Starting phenix.real_space_refine on Mon Jul 28 06:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kcq_22817/07_2025/7kcq_22817.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcq_22817/07_2025/7kcq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kcq_22817/07_2025/7kcq_22817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcq_22817/07_2025/7kcq_22817.map" model { file = "/net/cci-nas-00/data/ceres_data/7kcq_22817/07_2025/7kcq_22817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcq_22817/07_2025/7kcq_22817.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, D Time building chain proxies: 4.66, per 1000 atoms: 0.45 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.29 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: 3.41 Time building geometry restraints manager: 3.26 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.400 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.750 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP A 50 HIS 0.004 0.001 HIS C 138 PHE 0.008 0.002 PHE A 221 TYR 0.020 0.003 TYR B 258 ARG 0.005 0.001 ARG D 298 Details of bonding type rmsd hydrogen bonds : bond 0.15191 ( 380) hydrogen bonds : angle 7.52955 ( 1188) metal coordination : bond 0.11799 ( 28) metal coordination : angle 24.07529 ( 24) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.24164 ( 4) covalent geometry : bond 0.01058 (10540) covalent geometry : angle 0.79862 (14288) *********************** 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 : 1.148 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: 0.2274 time to fit residues: 51.2380 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 : 1.140 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 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 = 0.3311 r_free = 0.3311 target = 0.130164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.106014 restraints weight = 9493.993| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.01 r_work: 0.2833 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10570 Z= 0.108 Angle : 0.497 6.557 14316 Z= 0.248 Chirality : 0.044 0.137 1592 Planarity : 0.004 0.033 1844 Dihedral : 6.937 64.564 1552 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.89 % Allowed : 18.28 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1380 helix: -0.27 (0.23), residues: 444 sheet: -2.52 (0.27), residues: 224 loop : -1.62 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 50 HIS 0.002 0.001 HIS C 48 PHE 0.017 0.001 PHE A 210 TYR 0.015 0.001 TYR A 258 ARG 0.001 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 380) hydrogen bonds : angle 4.87767 ( 1188) metal coordination : bond 0.00608 ( 28) metal coordination : angle 3.85557 ( 24) SS BOND : bond 0.00837 ( 2) SS BOND : angle 0.58023 ( 4) covalent geometry : bond 0.00244 (10540) covalent geometry : angle 0.47149 (14288) *********************** 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 137 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.9019 (m-80) cc_final: 0.8290 (m-80) REVERT: A 44 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7709 (t-90) REVERT: A 86 ASP cc_start: 0.8270 (m-30) cc_final: 0.7944 (m-30) REVERT: A 193 MET cc_start: 0.9335 (mtp) cc_final: 0.9064 (mtp) REVERT: A 236 ASP cc_start: 0.8232 (t70) cc_final: 0.7636 (t0) REVERT: A 347 LYS cc_start: 0.8105 (mttm) cc_final: 0.7786 (mtmt) REVERT: B 39 TYR cc_start: 0.9025 (m-80) cc_final: 0.8299 (m-80) REVERT: B 44 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7691 (t-90) REVERT: B 86 ASP cc_start: 0.8285 (m-30) cc_final: 0.7960 (m-30) REVERT: B 193 MET cc_start: 0.9334 (mtp) cc_final: 0.9067 (mtp) REVERT: B 236 ASP cc_start: 0.8178 (t70) cc_final: 0.7589 (t0) REVERT: B 347 LYS cc_start: 0.8097 (mttm) cc_final: 0.7778 (mtmt) REVERT: C 39 TYR cc_start: 0.9030 (m-80) cc_final: 0.8311 (m-80) REVERT: C 44 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7692 (t-90) REVERT: C 86 ASP cc_start: 0.8286 (m-30) cc_final: 0.7963 (m-30) REVERT: C 193 MET cc_start: 0.9337 (mtp) cc_final: 0.9069 (mtp) REVERT: C 236 ASP cc_start: 0.8183 (t70) cc_final: 0.7597 (t0) REVERT: C 347 LYS cc_start: 0.8101 (mttm) cc_final: 0.7780 (mtmt) REVERT: D 39 TYR cc_start: 0.9033 (m-80) cc_final: 0.8314 (m-80) REVERT: D 44 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7708 (t-90) REVERT: D 86 ASP cc_start: 0.8293 (m-30) cc_final: 0.7969 (m-30) REVERT: D 193 MET cc_start: 0.9336 (mtp) cc_final: 0.9070 (mtp) REVERT: D 236 ASP cc_start: 0.8195 (t70) cc_final: 0.7607 (t0) REVERT: D 347 LYS cc_start: 0.8118 (mttm) cc_final: 0.7798 (mtmt) outliers start: 31 outliers final: 23 residues processed: 137 average time/residue: 0.2317 time to fit residues: 45.0724 Evaluate side-chains 123 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 96 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS B 36 ASN B 44 HIS C 44 HIS