Starting phenix.real_space_refine on Thu Jul 2 07:18:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jv5_36668/07_2026/8jv5_36668.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jv5_36668/07_2026/8jv5_36668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_2026/8jv5_36668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_2026/8jv5_36668.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_2026/8jv5_36668.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_2026/8jv5_36668.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_2026/8jv5_36668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_2026/8jv5_36668.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.094 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 Br 6 7.06 5 S 51 5.16 5 C 4733 2.51 5 N 1249 2.21 5 O 1441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2428 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 297} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2428 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 297} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2435 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 298} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.74, per 1000 atoms: 0.23 Number of scatterers: 7480 At special positions: 0 Unit cell: (91.3, 85.49, 113.71, 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) Br 6 34.99 S 51 16.00 O 1441 8.00 N 1249 7.00 C 4733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 273 " distance=2.02 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 264 " - pdb=" SG CYS C 273 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 213 " " NAG A 503 " - " ASN A 187 " " NAG A 504 " - " ASN A 78 " " NAG B 502 " - " ASN B 213 " " NAG B 503 " - " ASN B 187 " " NAG B 504 " - " ASN B 78 " " NAG C 502 " - " ASN C 213 " " NAG C 503 " - " ASN C 187 " " NAG C 504 " - " ASN C 78 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 455.6 milliseconds 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 15 sheets defined 20.8% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.702A pdb=" N ILE A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.910A pdb=" N HIS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 245 through 253 removed outlier: 4.102A pdb=" N ARG A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 335 through 358 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 213 through 219 removed outlier: 3.905A pdb=" N HIS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 245 through 253 removed outlier: 4.105A pdb=" N ARG B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 335 through 358 Processing helix chain 'C' and resid 43 through 50 removed outlier: 3.803A pdb=" N ILE C 47 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 213 through 219 removed outlier: 3.902A pdb=" N HIS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 245 through 253 removed outlier: 4.110A pdb=" N ARG C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 335 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.784A pdb=" N GLY A 254 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASP A 323 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A 256 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET A 325 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 258 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 327 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A 260 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLN A 329 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP A 262 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY A 331 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N CYS A 264 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N PHE A 333 " --> pdb=" O CYS A 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 153 removed outlier: 10.061A pdb=" N VAL A 147 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N TRP A 167 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N THR A 149 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LEU A 165 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG A 151 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER