues: 19.6407 Evaluate side-chains 132 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 90 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.133408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.105710 restraints weight = 9417.641| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.20 r_work: 0.2828 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 10570 Z= 0.149 Angle : 0.481 5.003 14316 Z= 0.238 Chirality : 0.045 0.132 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.142 33.155 1504 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.22 % Allowed : 19.22 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1380 helix: 1.40 (0.24), residues: 460 sheet: -1.47 (0.33), residues: 224 loop : -0.64 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 211 TYR 0.017 0.001 TYR D 258 PHE 0.010 0.001 PHE B 210 TRP 0.004 0.001 TRP C 92 HIS 0.002 0.000 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00354 (10540) covalent geometry : angle 0.46417 (14288) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.49121 ( 4) hydrogen bonds : bond 0.02758 ( 380) hydrogen bonds : angle 4.37746 ( 1188) metal coordination : bond 0.00406 ( 28) metal coordination : angle 3.07110 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 107 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8789 (pp) REVERT: A 39 TYR cc_start: 0.8998 (m-80) cc_final: 0.8194 (m-80) REVERT: A 44 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7672 (t-90) REVERT: A 104 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8262 (mt-10) REVERT: A 219 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8325 (mp) REVERT: A 236 ASP cc_start: 0.8521 (t70) cc_final: 0.7926 (t0) REVERT: A 347 LYS cc_start: 0.8086 (mttm) cc_final: 0.7754 (mtmt) REVERT: B 33 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 39 TYR cc_start: 0.8992 (m-80) cc_final: 0.8185 (m-80) REVERT: B 44 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7696 (t-90) REVERT: B 104 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8275 (mt-10) REVERT: B 219 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8321 (mp) REVERT: B 236 ASP cc_start: 0.8511 (t70) cc_final: 0.7917 (t0) REVERT: B 347 LYS cc_start: 0.8081 (mttm) cc_final: 0.7749 (mtmt) REVERT: C 33 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8785 (pp) REVERT: C 39 TYR cc_start: 0.8993 (m-80) cc_final: 0.8187 (m-80) REVERT: C 44 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7687 (t-90) REVERT: C 104 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8251 (mt-10) REVERT: C 219 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8308 (mp) REVERT: C 236 ASP cc_start: 0.8473 (t70) cc_final: 0.7887 (t0) REVERT: C 347 LYS cc_start: 0.8079 (mttm) cc_final: 0.7738 (mtmt) REVERT: D 33 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8785 (pp) REVERT: D 39 TYR cc_start: 0.9004 (m-80) cc_final: 0.8200 (m-80) REVERT: D 44 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7682 (t-90) REVERT: D 104 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 219 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8305 (mp) REVERT: D 236 ASP cc_start: 0.8496 (t70) cc_final: 0.7909 (t0) REVERT: D 347 LYS cc_start: 0.8082 (mttm) cc_final: 0.7745 (mtmt) outliers start: 56 outliers final: 38 residues processed: 163 average time/residue: 0.0956 time to fit residues: 22.2404 Evaluate side-chains 150 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.136334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.108917 restraints weight = 9398.124| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.19 r_work: 0.2870 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 10570 Z= 0.101 Angle : 0.450 4.958 14316 Z= 0.223 Chirality : 0.044 0.130 1592 Planarity : 0.003 0.022 1844 Dihedral : 4.872 34.413 1504 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.34 % Allowed : 18.84 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1380 helix: 1.64 (0.25), residues: 460 sheet: -1.32 (0.33), residues: 224 loop : -0.53 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 298 TYR 0.017 0.001 TYR B 20 PHE 0.011 0.001 PHE B 210 TRP 0.002 0.001 TRP A 172 HIS 0.002 0.000 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00238 (10540) covalent geometry : angle 0.43423 (14288) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.40216 ( 4) hydrogen bonds : bond 0.02398 ( 380) hydrogen bonds : angle 4.13419 ( 1188) metal coordination : bond 0.00297 ( 28) metal coordination : angle 2.95167 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 100 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8731 (pp) REVERT: A 44 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7586 (t-90) REVERT: A 104 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 219 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 236 ASP cc_start: 0.8455 (t70) cc_final: 0.7876 (t0) REVERT: A 327 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: A 347 LYS cc_start: 0.8056 (mttm) cc_final: 0.7727 (mtmt) REVERT: B 33 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8738 (pp) REVERT: B 44 