D 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.128644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.100371 restraints weight = 9721.492| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.23 r_work: 0.2757 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10570 Z= 0.143 Angle : 0.486 6.392 14316 Z= 0.241 Chirality : 0.044 0.134 1592 Planarity : 0.003 0.027 1844 Dihedral : 5.494 33.718 1508 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.08 % Allowed : 19.12 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1380 helix: 0.45 (0.23), residues: 460 sheet: -2.33 (0.28), residues: 224 loop : -1.23 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 92 HIS 0.005 0.001 HIS D 44 PHE 0.012 0.001 PHE B 210 TYR 0.016 0.001 TYR A 258 ARG 0.001 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 380) hydrogen bonds : angle 4.66603 ( 1188) metal coordination : bond 0.00493 ( 28) metal coordination : angle 3.70506 ( 24) SS BOND : bond 0.00683 ( 2) SS BOND : angle 0.78735 ( 4) covalent geometry : bond 0.00336 (10540) covalent geometry : angle 0.46156 (14288) *********************** 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 135 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8821 (pp) REVERT: A 39 TYR cc_start: 0.9057 (m-80) cc_final: 0.8290 (m-80) REVERT: A 219 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 236 ASP cc_start: 0.8365 (t70) cc_final: 0.7758 (t0) REVERT: A 347 LYS cc_start: 0.8039 (mttm) cc_final: 0.7701 (mtmt) REVERT: B 33 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8829 (pp) REVERT: B 39 TYR cc_start: 0.9058 (m-80) cc_final: 0.8294 (m-80) REVERT: B 219 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8251 (mp) REVERT: B 236 ASP cc_start: 0.8326 (t70) cc_final: 0.7720 (t0) REVERT: B 347 LYS cc_start: 0.8043 (mttm) cc_final: 0.7709 (mtmt) REVERT: C 33 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8816 (pp) REVERT: C 39 TYR cc_start: 0.9064 (m-80) cc_final: 0.8301 (m-80) REVERT: C 219 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8252 (mp) REVERT: C 236 ASP cc_start: 0.8348 (t70) cc_final: 0.7745 (t0) REVERT: C 347 LYS cc_start: 0.8033 (mttm) cc_final: 0.7695 (mtmt) REVERT: D 33 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8816 (pp) REVERT: D 39 TYR cc_start: 0.9061 (m-80) cc_final: 0.8295 (m-80) REVERT: D 219 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8252 (mp) REVERT: D 236 ASP cc_start: 0.8377 (t70) cc_final: 0.7773 (t0) REVERT: D 347 LYS cc_start: 0.8036 (mttm) cc_final: 0.7701 (mtmt) outliers start: 33 outliers final: 25 residues processed: 131 average time/residue: 0.2404 time to fit residues: 44.1047 Evaluate side-chains 131 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 313 VAL Chi-restraints excluded: chain A residue 314 LYS 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 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 96 SER 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 313 VAL Chi-restraints excluded: chain C residue 314 LYS 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 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 22 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.127829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.098953 restraints weight = 9676.618| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.25 r_work: 0.2731 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1593 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= 0.182 Angle : 0.501 5.391 14316 Z= 0.251 Chirality : 0.045 0.135 1592 Planarity : 0.003 0.025 1844 Dihedral : 5.529 33.129 1508 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.32 % Allowed : 16.51 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1380 helix: 0.72 (0.23), residues: 460 sheet: -2.09 (0.29), residues: 224 loop : -1.06 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 92 HIS 0.001 0.000 HIS D 138 PHE 0.010 0.001 PHE D 210 TYR 0.017 0.001 TYR B 258 ARG 0.002 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 380) hydrogen bonds : angle 4.68458 ( 1188) metal coordination : bond 0.00562 ( 28) metal coordination : angle 3.38080 ( 24) SS BOND : bond 0.00018 ( 2) SS BOND : angle 0.67977 ( 4) covalent geometry : bond 0.00431 (10540) covalent geometry : angle 0.48178 (14288) *********************** 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 157 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 100 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.8229 (t-90) REVERT: A 33 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8792 (pp) REVERT: A 39 TYR cc_start: 0.9055 (m-80) cc_final: 0.8309 (m-80) REVERT: A 44 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7695 (t-90) REVERT: A 86 ASP cc_start: 0.8294 (m-30) cc_final: 0.7945 (m-30) REVERT: A 104 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8354 (mt-10) REVERT: A 219 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 236 ASP cc_start: 0.8415 (t70) cc_final: 0.7827 (t0) REVERT: A 347 LYS cc_start: 0.8099 (mttm) cc_final: 0.7750 (mtmt) REVERT: B 15 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.8232 (t-90) REVERT: B 33 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8786 (pp) REVERT: B 39 TYR cc_start: 0.9058 (m-80) cc_final: 0.8315 (m-80) REVERT: B 44 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7722 (t-90) REVERT: B 86 ASP cc_start: 0.8281 (m-30) cc_final: 0.7928 (m-30) REVERT: B 104 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 219 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 236 ASP cc_start: 0.8389 (t70) cc_final: 0.7802 (t0) REVERT: B 347 LYS cc_start: 0.8100 (mttm) cc_final: 0.7753 (mtmt) REVERT: C 15 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.8231 (t-90) REVERT: C 33 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8793 (pp) REVERT: C 39 TYR cc_start: 0.9061 (m-80) cc_final: 0.8318 (m-80) REVERT: C 44 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7687 (t-90) REVERT: C 86 ASP cc_start: 0.8303 (m-30) cc_final: 0.7954 (m-30) REVERT: C 104 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8369 (mt-10) REVERT: C 219 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8279 (mp) REVERT: C 236 ASP cc_start: 0.8423 (t70) cc_final: 0.7837 (t0) REVERT: C 347 LYS cc_start: 0.8097 (mttm) cc_final: 0.7743 (mtmt) REVERT: D 15 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.8219 (t-90) REVERT: D 33 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8785 (pp) REVERT: D 39 TYR cc_start: 0.9067 (m-80) cc_final: 0.8327 (m-80) REVERT: D 44 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7701 (t-90) REVERT: D 86 ASP cc_start: 0.8295 (m-30) cc_final: 0.7947 (m-30) REVERT: D 104 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8370 (mt-10) REVERT: D 219 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8280 (mp) REVERT: D 236 ASP cc_start: 0.8417 (t70) cc_final: 0.7837 (t0) REVERT: D 347 LYS cc_start: 0.8104 (mttm) cc_final: 0.7756 (mtmt) outliers start: 57 outliers final: 29 residues processed: 153 average time/residue: 0.2212 time to fit residues: 48.3540 Evaluate side-chains 145 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 44 HIS 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 15 HIS 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 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 15 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 96 SER 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 15 HIS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 28 optimal weight: 0.3980 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.130874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.103530 restraints weight = 9358.146| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.19 r_work: 0.2801 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 10570 Z= 0.192 Angle : 0.516 5.825 14316 Z= 0.255 Chirality : 0.046 0.133 1592 Planarity : 0.003 0.024 1844 Dihedral : 5.513 32.783 1508 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.20 % Allowed : 17.44 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1380 helix: 0.84 (0.23), residues: 460 sheet: -1.82 (0.31), residues: 224 loop : -0.92 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 92 HIS 0.002 0.000 HIS C 138 PHE 0.010 0.001 PHE A 210 TYR 0.017 0.002 TYR D 258 ARG 0.002 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 380) hydrogen bonds : angle 4.62747 ( 1188) metal coordination : bond 0.00531 ( 28) metal coordination : angle 3.20522 ( 24) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.66258 ( 4) covalent geometry : bond 0.00458 (10540) covalent geometry : angle 0.49906 (14288) *********************** 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 149 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8252 (t-90) REVERT: A 33 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8809 (pp) REVERT: A 39 TYR cc_start: 0.9043 (m-80) cc_final: 0.8326 (m-80) REVERT: A 44 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7655 (t-90) REVERT: A 86 ASP cc_start: 0.8322 (m-30) cc_final: 0.7992 (m-30) REVERT: A 104 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 219 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 236 ASP cc_start: 0.8550 (t70) cc_final: 0.7946 (t0) REVERT: A 347 LYS cc_start: 0.8126 (mttm) cc_final: 0.7791 (mtmt) REVERT: B 15 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.8255 (t-90) REVERT: B 33 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8815 (pp) REVERT: B 39 TYR cc_start: 0.9035 (m-80) cc_final: 0.8313 (m-80) REVERT: B 44 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7674 (t-90) REVERT: B 86 ASP cc_start: 0.8314 (m-30) cc_final: 0.7985 (m-30) REVERT: B 104 