A 101 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 324 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 103 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE A 322 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 105 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 320 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 113 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG A 312 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR A 115 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLU A 310 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.784A pdb=" N GLY B 254 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP B 323 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET B 256 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N MET B 325 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 258 " --> pdb=" O MET B 325 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE B 327 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE B 260 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN B 329 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP B 262 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLY B 331 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N CYS B 264 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N PHE B 333 " --> pdb=" O CYS B 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 153 removed outlier: 10.057A pdb=" N VAL B 147 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N TRP B 167 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N THR B 149 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LEU B 165 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG B 151 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER B 101 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 324 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE B 103 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE B 322 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 105 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 320 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 113 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG B 312 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR B 115 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLU B 310 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 77 Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.769A pdb=" N GLY C 254 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASP C 323 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET C 256 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET C 325 " --> pdb=" O MET C 256 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 258 " --> pdb=" O MET C 325 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE C 327 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE C 260 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLN C 329 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP C 262 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY C 331 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N CYS C 264 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N PHE C 333 " --> pdb=" O CYS C 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 147 through 153 removed outlier: 10.058A pdb=" N VAL C 147 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N TRP C 167 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR C 149 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU C 165 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG C 151 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER C 101 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 324 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE C 103 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE C 322 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU C 105 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 320 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN C 113 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ARG C 312 " --> pdb=" O ASN C 113 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR C 115 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU C 310 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 72 Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 77 300 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2065 1.33 - 1.48: 2359 1.48 - 1.63: 3155 1.63 - 1.79: 7 1.79 - 1.94: 65 Bond restraints: 7651 Sorted by residual: bond pdb=" C10 P73 A 501 " pdb=" N11 P73 A 501 " ideal model delta sigma weight residual 1.373 1.454 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C10 P73 B 501 " pdb=" N11 P73 B 501 " ideal model delta sigma weight residual 1.373 1.453 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C10 P73 C 501 " pdb=" N11 P73 C 501 " ideal model delta sigma weight residual 1.373 1.452 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C10 P73 B 501 " pdb=" N09 P73 B 501 " ideal model delta sigma weight residual 1.377 1.454 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C10 P73 C 501 " pdb=" N09 P73 C 501 " ideal model delta sigma weight residual 1.377 1.453 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 7646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 10043 1.41 - 2.81: 314 2.81 - 4.22: 65 4.22 - 5.62: 10 5.62 - 7.03: 6 Bond angle restraints: 10438 Sorted by residual: angle pdb=" C ASP B 229 " pdb=" N CYS B 230 " pdb=" CA CYS B 230 " ideal model delta sigma weight residual 120.67 117.43 3.24 1.34e+00 5.57e-01 5.84e+00 angle pdb=" C ASP C 229 " pdb=" N CYS C 230 " pdb=" CA CYS C 230 " ideal model delta sigma weight residual 120.67 117.48 3.19 1.34e+00 5.57e-01 5.68e+00 angle pdb=" CA CYS B 220 " pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " ideal model delta sigma weight residual 114.40 119.86 -5.46 2.30e+00 1.89e-01 5.64e+00 angle pdb=" CA CYS C 220 " pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " ideal model delta sigma weight residual 114.40 119.85 -5.45 2.30e+00 1.89e-01 5.61e+00 angle pdb=" N09 P73 C 501 " pdb=" C10 P73 C 501 " pdb=" N11 P73 C 501 " ideal model delta sigma weight residual 113.26 120.29 -7.03 3.00e+00 1.11e-01 5.48e+00 ... (remaining 10433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 4056 15.23 - 30.47: 329 30.47 - 45.70: 74 45.70 - 60.94: 12 60.94 - 76.17: 12 Dihedral angle restraints: 4483 sinusoidal: 1738 harmonic: 2745 Sorted by residual: dihedral pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.49 -64.49 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.43 -64.43 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.33 -64.33 1 1.00e+01 1.00e-02 5.44e+01 ... (remaining 4480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 638 0.026 - 0.053: 315 0.053 - 0.079: 106 0.079 - 0.106: 85 0.106 - 0.132: 46 Chirality restraints: 1190 Sorted by residual: chirality pdb=" CA ILE B 94 " pdb=" N ILE B 94 " pdb=" C ILE B 94 " pdb=" CB ILE B 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE C 94 " pdb=" N ILE C 94 " pdb=" C ILE C 94 " pdb=" CB ILE C 94 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1187 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 198 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO C 199 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 199 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 199 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 198 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 199 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 198 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 199 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " 0.023 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2290 2.83 - 3.35: 6419 3.35 - 3.86: 11685 3.86 - 4.38: 13688 4.38 - 4.90: 24128 Nonbonded interactions: 58210 Sorted by model distance: nonbonded pdb=" NE ARG B 281 " pdb=" OD1 ASP B 283 " model vdw 2.312 3.120 nonbonded pdb=" NE ARG A 281 " pdb=" OD1 ASP A 283 " model vdw 2.318 3.120 nonbonded pdb=" OD2 ASP B 99 " pdb=" OH TYR C 295 " model vdw 2.322 3.040 nonbonded pdb=" NE ARG C 281 " pdb=" OD1 ASP C 283 " model vdw 2.322 3.120 nonbonded pdb=" OD2 ASP A 99 " pdb=" OH TYR B 295 " model vdw 2.326 3.040 ... (remaining 58205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 43 through 504) } 