Starting phenix.real_space_refine on Fri Feb 14 10:29:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kcq_22817/02_2025/7kcq_22817.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcq_22817/02_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_22817/02_2025/7kcq_22817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcq_22817/02_2025/7kcq_22817.map" model { file = "/net/cci-nas-00/data/ceres_data/7kcq_22817/02_2025/7kcq_22817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcq_22817/02_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-5592/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: 4.87, per 1000 atoms: 0.47 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=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.2 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: 1.31 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: 3.36 Time building geometry restraints manager: 2.87 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: 5416 17.18 - 34.37: 552 34.37 - 51.55: 148 51.55 - 68.73: 40 68.73 - 85.91: 16 Dihedral angle restraints: 6172 sinusoidal: 2308 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 6169 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: 70 2.57 - 3.15: 8460 3.15 - 3.73: 15853 3.73 - 4.32: 24945 4.32 - 4.90: 42082 Nonbonded interactions: 91410 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=" SG CYS C 277 " pdb=" SG CYS D 277 " model vdw 2.031 3.760 ... (remaining 91405 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: 0.08 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: 0.330 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.830 Find NCS groups from input model: 0.190 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- 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 : 0.011 0.062 10540 Z= 0.707 Angle : 0.799 7.429 14288 Z= 0.490 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 *********************** 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 : 1.175 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: 0.2399 time to fit residues: 53.9462 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 : 1.049 ------------------------------------------------------------------------------- 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: 4.9990 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 = 0.3308 r_free = 0.3308 target = 0.129691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.105921 restraints weight = 9508.443| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 0.98 r_work: 0.2792 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 10540 Z= 0.154 Angle : 0.472 4.924 14288 Z= 0.247 Chirality : 0.044 0.138 1592 Planarity : 0.004 0.033 1844 Dihedral : 6.941 64.485 1552 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.80 % Allowed : 18.28 % Favored : 78.92 % 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: -2.02 (0.21), residues: 1380 helix: -0.23 (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 0.003 0.001 HIS B 66 PHE 0.016 0.001 PHE B 210 TYR 0.015 0.001 TYR B 258 ARG 0.002 0.000 ARG B 260 *********************** 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 132 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 1.086 Fit side-chains REVERT: A 39 TYR cc_start: 0.9065 (m-80) cc_final: 0.8372 (m-80) REVERT: A 44 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7885 (t-90) REVERT: A 86 ASP cc_start: 0.8370 (m-30) cc_final: 0.8058 (m-30) REVERT: A 193 MET cc_start: 0.9342 (mtp) cc_final: 0.9075 (mtp) REVERT: A 236 ASP cc_start: 0.8418 (t70) cc_final: 0.7838 (t0) REVERT: A 347 LYS cc_start: 0.8141 (mttm) cc_final: 0.7817 (mtmt) REVERT: B 39 TYR cc_start: 0.9057 (m-80) cc_final: 0.8365 (m-80) REVERT: B 44 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7867 (t-90) REVERT: B 86 ASP cc_start: 0.8379 (m-30) cc_final: 0.8066 (m-30) REVERT: B 193 MET cc_start: 0.9339 (mtp) cc_final: 0.9075 (mtp) REVERT: B 236 ASP cc_start: 0.8336 (t70) cc_final: 0.7762 (t0) REVERT: B 347 LYS cc_start: 0.8138 (mttm) cc_final: 0.7820 (mtmt) REVERT: C 39 TYR cc_start: 0.9072 (m-80) cc_final: 0.8389 (m-80) REVERT: C 44 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7864 (t-90) REVERT: C 86 ASP cc_start: 0.8374 (m-30) cc_final: 0.8067 (m-30) REVERT: C 193 MET cc_start: 0.9338 (mtp) cc_final: 0.9075 (mtp) REVERT: C 236 ASP cc_start: 0.8347 (t70) cc_final: 0.7777 (t0) REVERT: C 347 LYS cc_start: 0.8126 (mttm) cc_final: 0.7799 (mtmt) REVERT: D 39 TYR cc_start: 0.9064 (m-80) cc_final: 0.8385 (m-80) REVERT: D 44 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7878 (t-90) REVERT: D 86 ASP cc_start: 0.8380 (m-30) cc_final: 0.8068 (m-30) REVERT: D 193 MET cc_start: 0.9338 (mtp) cc_final: 0.9075 (mtp) REVERT: D 236 ASP cc_start: 0.8373 (t70) cc_final: 0.7802 (t0) REVERT: D 347 LYS cc_start: 0.8159 (mttm) cc_final: 0.7845 (mtmt) outliers start: 30 outliers final: 22 residues processed: 132 average time/residue: 0.2418 time to fit residues: 45.0419 Evaluate side-chains 118 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 126 