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 219 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8356 (mp) REVERT: B 236 ASP cc_start: 0.8544 (t70) cc_final: 0.7936 (t0) REVERT: B 347 LYS cc_start: 0.8125 (mttm) cc_final: 0.7788 (mtmt) REVERT: C 15 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.8250 (t-90) REVERT: C 33 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8808 (pp) REVERT: C 39 TYR cc_start: 0.9038 (m-80) cc_final: 0.8322 (m-80) REVERT: C 44 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7669 (t-90) REVERT: C 86 ASP cc_start: 0.8310 (m-30) cc_final: 0.7979 (m-30) REVERT: C 104 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8288 (mt-10) REVERT: C 219 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8350 (mp) REVERT: C 236 ASP cc_start: 0.8524 (t70) cc_final: 0.7927 (t0) REVERT: C 347 LYS cc_start: 0.8123 (mttm) cc_final: 0.7784 (mtmt) REVERT: D 15 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.8247 (t-90) REVERT: D 33 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8809 (pp) REVERT: D 39 TYR cc_start: 0.9036 (m-80) cc_final: 0.8319 (m-80) REVERT: D 44 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7676 (t-90) REVERT: D 86 ASP cc_start: 0.8333 (m-30) cc_final: 0.8012 (m-30) REVERT: D 104 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8294 (mt-10) REVERT: D 219 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8342 (mp) REVERT: D 236 ASP cc_start: 0.8532 (t70) cc_final: 0.7933 (t0) REVERT: D 347 LYS cc_start: 0.8136 (mttm) cc_final: 0.7805 (mtmt) outliers start: 45 outliers final: 29 residues processed: 149 average time/residue: 0.2361 time to fit residues: 49.1583 Evaluate side-chains 137 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 44 HIS 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 15 HIS 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 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 15 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 96 SER 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 15 HIS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.133306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.105600 restraints weight = 9400.999| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.23 r_work: 0.2830 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10570 Z= 0.130 Angle : 0.473 5.226 14316 Z= 0.233 Chirality : 0.044 0.131 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.272 33.940 1508 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.32 % Allowed : 17.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1380 helix: 1.24 (0.24), residues: 460 sheet: -1.51 (0.33), residues: 220 loop : -0.76 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 172 HIS 0.002 0.000 HIS D 121 PHE 0.011 0.001 PHE A 210 TYR 0.016 0.001 TYR D 258 ARG 0.001 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.02674 ( 380) hydrogen bonds : angle 4.34149 ( 1188) metal coordination : bond 0.00371 ( 28) metal coordination : angle 3.08219 ( 24) SS BOND : bond 0.00004 ( 2) SS BOND : angle 0.53318 ( 4) covalent geometry : bond 0.00305 (10540) covalent geometry : angle 0.45637 (14288) *********************** 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 152 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 95 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.8284 (t-90) REVERT: A 33 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8769 (pp) REVERT: A 39 TYR cc_start: 0.9001 (m-80) cc_final: 0.8208 (m-80) REVERT: A 44 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7592 (t-90) REVERT: A 104 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 219 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 236 ASP cc_start: 0.8536 (t70) cc_final: 0.7939 (t0) REVERT: A 347 LYS cc_start: 0.8081 (mttm) cc_final: 0.7725 (mtmt) REVERT: B 33 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8770 (pp) REVERT: B 39 TYR cc_start: 0.8992 (m-80) cc_final: 0.8196 (m-80) REVERT: B 44 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7619 (t-90) REVERT: B 104 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 219 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8296 (mp) REVERT: B 236 ASP cc_start: 0.8527 (t70) cc_final: 0.7926 (t0) REVERT: B 347 LYS cc_start: 0.8077 (mttm) cc_final: 0.7729 (mtmt) REVERT: C 15 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.8291 (t-90) REVERT: C 33 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8769 (pp) REVERT: C 39 TYR cc_start: 0.9000 (m-80) cc_final: 0.8205 (m-80) REVERT: C 44 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7614 (t-90) REVERT: C 104 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 219 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8291 (mp) REVERT: C 236 ASP cc_start: 0.8510 (t70) cc_final: 0.7919 (t0) REVERT: C 347 LYS cc_start: 0.8082 (mttm) cc_final: 0.7726 (mtmt) REVERT: D 15 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.8287 (t-90) REVERT: D 33 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8772 (pp) REVERT: D 39 TYR cc_start: 0.9010 (m-80) cc_final: 0.8216 (m-80) REVERT: D 44 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7619 (t-90) REVERT: D 104 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8256 (mt-10) REVERT: D 219 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8283 (mp) REVERT: D 236 ASP cc_start: 0.8517 (t70) cc_final: 0.7927 (t0) REVERT: D 347 LYS cc_start: 0.8089 (mttm) cc_final: 0.7732 (mtmt) outliers start: 57 outliers final: 33 residues processed: 152 average time/residue: 0.2297 time to fit residues: 49.5529 Evaluate side-chains 140 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 44 HIS Chi-restraints excluded: chain A residue 117 SER 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 33 LEU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 117 SER 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 15 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 117 SER 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 15 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 111 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.132472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.104607 restraints weight = 9555.834| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.23 r_work: 0.2817 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 10570 Z= 0.151 Angle : 0.479 4.982 14316 Z= 0.237 Chirality : 0.044 0.132 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.306 33.259 1508 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.16 % Allowed : 16.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1380 helix: 1.31 (0.24), residues: 460 sheet: -1.52 (0.33), residues: 224 loop : -0.66 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 172 HIS 0.002 0.000 HIS C 121 PHE 0.010 0.001 PHE C 210 TYR 0.016 0.001 TYR A 258 ARG 0.001 0.000 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 380) hydrogen bonds : angle 4.40674 ( 1188) metal coordination : bond 0.00412 ( 28) metal coordination : angle 3.07169 ( 24) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.53539 ( 4) covalent geometry : bond 0.00357 (10540) covalent geometry : angle 0.46299 (14288) *********************** 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 161 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 95 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 39 TYR cc_start: 0.9012 (m-80) cc_final: 0.8279 (m-80) REVERT: A 44 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7603 (t-90) REVERT: A 104 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 219 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 236 ASP cc_start: 0.8550 (t70) cc_final: 0.7955 (t0) REVERT: A 327 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.5337 (mp0) REVERT: A 347 LYS cc_start: 0.8086 (mttm) cc_final: 0.7739 (mtmt) REVERT: B 33 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8794 (pp) REVERT: B 39 TYR cc_start: 0.8998 (m-80) cc_final: 0.8260 (m-80) REVERT: B 44 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7612 (t-90) REVERT: B 104 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 219 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 236 ASP cc_start: 0.8561 (t70) cc_final: 0.7965 (t0) REVERT: B 327 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.5339 (mp0) REVERT: B 347 LYS cc_start: 0.8079 (mttm) cc_final: 0.7738 (mtmt) REVERT: C 33 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8792 (pp) REVERT: C 39 TYR cc_start: 0.9011 (m-80) cc_final: 0.8278 (m-80) REVERT: C 44 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7620 (t-90) REVERT: C 104 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8256 (mt-10) REVERT: C 219 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8284 (mp) REVERT: C 224 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: C 236 ASP cc_start: 0.8524 (t70) cc_final: 0.7930 (t0) REVERT: C 327 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.5357 (mp0) REVERT: C 347 LYS cc_start: 0.8085 (mttm) cc_final: 0.7738 (mtmt) REVERT: D 33 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8794 (pp) REVERT: D 39 TYR cc_start: 0.9017 (m-80) cc_final: 0.8286 (m-80) REVERT: D 44 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7623 (t-90) REVERT: D 104 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8255 (mt-10) REVERT: D 219 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8288 (mp) REVERT: D 224 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: D 236 ASP cc_start: 0.8549 (t70) cc_final: 0.7960 (t0) REVERT: D 327 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.5354 (mp0) REVERT: D 347 LYS cc_start: 0.8089 (mttm) cc_final: 0.7742 (mtmt) outliers start: 66 outliers final: 37 residues