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7599 (t-90) REVERT: B 104 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 219 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 236 ASP cc_start: 0.8439 (t70) cc_final: 0.7857 (t0) REVERT: B 327 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: B 347 LYS cc_start: 0.8053 (mttm) cc_final: 0.7725 (mtmt) REVERT: C 33 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8734 (pp) REVERT: C 44 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7588 (t-90) REVERT: C 104 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8238 (mt-10) REVERT: C 219 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8345 (mp) REVERT: C 236 ASP cc_start: 0.8411 (t70) cc_final: 0.7837 (t0) REVERT: C 327 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: C 347 LYS cc_start: 0.8045 (mttm) cc_final: 0.7713 (mtmt) REVERT: D 33 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8729 (pp) REVERT: D 44 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7602 (t-90) REVERT: D 104 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8229 (mt-10) REVERT: D 219 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8348 (mp) REVERT: D 236 ASP cc_start: 0.8423 (t70) cc_final: 0.7846 (t0) REVERT: D 327 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.5815 (mp0) REVERT: D 347 LYS cc_start: 0.8058 (mttm) cc_final: 0.7689 (mtmt) outliers start: 68 outliers final: 47 residues processed: 164 average time/residue: 0.0918 time to fit residues: 21.6174 Evaluate side-chains 163 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 100 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.131475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.103587 restraints weight = 9502.268| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.20 r_work: 0.2797 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10570 Z= 0.213 Angle : 0.518 5.430 14316 Z= 0.259 Chirality : 0.047 0.135 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.304 32.072 1504 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.25 % Allowed : 18.10 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1380 helix: 1.30 (0.24), residues: 460 sheet: -1.34 (0.34), residues: 220 loop : -0.66 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 211 TYR 0.017 0.002 TYR A 258 PHE 0.008 0.001 PHE B 210 TRP 0.006 0.001 TRP C 92 HIS 0.001 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00508 (10540) covalent geometry : angle 0.50237 (14288) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.60669 ( 4) hydrogen bonds : bond 0.03047 ( 380) hydrogen bonds : angle 4.56666 ( 1188) metal coordination : bond 0.00521 ( 28) metal coordination : angle 3.13167 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 106 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8809 (pp) REVERT: A 39 TYR cc_start: 0.9020 (m-80) cc_final: 0.8280 (m-80) REVERT: A 44 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7708 (t-90) REVERT: A 104 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8297 (mt-10) REVERT: A 219 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 236 ASP cc_start: 0.8585 (t70) cc_final: 0.7980 (t0) REVERT: A 327 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.5776 (mp0) REVERT: A 347 LYS cc_start: 0.8135 (mttm) cc_final: 0.7788 (mtmt) REVERT: B 33 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8804 (pp) REVERT: B 39 TYR cc_start: 0.9017 (m-80) cc_final: 0.8274 (m-80) REVERT: B 44 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7739 (t-90) REVERT: B 104 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8321 (mt-10) REVERT: B 219 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 236 ASP cc_start: 0.8580 (t70) cc_final: 0.7972 (t0) REVERT: B 327 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.5781 (mp0) REVERT: B 347 LYS cc_start: 0.8138 (mttm) cc_final: 0.7793 (mtmt) REVERT: C 33 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8809 (pp) REVERT: C 39 TYR cc_start: 0.9023 (m-80) cc_final: 0.8283 (m-80) REVERT: C 44 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7706 (t-90) REVERT: C 104 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8294 (mt-10) REVERT: C 219 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 236 ASP cc_start: 0.8535 (t70) cc_final: 0.7933 (t0) REVERT: C 327 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: C 347 LYS cc_start: 0.8140 (mttm) cc_final: 0.7791 (mtmt) REVERT: D 33 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8810 (pp) REVERT: D 39 TYR cc_start: 0.9023 (m-80) cc_final: 0.8283 (m-80) REVERT: D 44 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7712 (t-90) REVERT: D 104 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8302 (mt-10) REVERT: D 219 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8360 (mp) REVERT: D 236 ASP cc_start: 0.8558 (t70) cc_final: 0.7959 (t0) REVERT: D 327 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.5785 (mp0) REVERT: D 347 LYS cc_start: 0.8098 (mttm) cc_final: 0.7753 (mtmt) outliers start: 67 outliers final: 43 residues processed: 169 average time/residue: 