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 96 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS B 44 HIS C 44 HIS D 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.132353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.106946 restraints weight = 9566.898| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.07 r_work: 0.2838 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 10540 Z= 0.136 Angle : 0.431 4.934 14288 Z= 0.224 Chirality : 0.043 0.132 1592 Planarity : 0.003 0.026 1844 Dihedral : 5.175 34.391 1508 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.36 % Allowed : 19.12 % Favored : 77.52 % 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: -1.08 (0.23), residues: 1380 helix: 0.71 (0.24), residues: 460 sheet: -2.25 (0.28), residues: 232 loop : -1.09 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 92 HIS 0.007 0.001 HIS A 44 PHE 0.014 0.001 PHE A 210 TYR 0.014 0.001 TYR C 258 ARG 0.001 0.000 ARG B 211 *********************** 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 138 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 1.245 Fit side-chains REVERT: A 15 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8242 (t-90) REVERT: A 33 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8812 (pp) REVERT: A 219 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8193 (mp) REVERT: A 236 ASP cc_start: 0.8258 (t70) cc_final: 0.7630 (t0) REVERT: A 347 LYS cc_start: 0.8036 (mttm) cc_final: 0.7689 (mtmt) REVERT: B 15 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.8253 (t-90) REVERT: B 33 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8815 (pp) REVERT: B 219 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8201 (mp) REVERT: B 236 ASP cc_start: 0.8244 (t70) cc_final: 0.7620 (t0) REVERT: B 347 LYS cc_start: 0.8051 (mttm) cc_final: 0.7707 (mtmt) REVERT: C 15 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8245 (t-90) REVERT: C 33 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8811 (pp) REVERT: C 219 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8204 (mp) REVERT: C 236 ASP cc_start: 0.8272 (t70) cc_final: 0.7643 (t0) REVERT: C 347 LYS cc_start: 0.8034 (mttm) cc_final: 0.7687 (mtmt) REVERT: D 15 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8241 (t-90) REVERT: D 33 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8809 (pp) REVERT: D 219 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8198 (mp) REVERT: D 236 ASP cc_start: 0.8279 (t70) cc_final: 0.7651 (t0) REVERT: D 347 LYS cc_start: 0.8037 (mttm) cc_final: 0.7690 (mtmt) outliers start: 36 outliers final: 24 residues processed: 138 average time/residue: 0.2421 time to fit residues: 47.0119 Evaluate side-chains 128 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 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 219 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 22 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 36 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.125204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.095702 restraints weight = 9814.432| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.29 r_work: 0.2682 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 10540 Z= 0.522 Angle : 0.586 6.396 14288 Z= 0.301 Chirality : 0.050 0.139 1592 Planarity : 0.004 0.027 1844 Dihedral : 6.042 36.156 1508 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.60 % Allowed : 17.72 % Favored : 76.68 % 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: -1.39 (0.22), residues: 1380 helix: 0.30 (0.23), residues: 460 sheet: -2.14 (0.29), residues: 220 loop : -1.29 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 92 HIS 0.002 0.001 HIS B 138 PHE 0.008 0.002 PHE D 11 TYR 0.019 0.002 TYR D 258 ARG 0.003 0.001 ARG B 211 *********************** 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 168 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 108 time to evaluate : 1.117 Fit side-chains REVERT: A 15 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.8296 (t-90) REVERT: A 33 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8815 (pp) REVERT: A 39 TYR cc_start: 0.9101 (m-80) cc_final: 0.8400 (m-80) REVERT: A 44 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7754 (t-90) REVERT: A 86 ASP cc_start: 0.8347 (m-30) cc_final: 0.7943 (m-30) REVERT: A 219 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 236 ASP cc_start: 0.8547 (t70) cc_final: 0.7944 (t0) REVERT: A 277 CYS cc_start: 0.8907 (m) cc_final: 0.8700 (m) REVERT: A 347 LYS cc_start: 0.8158 (mttm) cc_final: 0.7816 (mtmt) REVERT: B 15 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.8293 (t-90) REVERT: B 33 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8834 (pp) REVERT: B 39 TYR cc_start: 0.9099 (m-80) cc_final: 0.8395 (m-80) REVERT: B 44 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7758 (t-90) REVERT: B 86 ASP cc_start: 0.8313 (m-30) cc_final: 0.7899 (m-30) REVERT: B 193 MET cc_start: 0.9349 (mtp) cc_final: 0.8997 (mtp) REVERT: B 219 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8317 (mp) REVERT: B 236 ASP cc_start: 0.8540 (t70) cc_final: 0.7946 (t0) REVERT: B 347 LYS cc_start: 0.8170 (mttm) cc_final: 0.7826 (mtmt) REVERT: C 15 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8302 (t-90) REVERT: C 33 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8821 (pp) REVERT: C 39 TYR cc_start: 0.9105 (m-80) cc_final: 0.8407 (m-80) REVERT: C 44 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7756 (t-90) REVERT: C 86 ASP cc_start: 0.8326 (m-30) cc_final: 0.7909 (m-30) REVERT: C 219 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 236 ASP cc_start: 0.8544 (t70) cc_final: 0.7952 (t0) REVERT: C 277 CYS cc_start: 0.8900 (m) cc_final: 0.8681 (m) REVERT: C 347 LYS cc_start: 0.8162 (mttm) cc_final: 0.7809 (mtmt) REVERT: D 15 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8278 (t-90) REVERT: D 33 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8818 (pp) REVERT: D 39 TYR cc_start: 0.9111 (m-80) cc_final: 0.8415 (m-80) REVERT: D 44 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7748 (t-90) REVERT: D 86 ASP cc_start: 0.8339 (m-30) cc_final: 0.7914 (m-30) REVERT: D 193 MET cc_start: 0.9352 (mtp) cc_final: 0.8999 (mtp) REVERT: D 219 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8316 (mp) REVERT: D 236 ASP cc_start: 0.8511 (t70) cc_final: 0.7910 (t0) REVERT: D 347 LYS cc_start: 0.8166 (mttm) cc_final: 0.7821 (mtmt) outliers start: 60 outliers final: 30 residues processed: 164 average time/residue: 0.2379 time to fit residues: 54.4376 Evaluate side-chains 160 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 96 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.129074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.100771 restraints weight = 9678.786| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.24 r_work: 0.2762 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10540 Z= 0.213 Angle : 0.479 6.690 14288 Z= 0.242 Chirality : 0.044 0.134 1592 Planarity : 0.003 0.024 1844 Dihedral : 5.421 33.691 1508 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.92 % Allowed : 19.68 % Favored : 76.40 % 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: -0.80 (0.23), residues: 1380 helix: 0.83 (0.23), residues: 460 sheet: -1.82 (0.31), residues: 224 loop : -0.96 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 172 HIS 0.002 0.000 HIS A 121 PHE 0.012 0.001 PHE B 210 TYR 0.017 0.001 TYR C 258 ARG 0.001 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 1.152 Fit side-chains REVERT: A 15 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8286 (t-90) REVERT: A 33 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8806 (pp) REVERT: A 39 TYR cc_start: 0.9036 (m-80) cc_final: 0.8291 (m-80) REVERT: A 44 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7688 (t-90) REVERT: A 104 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8358 (mt-10) REVERT: A 219 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8242 (mp) REVERT: A 236 ASP cc_start: 0.8462 (t70) cc_final: 0.7835 (t0) REVERT: A 347 LYS cc_start: 0.8097 (mttm) cc_final: 0.7738 (mtmt) REVERT: B 15 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8296 (t-90) REVERT: B 33 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8810 (pp) REVERT: B 39 TYR cc_start: 0.9030 (m-80) cc_final: 0.8280 (m-80) REVERT: B 44 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7700 (t-90) REVERT: B 104 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 193 MET cc_start: 0.9315 (mtp) cc_final: 0.9024 (mtp) REVERT: B 219 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8245 (mp) REVERT: B 236 ASP cc_start: 0.8452 (t70) cc_final: 0.7822 (t0) REVERT: B 347 LYS cc_start: 0.8090 (mttm) cc_final: 0.7729 (mtmt) REVERT: C 15 HIS cc_start: 0.8499 (OUTLIER) cc_final: 0.8292 (t-90) REVERT: C 33 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8800 (pp) REVERT: C 39 TYR cc_start: 0.9035 (m-80) cc_final: 0.8293 (m-80) REVERT: C 44 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7686 (t-90) REVERT: C 104 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8370 (mt-10) REVERT: C 219 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8237 (mp) REVERT: C 236 ASP cc_start: 0.8470 (t70) cc_final: 0.7849 (t0) REVERT: C 347 LYS cc_start: 0.8092 (mttm) cc_final: 0.7733 (mtmt) REVERT: D 15 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.8287 (t-90) REVERT: D 33 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8800 (pp) REVERT: D 39 TYR cc_start: 0.9036 (m-80) cc_final: 0.8293 (m-80) REVERT: D 44 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7693 (t-90) REVERT: D 104 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8354 (mt-10) REVERT: D 193 MET cc_start: 0.9330 (mtp) cc_final: 0.9038 (mtp) REVERT: D 219 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8241 (mp) REVERT: D 236 ASP cc_start: 0.8478 (t70) cc_final: 0.7852 (t0) REVERT: D 347 LYS cc_start: 0.8094 (mttm) cc_final: 0.7733 (mtmt) outliers start: 42 outliers final: 24 residues processed: 140 average time/residue: 0.2458 time to fit residues: 48.0628 Evaluate side-chains 138 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 