processed: 157 average time/residue: 0.2907 time to fit residues: 63.7834 Evaluate side-chains 143 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 88 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 117 SER 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 117 SER 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 96 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 224 GLU 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 117 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 224 GLU 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 327 GLU 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 43 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 chunk 126 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.135180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.107579 restraints weight = 9381.865| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.21 r_work: 0.2856 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 10570 Z= 0.106 Angle : 0.451 4.945 14316 Z= 0.223 Chirality : 0.043 0.132 1592 Planarity : 0.003 0.022 1844 Dihedral : 5.053 34.542 1508 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.22 % Allowed : 17.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1380 helix: 1.59 (0.25), residues: 460 sheet: -1.40 (0.33), residues: 224 loop : -0.54 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 172 HIS 0.002 0.000 HIS A 121 PHE 0.011 0.001 PHE C 210 TYR 0.015 0.001 TYR A 258 ARG 0.001 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.02487 ( 380) hydrogen bonds : angle 4.19749 ( 1188) metal coordination : bond 0.00312 ( 28) metal coordination : angle 3.01763 ( 24) SS BOND : bond 0.00014 ( 2) SS BOND : angle 0.41216 ( 4) covalent geometry : bond 0.00246 (10540) covalent geometry : angle 0.43395 (14288) *********************** 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 152 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 96 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8755 (pp) REVERT: A 104 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 219 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 224 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: A 236 ASP cc_start: 0.8507 (t70) cc_final: 0.7932 (t0) REVERT: A 327 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.5811 (mp0) REVERT: A 347 LYS cc_start: 0.8100 (mttm) cc_final: 0.7751 (mtmt) REVERT: B 33 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8766 (pp) REVERT: B 104 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 219 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B 224 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: B 236 ASP cc_start: 0.8500 (t70) cc_final: 0.7927 (t0) REVERT: B 327 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.5829 (mp0) REVERT: B 347 LYS cc_start: 0.8099 (mttm) cc_final: 0.7755 (mtmt) REVERT: C 33 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8762 (pp) REVERT: C 104 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8254 (mt-10) REVERT: C 219 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 224 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: C 236 ASP cc_start: 0.8471 (t70) cc_final: 0.7908 (t0) REVERT: C 327 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.5845 (mp0) REVERT: C 347 LYS cc_start: 0.8101 (mttm) cc_final: 0.7753 (mtmt) REVERT: D 33 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8757 (pp) REVERT: D 104 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8257 (mt-10) REVERT: D 219 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8296 (mp) REVERT: D 224 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: D 236 ASP cc_start: 0.8493 (t70) cc_final: 0.7927 (t0) REVERT: D 327 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.5839 (mp0) REVERT: D 347 LYS cc_start: 0.8098 (mttm) cc_final: 0.7752 (mtmt) outliers start: 56 outliers final: 40 residues processed: 152 average time/residue: 0.2564 time to fit residues: 54.9678 Evaluate side-chains 149 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 93 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 117 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 GLU 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 117 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 224 GLU 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 117 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 224 GLU 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 117 SER Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 224 GLU 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 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 133 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.131515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.103835 restraints weight = 9587.466| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.22 r_work: 