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: 1.160 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 7675 Z= 0.235 Angle : 0.635 7.026 10495 Z= 0.322 Chirality : 0.045 0.132 1190 Planarity : 0.005 0.044 1354 Dihedral : 12.438 76.169 2678 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.76 % Allowed : 3.29 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.27), residues: 943 helix: 1.17 (0.44), residues: 174 sheet: 1.29 (0.29), residues: 330 loop : -0.16 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 276 TYR 0.008 0.001 TYR C 318 PHE 0.011 0.001 PHE B 327 TRP 0.011 0.001 TRP B 262 HIS 0.000 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.24 ( 7651) covalent geometry : angle 0.62938 / 0.32 (10438) SS BOND : bond 0.00306 / 0.21 ( 15) SS BOND : angle 1.44619 / 0.87 ( 30) hydrogen bonds : bond 0.12802 / 8.86 ( 270) hydrogen bonds : angle 5.68562 / 3.85 ( 774) link_NAG-ASN : bond 0.00248 / 0.13 ( 9) link_NAG-ASN : angle 1.10061 / 0.63 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.6841 (mtp85) cc_final: 0.6515 (mtm180) REVERT: B 72 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7578 (mtpp) outliers start: 6 outliers final: 0 residues processed: 155 average time/residue: 0.1102 time to fit residues: 22.0574 Evaluate side-chains 95 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 247 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 270 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.190003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126382 restraints weight = 7094.191| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.69 r_work: 0.3240 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7675 Z= 0.121 Angle : 0.552 6.331 10495 Z= 0.289 Chirality : 0.045 0.154 1190 Planarity : 0.004 0.036 1354 Dihedral : 4.749 20.180 1042 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.76 % Allowed : 9.75 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.28), residues: 943 helix: 1.13 (0.43), residues: 194 sheet: 1.43 (0.29), residues: 332 loop : -0.34 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 298 TYR 0.010 0.001 TYR C 318 PHE 0.009 0.001 PHE C 103 TRP 0.014 0.002 TRP C 262 HIS 0.000 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7651) covalent geometry : angle 0.54481 / 0.29 (10438) SS BOND : bond 0.00243 / 0.18 ( 15) SS BOND : angle 1.69245 / 1.04 ( 30) hydrogen bonds : bond 0.03470 / 2.24 ( 270) hydrogen bonds : angle 4.91743 / 3.30 ( 774) link_NAG-ASN : bond 0.00321 / 0.18 ( 9) link_NAG-ASN : angle 0.76428 / 0.48 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7680 (t0) cc_final: 0.7443 (t0) REVERT: A 72 LYS cc_start: 0.7550 (mtmm) cc_final: 0.7283 (mtpp) REVERT: A 200 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8219 (ttmm) REVERT: A 276 ARG cc_start: 0.6717 (mtp85) cc_final: 0.5972 (mtm-85) REVERT: B 72 LYS cc_start: 0.7542 (mtmm) cc_final: 0.7267 (mtpp) REVERT: B 301 LYS cc_start: 0.8428 (mttm) cc_final: 0.8150 (mttm) REVERT: C 261 ARG cc_start: 0.8337 (ttt-90) cc_final: 0.8032 (ttt180) REVERT: C 268 MET cc_start: 0.7740 (mmm) cc_final: 0.7296 (mmm) outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.1168 time to fit residues: 16.4572 Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 221 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 39 optimal weight: 30.0000 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.186301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120596 restraints weight = 6886.694| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.86 r_work: 0.3146 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7675 Z= 0.152 Angle : 0.551 5.947 10495 Z= 0.290 Chirality : 0.045 0.141 1190 Planarity : 0.004 0.034 1354 Dihedral : 5.012 21.313 1042 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.53 % Allowed : 10.38 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 943 helix: 1.37 (0.43), residues: 183 sheet: 1.22 (0.29), residues: 334 loop : -0.50 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 298 TYR 0.010 0.001 TYR C 318 PHE 0.012 0.002 PHE B 103 TRP 0.015 0.002 TRP A 167 HIS 0.000 0.000 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 7651) covalent