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 219 ILE Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 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 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: 0.8980 chunk 13 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.127729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.098925 restraints weight = 9751.741| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.25 r_work: 0.2730 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10540 Z= 0.297 Angle : 0.497 6.020 14288 Z= 0.252 Chirality : 0.045 0.134 1592 Planarity : 0.003 0.025 1844 Dihedral : 5.498 32.819 1508 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.85 % Allowed : 18.84 % Favored : 76.31 % 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: -0.64 (0.23), residues: 1380 helix: 0.98 (0.23), residues: 460 sheet: -1.65 (0.32), residues: 220 loop : -0.92 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 92 HIS 0.002 0.000 HIS A 121 PHE 0.010 0.001 PHE C 210 TYR 0.017 0.001 TYR A 258 ARG 0.001 0.000 ARG B 211 *********************** 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: 52 poor density : 100 time to evaluate : 1.069 Fit side-chains REVERT: A 15 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8294 (t-90) REVERT: A 33 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8813 (pp) REVERT: A 39 TYR cc_start: 0.9058 (m-80) cc_final: 0.8354 (m-80) REVERT: A 44 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7697 (t-90) REVERT: A 104 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 219 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 236 ASP cc_start: 0.8524 (t70) cc_final: 0.7904 (t0) REVERT: A 347 LYS cc_start: 0.8116 (mttm) cc_final: 0.7757 (mtmt) REVERT: B 33 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8821 (pp) REVERT: B 39 TYR cc_start: 0.9065 (m-80) cc_final: 0.8363 (m-80) REVERT: B 44 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7694 (t-90) REVERT: B 104 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 193 MET cc_start: 0.9319 (mtp) cc_final: 0.9022 (mtp) REVERT: B 219 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8274 (mp) REVERT: B 236 ASP cc_start: 0.8503 (t70) cc_final: 0.7883 (t0) REVERT: B 347 LYS cc_start: 0.8101 (mttm) cc_final: 0.7742 (mtmt) REVERT: C 33 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8817 (pp) REVERT: C 39 TYR cc_start: 0.9067 (m-80) cc_final: 0.8366 (m-80) REVERT: C 44 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7691 (t-90) REVERT: C 104 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8328 (mt-10) REVERT: C 219 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8266 (mp) REVERT: C 236 ASP cc_start: 0.8526 (t70) cc_final: 0.7910 (t0) REVERT: C 347 LYS cc_start: 0.8117 (mttm) cc_final: 0.7753 (mtmt) REVERT: D 33 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8812 (pp) REVERT: D 39 TYR cc_start: 0.9063 (m-80) cc_final: 0.8361 (m-80) REVERT: D 44 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7670 (t-90) REVERT: D 104 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8321 (mt-10) REVERT: D 193 MET cc_start: 0.9334 (mtp) cc_final: 0.9046 (mtp) REVERT: D 219 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8271 (mp) REVERT: D 236 ASP cc_start: 0.8518 (t70) cc_final: 0.7897 (t0) REVERT: D 347 LYS cc_start: 0.8106 (mttm) cc_final: 0.7748 (mtmt) outliers start: 52 outliers final: 32 residues processed: 152 average time/residue: 0.2354 time to fit residues: 50.0208 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 : 1.130 ------------------------------------------------------------------------------- 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 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 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 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: 0.5980 chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.130237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.101871 restraints weight = 9836.937| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.26 r_work: 0.2779 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 10540 Z= 0.178 Angle : 0.450 5.438 14288 Z= 0.229 Chirality : 0.043 0.133 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.194 34.678 1508 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.88 % Allowed : 17.63 % Favored : 76.49 % 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: 1.34 (0.24), residues: 460 sheet: -1.55 (0.33), residues: 224 loop : -0.68 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 172 HIS 0.002 0.000 HIS A 121 PHE 0.012 0.001 PHE A 210 TYR 0.016 0.001 TYR D 258 ARG 0.001 0.000 ARG A 298 *********************** 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 157 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 94 time to evaluate : 1.173 Fit side-chains REVERT: A 15 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.8263 (t-90) REVERT: A 33 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8764 (pp) REVERT: A 44 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7607 (t-90) REVERT: A 104 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8351 (mt-10) REVERT: A 219 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 236 ASP cc_start: 0.8464 (t70) cc_final: 0.7839 (t0) REVERT: A 327 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.5455 (mp0) REVERT: A 347 LYS cc_start: 0.8071 (mttm) cc_final: 0.7666 (mtmt) REVERT: B 33 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8761 (pp) REVERT: B 44 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7595 (t-90) REVERT: B 104 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 193 MET cc_start: 0.9343 (mtp) cc_final: 0.9101 (mtp) REVERT: B 219 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 236 ASP cc_start: 0.8412 (t70) cc_final: 0.7781 (t0) REVERT: B 327 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: B 347 LYS cc_start: 0.8063 (mttm) cc_final: 0.7656 (mtmt) REVERT: C 33 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8763 (pp) REVERT: C 44 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7602 (t-90) REVERT: C 104 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8354 (mt-10) REVERT: C 219 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8213 (mp) REVERT: C 224 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: C 236 ASP cc_start: 0.8450 (t70) cc_final: 0.7827 (t0) REVERT: C 327 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.5441 (mp0) REVERT: C 347 LYS cc_start: 0.8077 (mttm) cc_final: 0.7676 (mtmt) REVERT: D 33 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8763 (pp) REVERT: D 44 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7597 (t-90) REVERT: D 104 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8354 (mt-10) REVERT: D 193 MET cc_start: 0.9352 (mtp) cc_final: 0.9119 (mtp) REVERT: D 219 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8215 (mp) REVERT: D 224 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: D 236 ASP cc_start: 0.8467 (t70) cc_final: 0.7837 (t0) REVERT: D 327 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.5410 (mp0) REVERT: D 347 LYS cc_start: 0.8074 (mttm) cc_final: 0.7670 (mtmt) outliers start: 63 outliers final: 40 residues processed: 157 average time/residue: 0.2415 time to fit residues: 53.6544 Evaluate side-chains 153 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 94 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 175 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 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 33 LEU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 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: 7.9990 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.131988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.106334 restraints weight = 9668.531| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.12 r_work: 0.2848 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 10540 Z= 0.143 Angle : 0.430 5.093 14288 Z= 0.218 Chirality : 0.043 0.131 1592 Planarity : 0.003 0.023 1844 Dihedral : 4.911 35.130 1508 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.22 % Allowed : 18.28 % Favored : 76.49 % 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: 0.02 (0.24), residues: 1380 helix: 1.62 (0.25), residues: 460 sheet: -1.34 (0.33), residues: 224 loop : -0.56 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 172 HIS 0.002 0.000 HIS A 121 PHE 0.012 0.001 PHE C 210 TYR 0.015 0.001 TYR C 258 ARG 0.001 0.000 ARG C 298 *********************** 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 159 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 103 time to evaluate : 1.329 Fit side-chains REVERT: A 33 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8745 (pp) REVERT: A 104 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 219 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 224 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: A 236 ASP cc_start: 0.8341 (t70) cc_final: 0.7757 (t0) REVERT: A 327 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.5853 (mp0) REVERT: A 347 LYS cc_start: 0.8082 (mttm) cc_final: 0.7753 (mtmt) REVERT: B 33 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8754 (pp) REVERT: B 104 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8313 (mt-10) REVERT: B 193 MET cc_start: 0.9318 (mtp) cc_final: 0.9088 (mtp) REVERT: B 219 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8302 (mp) REVERT: B 224 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: B 236 ASP cc_start: 0.8322 (t70) cc_final: 0.7735 (t0) REVERT: B 327 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: B 347 LYS cc_start: 0.8084 (mttm) cc_final: 0.7754 (mtmt) REVERT: C 33 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8738 (pp) REVERT: C 104 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8345 (mt-10) REVERT: C 219 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8288 (mp) REVERT: C 224 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: C 236 ASP cc_start: 0.8360 (t70) cc_final: 0.7777 (t0) REVERT: C 327 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.5856 (mp0) REVERT: C 347 LYS cc_start: 0.8097 (mttm) cc_final: 0.7771 (mtmt) REVERT: D 33 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8742 (pp) REVERT: D 104 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8303 (mt-10) REVERT: D 193 MET cc_start: 0.9325 (mtp) cc_final: 0.9106 (mtp) REVERT: D 219 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8290 (mp) REVERT: D 224 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: D 236 ASP cc_start: 0.8355 (t70) cc_final: 0.7772 (t0) REVERT: D 327 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5838 (mp0) REVERT: D 347 LYS cc_start: 0.8088 (mttm) cc_final: 0.7762 (mtmt) outliers start: 56 outliers final: 40 residues processed: 159 average time/residue: 0.2317 time to fit residues: 52.4034 Evaluate side-chains 154 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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: 3.9990 chunk 102 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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** A 113 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.129231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.100767 restraints weight = 9935.574| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.51 r_work: 0.2766 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 10540 Z= 0.317 Angle : 0.498 5.330 14288 Z= 0.253 Chirality : 0.046 0.134 1592 Planarity : 0.003 0.024 1844 Dihedral : 5.309 32.708 1504 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.06 % Allowed : 18.10 % Favored : 75.84 % 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: -0.22 (0.23), residues: 1380 helix: 1.31 (0.24), residues: 460 sheet: -1.35 (0.34), residues: 220 loop : -0.68 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 92 HIS 0.002 0.001 HIS B 113 PHE 0.008 0.001 PHE A 210 TYR 0.017 0.002 TYR B 258 ARG 0.002 0.000 ARG D 211 *********************** 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 163 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 98 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8835 (pp) REVERT: A 39 TYR cc_start: 0.9054 (m-80) cc_final: 0.8328 (m-80) REVERT: A 44 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7676 (t-90) REVERT: A 104 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 219 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8319 (mp) REVERT: A 224 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: A 236 ASP cc_start: 0.8598 (t70) cc_final: 0.8006 (t0) REVERT: A 347 LYS cc_start: 0.8135 (mttm) cc_final: 0.7763 (mtmt) REVERT: B 33 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8835 (pp) REVERT: B 39 TYR cc_start: 0.9062 (m-80) cc_final: 0.8344 (m-80) REVERT: B 44 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7699 (t-90) REVERT: B 104 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 193 MET cc_start: 0.9337 (mtp) cc_final: 0.9035 (mtp) REVERT: B 219 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8321 (mp) REVERT: B 224 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: B 236 ASP cc_start: 0.8560 (t70) cc_final: 0.7976 (t0) REVERT: B 347 LYS cc_start: 0.8138 (mttm) cc_final: 0.7765 (mtmt) REVERT: C 33 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8833 (pp) REVERT: C 39 TYR cc_start: 0.9057 (m-80) cc_final: 0.8338 (m-80) REVERT: C 44 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7677 (t-90) REVERT: C 104 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8427 (mt-10) REVERT: C 219 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8302 (mp) REVERT: C 236 ASP cc_start: 0.8610 (t70) cc_final: 0.8031 (t0) REVERT: C 347 LYS cc_start: 0.8158 (mttm) cc_final: 0.7792 (mtmt) REVERT: D 33 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8837 (pp) REVERT: D 39 TYR cc_start: 0.9071 (m-80) cc_final: 0.8356 (m-80) REVERT: D 44 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7665 (t-90) REVERT: D 104 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8409 (mt-10) REVERT: D 193 MET cc_start: 0.9345 (mtp) cc_final: 0.9052 (mtp) REVERT: D 219 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8308 (mp) REVERT: D 236 ASP cc_start: 0.8571 (t70) cc_final: 0.7977 (t0) REVERT: D 327 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.5696 (mp0) REVERT: D 347 LYS cc_start: 0.8130 (mttm) cc_final: 0.7757 (mtmt) outliers start: 65 outliers final: 42 residues processed: 163 average time/residue: 0.2353 time to fit residues: 53.5408 Evaluate side-chains 150 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 93 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 109 SER 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 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 109 SER 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 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 109 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 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 33 LEU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 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: 0.9990 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** A 113 