0.2801 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10570 Z= 0.189 Angle : 0.502 5.239 14316 Z= 0.249 Chirality : 0.046 0.133 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.400 32.618 1508 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.78 % Allowed : 18.28 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1380 helix: 1.36 (0.24), residues: 460 sheet: -1.38 (0.34), residues: 220 loop : -0.64 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.001 0.000 HIS A 138 PHE 0.008 0.001 PHE B 210 TYR 0.017 0.001 TYR B 258 ARG 0.001 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 380) hydrogen bonds : angle 4.51997 ( 1188) metal coordination : bond 0.00488 ( 28) metal coordination : angle 3.11504 ( 24) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.54815 ( 4) covalent geometry : bond 0.00449 (10540) covalent geometry : angle 0.48586 (14288) *********************** 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 158 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 96 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8820 (pp) REVERT: A 39 TYR cc_start: 0.9002 (m-80) cc_final: 0.8243 (m-80) REVERT: A 44 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7624 (t-90) REVERT: A 104 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 219 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 224 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: A 236 ASP cc_start: 0.8578 (t70) cc_final: 0.7976 (t0) REVERT: A 327 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.5644 (mp0) REVERT: A 347 LYS cc_start: 0.8097 (mttm) cc_final: 0.7744 (mtmt) REVERT: B 33 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8822 (pp) REVERT: B 39 TYR cc_start: 0.9002 (m-80) cc_final: 0.8239 (m-80) REVERT: B 44 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7637 (t-90) REVERT: B 104 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 219 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8376 (mp) REVERT: B 224 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: B 236 ASP cc_start: 0.8582 (t70) cc_final: 0.7976 (t0) REVERT: B 327 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.5654 (mp0) REVERT: B 347 LYS cc_start: 0.8116 (mttm) cc_final: 0.7771 (mtmt) REVERT: C 33 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8815 (pp) REVERT: C 39 TYR cc_start: 0.9012 (m-80) cc_final: 0.8254 (m-80) REVERT: C 44 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7630 (t-90) REVERT: C 104 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8273 (mt-10) REVERT: C 219 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8357 (mp) REVERT: C 224 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: C 236 ASP cc_start: 0.8545 (t70) cc_final: 0.7950 (t0) REVERT: C 327 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.5657 (mp0) REVERT: C 347 LYS cc_start: 0.8104 (mttm) cc_final: 0.7752 (mtmt) REVERT: D 33 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8820 (pp) REVERT: D 39 TYR cc_start: 0.9006 (m-80) cc_final: 0.8246 (m-80) REVERT: D 44 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7647 (t-90) REVERT: D 104 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8302 (mt-10) REVERT: D 219 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8353 (mp) REVERT: D 224 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: D 236 ASP cc_start: 0.8568 (t70) cc_final: 0.7976 (t0) REVERT: D 327 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.5643 (mp0) REVERT: D 347 LYS cc_start: 0.8117 (mttm) cc_final: 0.7764 (mtmt) outliers start: 62 outliers final: 38 residues processed: 158 average time/residue: 0.2241 time to fit residues: 50.3978 Evaluate side-chains 151 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 117 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 GLU 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 117 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 224 GLU 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 117 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 224 GLU 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 117 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 224 GLU 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 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 48 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.132646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.105344 restraints weight = 9473.182| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.19 r_work: 0.2825 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10570 Z= 0.153 Angle : 0.483 4.998 14316 Z= 0.239 Chirality : 0.045 0.132 1592 Planarity : 0.003 0.022 1844 Dihedral : 5.303 33.368 1508 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.04 % Allowed : 19.03 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1380 helix: 1.41 (0.24), residues: 460 sheet: -1.41 (0.34), residues: 224 loop : -0.57 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 172 HIS 0.002 0.000 HIS D 121 PHE 0.010 0.001 PHE B 210 TYR 0.016 0.001 TYR A 258 ARG 0.001 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 380) hydrogen bonds : angle 4.40564 ( 1188) metal coordination : bond 0.00424 ( 28) metal coordination : angle 3.09069 ( 24) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.51684 ( 4) covalent geometry : bond 0.00362 (10540) covalent geometry : angle 0.46655 (14288) ********************** 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 154 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8797 (pp) REVERT: A 39 TYR cc_start: 0.8989 (m-80) cc_final: 0.8235 (m-80) REVERT: A 104 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8282 (mt-10) REVERT: A 219 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 224 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 236 ASP cc_start: 0.8555 (t70) cc_final: 0.7949 (t0) REVERT: A 327 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.5629 (mp0) REVERT: A 347 LYS cc_start: 0.8090 (mttm) cc_final: 0.7744 (mtmt) REVERT: B 33 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8800 (pp) REVERT: B 39 TYR cc_start: 0.8987 (m-80) cc_final: 0.8235 (m-80) REVERT: B 104 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8303 (mt-10) REVERT: B 219 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 224 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: B 236 ASP cc_start: 0.8560 (t70) cc_final: 0.7953 (t0) REVERT: B 327 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.5643 (mp0) REVERT: B 347 LYS cc_start: 0.8105 (mttm) cc_final: 0.7766 (mtmt) REVERT: C 33 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8797 (pp) REVERT: C 39 TYR cc_start: 0.8996 (m-80) cc_final: 0.8248 (m-80) REVERT: C 104 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8284 (mt-10) REVERT: C 219 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8335 (mp) REVERT: C 224 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: C 236 ASP cc_start: 0.8517 (t70) cc_final: 0.7922 (t0) REVERT: C 327 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.5635 (mp0) REVERT: C 347 LYS cc_start: 0.8143 (mttm) cc_final: 0.7810 (mtmt) REVERT: D 33 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8803 (pp) REVERT: D 39 TYR cc_start: 0.9001 (m-80) cc_final: 0.8249 (m-80) REVERT: D 104 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8287 (mt-10) REVERT: D 219 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8318 (mp) REVERT: D 224 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: D 236 ASP cc_start: 0.8542 (t70) cc_final: 0.7950 (t0) REVERT: D 327 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.5633 (mp0) REVERT: D 347 LYS cc_start: 0.8107 (mttm) cc_final: 0.7762 (mtmt) outliers start: 54 outliers final: 38 residues processed: 154 average time/residue: 0.2273 time to fit residues: 49.6852 Evaluate side-chains 154 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 117 SER Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 GLU 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 117 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 224 GLU 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 117 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 224 GLU 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 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 224 GLU 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 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 70 optimal weight: 4.9990 chunk 125 optimal weight: 0.0040 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.131585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.104187 restraints weight = 9427.463| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.19 r_work: 0.2807 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10570 Z= 0.184 Angle : 0.502 5.129 14316 Z= 0.249 Chirality : 0.046 0.133 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.401 32.673 1508 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.88 % Allowed : 18.19 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1380 helix: 1.27 (0.24), residues: 460 sheet: -1.36 (0.34), residues: 220 loop : -0.65 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 92 HIS 0.002 0.001 HIS A 121 PHE 0.009 0.001 PHE C 210 TYR 0.017 0.001 TYR C 258 ARG 0.002 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.02941 ( 380) hydrogen bonds : angle 4.53056 ( 1188) metal coordination : bond 0.00488 ( 28) metal coordination : angle 3.16124 ( 24) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.56096 ( 4) covalent geometry : bond 0.00439 (10540) covalent geometry : angle 0.48572 (14288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5275.86 seconds wall clock time: 93 minutes 35.50 seconds (5615.50 seconds total)