0.0957 time to fit residues: 23.0538 Evaluate side-chains 161 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 102 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.133694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.106223 restraints weight = 9384.435| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.18 r_work: 0.2838 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10570 Z= 0.139 Angle : 0.478 4.988 14316 Z= 0.236 Chirality : 0.045 0.132 1592 Planarity : 0.003 0.021 1844 Dihedral : 5.111 33.345 1504 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.50 % Allowed : 18.84 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1380 helix: 1.53 (0.25), residues: 460 sheet: -1.33 (0.34), residues: 224 loop : -0.57 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 211 TYR 0.016 0.001 TYR B 258 PHE 0.011 0.001 PHE B 210 TRP 0.003 0.001 TRP D 172 HIS 0.002 0.000 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00330 (10540) covalent geometry : angle 0.46126 (14288) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.50745 ( 4) hydrogen bonds : bond 0.02657 ( 380) hydrogen bonds : angle 4.32316 ( 1188) metal coordination : bond 0.00390 ( 28) metal coordination : angle 3.05436 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 108 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8765 (pp) REVERT: A 39 TYR cc_start: 0.8989 (m-80) cc_final: 0.8252 (m-80) REVERT: A 44 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7653 (t-90) REVERT: A 104 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8243 (mt-10) REVERT: A 219 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 236 ASP cc_start: 0.8564 (t70) cc_final: 0.7955 (t0) REVERT: A 327 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: A 347 LYS cc_start: 0.8109 (mttm) cc_final: 0.7801 (mtmt) REVERT: B 33 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8774 (pp) REVERT: B 39 TYR cc_start: 0.8986 (m-80) cc_final: 0.8246 (m-80) REVERT: B 44 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7698 (t-90) REVERT: B 104 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 219 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 236 ASP cc_start: 0.8537 (t70) cc_final: 0.7928 (t0) REVERT: B 327 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.5723 (mp0) REVERT: B 347 LYS cc_start: 0.8113 (mttm) cc_final: 0.7803 (mtmt) REVERT: C 33 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8764 (pp) REVERT: C 39 TYR cc_start: 0.8991 (m-80) cc_final: 0.8258 (m-80) REVERT: C 44 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7676 (t-90) REVERT: C 104 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8239 (mt-10) REVERT: C 219 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8317 (mp) REVERT: C 236 ASP cc_start: 0.8520 (t70) cc_final: 0.7923 (t0) REVERT: C 327 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.5738 (mp0) REVERT: C 347 LYS cc_start: 0.8112 (mttm) cc_final: 0.7798 (mtmt) REVERT: D 33 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8764 (pp) REVERT: D 39 TYR cc_start: 0.8994 (m-80) cc_final: 0.8258 (m-80) REVERT: D 44 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7680 (t-90) REVERT: D 104 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8265 (mt-10) REVERT: D 219 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8315 (mp) REVERT: D 236 ASP cc_start: 0.8524 (t70) cc_final: 0.7924 (t0) REVERT: D 327 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: D 347 LYS cc_start: 0.8095 (mttm) cc_final: 0.7769 (mtmt) outliers start: 59 outliers final: 43 residues processed: 163 average time/residue: 0.0942 time to fit residues: 22.1065 Evaluate side-chains 167 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 108 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 9 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 110 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.132247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.104307 restraints weight = 9493.243| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.22 r_work: 0.2808 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10570 Z= 0.181 Angle : 0.502 5.174 14316 Z= 0.249 Chirality : 0.046 0.133 1592 Planarity : 0.003 0.022 1844 Dihedral : 5.223 32.481 1504 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.50 % Allowed : 18.47 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.23), residues: 1380 helix: 1.38 (0.24), residues: 460 sheet: -1.38 (0.34), residues: 224 loop : -0.61 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 211 TYR 0.017 0.002 TYR A 258 PHE 0.009 0.001 PHE B 210 TRP 0.005 0.001 TRP C 92 HIS 0.002 0.000 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00432 (10540) covalent geometry : angle 0.48527 (14288) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.55766 ( 4) hydrogen bonds : bond 0.02876 ( 380) hydrogen bonds : angle 4.47339 ( 1188) metal coordination : bond 0.00471 ( 28) metal coordination : angle 3.14029 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.70 seconds wall clock time: 38 minutes 24.19 seconds (2304.19 seconds total)