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.129783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.100523 restraints weight = 9802.148| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.29 r_work: 0.2740 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10540 Z= 0.273 Angle : 0.483 5.100 14288 Z= 0.245 Chirality : 0.045 0.133 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.249 33.155 1504 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.04 % Allowed : 19.12 % Favored : 75.84 % 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: 1.31 (0.24), residues: 460 sheet: -1.29 (0.34), residues: 220 loop : -0.64 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 92 HIS 0.002 0.001 HIS B 121 PHE 0.010 0.001 PHE C 210 TYR 0.017 0.001 TYR C 258 ARG 0.002 0.000 ARG D 211 ********************** 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 148 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 94 time to evaluate : 1.011 Fit side-chains REVERT: A 33 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8793 (pp) REVERT: A 39 TYR cc_start: 0.9031 (m-80) cc_final: 0.8300 (m-80) REVERT: A 104 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 219 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 224 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: A 236 ASP cc_start: 0.8515 (t70) cc_final: 0.7896 (t0) REVERT: A 327 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.5585 (mp0) REVERT: A 347 LYS cc_start: 0.8088 (mttm) cc_final: 0.7717 (mtmt) REVERT: B 33 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 39 TYR cc_start: 0.9037 (m-80) cc_final: 0.8317 (m-80) REVERT: B 104 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8346 (mt-10) REVERT: B 193 MET cc_start: 0.9327 (mtp) cc_final: 0.9031 (mtp) REVERT: B 219 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 224 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: B 236 ASP cc_start: 0.8446 (t70) cc_final: 0.7832 (t0) REVERT: B 327 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5183 (mp0) REVERT: B 347 LYS cc_start: 0.8089 (mttm) cc_final: 0.7719 (mtmt) REVERT: C 33 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8785 (pp) REVERT: C 39 TYR cc_start: 0.9037 (m-80) cc_final: 0.8315 (m-80) REVERT: C 104 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8355 (mt-10) REVERT: C 219 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8227 (mp) REVERT: C 236 ASP cc_start: 0.8520 (t70) cc_final: 0.7915 (t0) REVERT: C 327 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.5254 (mp0) REVERT: C 347 LYS cc_start: 0.8094 (mttm) cc_final: 0.7729 (mtmt) REVERT: D 33 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8795 (pp) REVERT: D 39 TYR cc_start: 0.9049 (m-80) cc_final: 0.8333 (m-80) REVERT: D 104 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8345 (mt-10) REVERT: D 193 MET cc_start: 0.9342 (mtp) cc_final: 0.9057 (mtp) REVERT: D 219 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8227 (mp) REVERT: D 236 ASP cc_start: 0.8497 (t70) cc_final: 0.7880 (t0) REVERT: D 327 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.5223 (mp0) REVERT: D 347 LYS cc_start: 0.8084 (mttm) cc_final: 0.7713 (mtmt) outliers start: 54 outliers final: 40 residues processed: 148 average time/residue: 0.2303 time to fit residues: 48.2215 Evaluate side-chains 148 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 94 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 109 SER 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 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 109 SER 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 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 109 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 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 109 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 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: 6.9990 chunk 125 optimal weight: 4.9990 chunk 44 optimal weight: 0.0050 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.2118 ------------------------------------------------------------------------------- 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** A 113 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.131499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.104390 restraints weight = 9748.810| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.38 r_work: 0.2776 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10540 Z= 0.200 Angle : 0.453 4.966 14288 Z= 0.230 Chirality : 0.044 0.131 1592 Planarity : 0.003 0.022 1844 Dihedral : 5.049 34.193 1504 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.06 % Allowed : 18.10 % Favored : 75.84 % 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: -0.02 (0.24), residues: 1380 helix: 1.50 (0.24), residues: 460 sheet: -1.23 (0.34), residues: 220 loop : -0.58 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 172 HIS 0.002 0.000 HIS A 121 PHE 0.011 0.001 PHE C 210 TYR 0.016 0.001 TYR C 258 ARG 0.001 0.000 ARG D 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4690.16 seconds wall clock time: 84 minutes 9.20 seconds (5049.20 seconds total)