geometry : angle 0.54390 / 0.29 (10438) SS BOND : bond 0.00415 / 0.28 ( 15) SS BOND : angle 1.41075 / 0.89 ( 30) hydrogen bonds : bond 0.03319 / 2.22 ( 270) hydrogen bonds : angle 4.93985 / 3.37 ( 774) link_NAG-ASN : bond 0.00263 / 0.14 ( 9) link_NAG-ASN : angle 1.11718 / 0.72 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7851 (t0) cc_final: 0.7617 (t0) REVERT: A 108 MET cc_start: 0.8745 (ptp) cc_final: 0.8392 (ptp) REVERT: A 166 SER cc_start: 0.7420 (t) cc_final: 0.7156 (m) REVERT: A 276 ARG cc_start: 0.6869 (mtp85) cc_final: 0.6059 (mtm-85) REVERT: B 72 LYS cc_start: 0.7508 (mtmm) cc_final: 0.7185 (mtpp) REVERT: B 164 VAL cc_start: 0.6408 (m) cc_final: 0.6150 (m) REVERT: B 261 ARG cc_start: 0.8368 (ttt-90) cc_final: 0.8063 (ttt-90) REVERT: C 79 THR cc_start: 0.7848 (t) cc_final: 0.7469 (p) REVERT: C 164 VAL cc_start: 0.6219 (m) cc_final: 0.5964 (m) REVERT: C 261 ARG cc_start: 0.8336 (ttt-90) cc_final: 0.8131 (ttt-90) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 0.1017 time to fit residues: 14.0255 Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 7.9990 chunk 75 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 87 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 259 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.185932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121817 restraints weight = 6774.613| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.75 r_work: 0.3161 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7675 Z= 0.127 Angle : 0.544 9.597 10495 Z= 0.284 Chirality : 0.044 0.147 1190 Planarity : 0.004 0.034 1354 Dihedral : 5.007 23.121 1042 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.03 % Allowed : 12.15 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.27), residues: 943 helix: 1.37 (0.43), residues: 183 sheet: 1.43 (0.29), residues: 315 loop : -0.59 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.010 0.001 TYR C 318 PHE 0.009 0.001 PHE B 103 TRP 0.015 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7651) covalent geometry : angle 0.53325 / 0.28 (10438) SS BOND : bond 0.00538 / 0.32 ( 15) SS BOND : angle 1.83230 / 1.16 ( 30) hydrogen bonds : bond 0.03075 / 2.05 ( 270) hydrogen bonds : angle 4.88218 / 3.30 ( 774) link_NAG-ASN : bond 0.00243 / 0.13 ( 9) link_NAG-ASN : angle 1.11580 / 0.73 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7824 (t0) cc_final: 0.7590 (t0) REVERT: A 166 SER cc_start: 0.7337 (t) cc_final: 0.7075 (m) REVERT: A 276 ARG cc_start: 0.6859 (mtp85) cc_final: 0.6035 (mtm-85) REVERT: C 79 THR cc_start: 0.7859 (t) cc_final: 0.7460 (p) REVERT: C 268 MET cc_start: 0.7835 (mmm) cc_final: 0.7594 (mmm) REVERT: C 270 GLN cc_start: 0.7712 (pp30) cc_final: 0.6849 (pm20) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.1031 time to fit residues: 13.0807 Evaluate side-chains 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 221 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.0030 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.186986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122526 restraints weight = 6764.657| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.77 r_work: 0.3191 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7675 Z= 0.111 Angle : 0.525 8.725 10495 Z= 0.274 Chirality : 0.044 0.146 1190 Planarity : 0.004 0.033 1354 Dihedral : 4.891 23.496 1042 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.53 % Allowed : 12.28 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 943 helix: 2.06 (0.45), residues: 165 sheet: 1.45 (0.29), residues: 315 loop : -0.43 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 298 TYR 0.007 0.001 TYR C 216 PHE 0.008 0.001 PHE C 103 TRP 0.015 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 7651) covalent geometry : angle 0.51643 / 0.27 (10438) SS BOND : bond 0.00362 / 0.21 ( 15) SS BOND : angle 1.58986 / 0.94 ( 30) hydrogen bonds : bond 0.02914 / 1.93 ( 270) hydrogen bonds : angle 4.75360 / 3.22 ( 774) link_NAG-ASN : bond 0.00208 / 0.11 ( 9) link_NAG-ASN : angle 1.14839 / 0.76 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7917 (t0) cc_final: 0.7681 (t0) REVERT: A 166 SER cc_start: 0.7364 (t) cc_final: 0.7010 (m) REVERT: A 276 ARG cc_start: 0.7040 (mtp85) cc_final: 0.6133 (mtm-85) REVERT: B 261 ARG cc_start: 0.8365 (ttt-90) cc_final: 0.8103 (ttt-90) REVERT: B 276 ARG cc_start: 0.7501 (mpp80) cc_final: 0.7270 (mtm-85) REVERT: C 79 THR cc_start: 0.7817 (t) cc_final: 0.7396 (p) REVERT: C 268 MET cc_start: 0.7910 (mmm) cc_final: 0.7625 (mmm) outliers start: 20 outliers final: 19 residues processed: 98 average time/residue: 0.1128 time to fit residues: 14.3356 Evaluate side-chains 106 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 202 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.180732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116719 restraints weight = 6726.422| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.71 r_work: 0.3138 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7675 Z= 0.235 Angle : 0.633 8.224 10495 Z= 0.331 Chirality : 0.046 0.135 1190 Planarity : 0.005 0.037 1354 Dihedral : 5.345 22.874 1042 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.29 % Allowed : 12.66 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 943 helix: 1.16 (0.42), residues: 185 sheet: 0.91 (0.29), residues: 330 loop : -0.40 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 224 TYR 0.011 0.002 TYR A 57 PHE 0.018 0.002 PHE A 103 TRP 0.017 0.002 TRP A 272 HIS 0.001 0.000 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.23 ( 7651) covalent geometry : angle 0.62051 / 0.33 (10438) SS BOND : bond 0.00438 / 0.32 ( 15) SS BOND : angle 1.86550 / 1.09 ( 30) hydrogen bonds : bond 0.03614 / 2.42 ( 270) hydrogen bonds : angle 5.02138 / 3.43 ( 774) link_NAG-ASN : bond 0.00431 / 0.22 ( 9) link_NAG-ASN : angle 1.68386 / 1.10 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8143 (t0) cc_final: 0.7907 (t0) REVERT: A 79 THR cc_start: 0.7806 (t) cc_final: 0.7257 (p) REVERT: A 166 SER cc_start: 0.7594 (t) cc_final: 0.7247 (m) REVERT: A 276 ARG cc_start: 0.7192 (mtp85) cc_final: 0.6321 (mtm-85) REVERT: A 286 ASP cc_start: 0.7297 (t70) cc_final: 0.6908 (t0) REVERT: B 164 VAL cc_start: 0.6782 (m) cc_final: 0.6553 (m) REVERT: B 286 ASP cc_start: 0.7498 (t70) cc_final: 0.7079 (t0) REVERT: C 61 ASP cc_start: 0.8142 (t0) cc_final: 0.7928 (t0) REVERT: C 79 THR cc_start: 0.7683 (t) cc_final: 0.7199 (p) REVERT: C 268 MET cc_start: 0.7976 (mmm) cc_final: 0.7623 (mtt) outliers start: 26 outliers final: 17 residues processed: 104 average time/residue: 0.1025 time to fit residues: 14.0481 Evaluate side-chains 102 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 67 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 259 GLN ** 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 = 0.4082 r_free = 0.4082 target = 0.184929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123317 restraints weight = 6693.057| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.55 r_work: 0.3244 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7675 Z= 0.118 Angle : 0.544 7.175 10495 Z= 0.284 Chirality : 0.044 0.146 1190 Planarity : 0.004 0.035 1354 Dihedral : 5.046 23.473 1042 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.53 % Allowed : 15.19 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 943 helix: 1.90 (0.45), residues: 165 sheet: 1.25 (0.29), residues: 311 loop : -0.40 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 261 TYR 0.013 0.001 TYR C 318 PHE 0.009 0.001 PHE C 103 TRP 0.014 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7651) covalent geometry : angle 0.53397 / 0.28 (10438) SS BOND : bond 0.00330 / 0.20 ( 15) SS BOND : angle 1.53136 / 0.87 ( 30) hydrogen bonds : bond 0.03078 / 2.03 ( 270) hydrogen bonds : angle 4.75042 / 3.23 ( 774) link_NAG-ASN : bond 0.00255 / 0.14 ( 9) link_NAG-ASN : angle 1.43239 / 0.96 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7865 (t0) cc_final: 0.7656 (t0) REVERT: A 79 THR cc_start: 0.7765 (t) cc_final: 0.7203 (p) REVERT: A 166 SER cc_start: 0.7467 (t) cc_final: 0.7087 (m) REVERT: A 276 ARG cc_start: 0.7158 (mtp85) cc_final: 0.6297 (mtm-85) REVERT: A 286 ASP cc_start: 0.7342 (t70) cc_final: 0.6984 (t0) REVERT: B 118 LYS cc_start: 0.7447 (mtpt) cc_final: 0.7225 (ttmm) REVERT: B 164 VAL cc_start: 0.6796 (m) cc_final: 0.6560 (m) REVERT: B 276 ARG cc_start: 0.7610 (mpp80) cc_final: 0.7355 (mtm-85) REVERT: B 286 ASP cc_start: 0.7554 (t70) cc_final: 0.7159 (t0) REVERT: C 61 ASP cc_start: 0.7865 (t0) cc_final: 0.7644 (t0) REVERT: C 79 THR cc_start: 0.7641 (t) cc_final: 0.7137 (p) REVERT: C 268 MET cc_start: 0.7978 (mmm) cc_final: 0.7649 (mtt) REVERT: C 286 ASP cc_start: 0.7268 (t70) cc_final: 0.6950 (t0) outliers start: 20 outliers final: 19 residues processed: 106 average time/residue: 0.0924 time to fit residues: 13.1586 Evaluate side-chains 110 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123846 restraints weight = 7010.078| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.66 r_work: 0.3202 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7675 Z= 0.179 Angle : 0.596 10.026 10495 Z= 0.309 Chirality : 0.045 0.141 1190 Planarity : 0.004 0.034 1354 Dihedral : 5.202 29.362 1042 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.54 % Allowed : 13.67 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 943 helix: 1.30 (0.42), residues: 179 sheet: 0.95 (0.29), residues: 322 loop : -0.45 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 276 TYR 0.011 0.001 TYR C 318 PHE 0.014 0.002 PHE B 103 TRP 0.013 0.002 TRP A 272 HIS 0.000 0.000 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 7651) covalent geometry : angle 0.58328 / 0.31 (10438) SS BOND : bond 0.00377 / 0.27 ( 15) SS BOND : angle 1.80519 / 1.03 ( 30) hydrogen bonds : bond 0.03362 / 2.24 ( 270) hydrogen bonds : angle 4.86715 / 3.33 ( 774) link_NAG-ASN : bond 0.00266 / 0.13 ( 9) link_NAG-ASN : angle 1.65714 / 1.10 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7964 (t0) cc_final: 0.7731 (t0) REVERT: A 79 THR cc_start: 0.7724 (t) cc_final: 0.7155 (p) REVERT: A 166 SER cc_start: 0.7541 (t) cc_final: 0.7185 (m) REVERT: A 276 ARG cc_start: 0.7243 (mtp85) cc_final: 0.6416 (mtm-85) REVERT: A 286 ASP cc_start: 0.7428 (t70) cc_final: 0.7066 (t0) REVERT: B 118 LYS cc_start: 0.7393 (mtpt) cc_final: 0.6990 (mttm) REVERT: B 191 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7896 (tp) REVERT: B 276 ARG cc_start: 0.7726 (mpp80) cc_final: 0.7521 (mtm-85) REVERT: B 286 ASP cc_start: 0.7634 (t70) cc_final: 0.7238 (t0) REVERT: C 61 ASP cc_start: 0.7985 (t0) cc_final: 0.7771 (t0) REVERT: C 79 THR cc_start: 0.7658 (t) cc_final: 0.7135 (p) REVERT: C 191 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7881 (tp) REVERT: C 268 MET cc_start: 0.8011 (mmm) cc_final: 0.7664 (mtt) REVERT: C 286 ASP cc_start: 0.7353 (t70) cc_final: 0.7021 (t0) outliers start: 28 outliers final: 20 residues processed: 106 average time/residue: 0.0858 time to fit residues: 12.1921 Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 70 optimal weight: 0.0570 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 92 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.189238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126862 restraints weight = 6872.901| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.68 r_work: 0.3237 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7675 Z= 0.107 Angle : 0.544 8.393 10495 Z= 0.281 Chirality : 0.044 0.145 1190 Planarity : 0.004 0.034 1354 Dihedral : 4.933 28.139 1042 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.53 % Allowed : 15.44 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 943 helix: 1.89 (0.45), residues: 165 sheet: 1.28 (0.29), residues: 312 loop : -0.35 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 261 TYR 0.008 0.001 TYR B 92 PHE 0.010 0.001 PHE C 103 TRP 0.016 0.001 TRP A 167 HIS 0.000 0.000 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7651) covalent geometry : angle 0.53418 / 0.28 (10438) SS BOND : bond 0.00191 / 0.14 ( 15) SS BOND : angle 1.51488 / 0.86 ( 30) hydrogen bonds : bond 0.02965 / 1.96 ( 270) hydrogen bonds : angle 4.69442 / 3.19 ( 774) link_NAG-ASN : bond 0.00244 / 0.14 ( 9) link_NAG-ASN : angle 1.43496 / 0.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7801 (t0) cc_final: 0.7575 (t0) REVERT: A 79 THR cc_start: 0.7757 (t) cc_final: 0.7175 (p) REVERT: A 166 SER cc_start: 0.7446 (t) cc_final: 0.7065 (m) REVERT: A 276 ARG cc_start: 0.7160 (mtp85) cc_final: 0.6286 (mtm-85) REVERT: A 286 ASP cc_start: 0.7399 (t70) cc_final: 0.7028 (t0) REVERT: B 118 LYS cc_start: 0.7326 (mtpt) cc_final: 0.7071 (mttp) REVERT: B 286 ASP cc_start: 0.7547 (t70) cc_final: 0.7170 (t0) REVERT: C 61 ASP cc_start: 0.7838 (t0) cc_final: 0.7632 (t0) REVERT: C 79 THR cc_start: 0.7662 (t) cc_final: 0.7110 (p) REVERT: C 147 VAL cc_start: 0.8202 (m) cc_final: 0.7876 (p) REVERT: C 268 MET cc_start: 0.7993 (mmm) cc_final: 0.7644 (mtt) REVERT: C 286 ASP cc_start: 0.7300 (t70) cc_final: 0.6979 (t0) REVERT: C 288 ASP cc_start: 0.8161 (m-30) cc_final: 0.7455 (t70) outliers start: 20 outliers final: 18 residues processed: 106 average time/residue: 0.0847 time to fit residues: 12.1954 Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124212 restraints weight = 6828.260| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.63 r_work: 0.3237 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7675 Z= 0.188 Angle : 0.608 7.960 10495 Z= 0.315 Chirality : 0.045 0.148 1190 Planarity : 0.004 0.033 1354 Dihedral : 5.164 27.947 1042 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.78 % Allowed : 15.19 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.27), residues: 943 helix: 1.10 (0.42), residues: 185 sheet: 0.81 (0.29), residues: 330 loop : -0.47 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 261 TYR 0.011 0.001 TYR C 318 PHE 0.015 0.002 PHE B 103 TRP 0.014 0.002 TRP B 272 HIS 0.000 0.000 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 7651) covalent geometry : angle 0.59545 / 0.31 (10438) SS BOND : bond 0.00381 / 0.28 ( 15) SS BOND : angle 1.78045 / 1.02 ( 30) hydrogen bonds : bond 0.03368 / 2.23 ( 270) hydrogen bonds : angle 4.80029 / 3.28 ( 774) link_NAG-ASN : bond 0.00302 / 0.16 ( 9) link_NAG-ASN : angle 1.71292 / 1.14 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7942 (t0) cc_final: 0.7714 (t0) REVERT: A 79 THR cc_start: 0.7818 (t) cc_final: 0.7196 (p) REVERT: A 166 SER cc_start: 0.7621 (t) cc_final: 0.7232 (m) REVERT: A 276 ARG cc_start: 0.7229 (mtp85) cc_final: 0.6460 (mtm-85) REVERT: A 286 ASP cc_start: 0.7522 (t70) cc_final: 0.7200 (t0) REVERT: A 288 ASP cc_start: 0.8162 (m-30) cc_final: 0.7636 (t70) REVERT: B 118 LYS cc_start: 0.7562 (mtpt) cc_final: 0.7244 (mttp) REVERT: B 256 MET cc_start: 0.8317 (tpp) cc_final: 0.7988 (mtp) REVERT: B 286 ASP cc_start: 0.7651 (t70) cc_final: 0.7297 (t0) REVERT: B 288 ASP cc_start: 0.8173 (m-30) cc_final: 0.7594 (t70) REVERT: C 61 ASP cc_start: 0.7973 (t0) cc_final: 0.7758 (t0) REVERT: C 79 THR cc_start: 0.7729 (t) cc_final: 0.7127 (p) REVERT: C 147 VAL cc_start: 0.8530 (m) cc_final: 0.8139 (p) REVERT: C 268 MET cc_start: 0.8041 (mmm) cc_final: 0.7807 (mmm) REVERT: C 286 ASP cc_start: 0.7401 (t70) cc_final: 0.7107 (t0) REVERT: C 288 ASP cc_start: 0.8163 (m-30) cc_final: 0.7536 (t70) outliers start: 22 outliers final: 19 residues processed: 103 average time/residue: 0.0751 time to fit residues: 10.5115 Evaluate side-chains 106 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 CYS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 278 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 0.0170 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.188639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126697 restraints weight = 6887.791| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.63 r_work: 0.3261 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7675 Z= 0.115 Angle : 0.550 8.299 10495 Z= 0.284 Chirality : 0.044 0.144 1190 Planarity : 0.004 0.034 1354 Dihedral : 4.923 27.615 1042 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.28 % Allowed : 15.32 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 943 helix: 1.90 (0.45), residues: 165 sheet: 1.25 (0.29), residues: 312 loop : -0.34 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 261 TYR 0.007 0.001 TYR B 92 PHE 0.010 0.001 PHE C 103 TRP 0.015 0.001 TRP A 167 HIS 0.000 0.000 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 7651) covalent geometry : angle 0.54011 / 0.28 (10438) SS BOND : bond 0.00231 / 0.17 ( 15) SS BOND : angle 1.50342 / 0.86 ( 30) hydrogen bonds : bond 0.02988 / 1.98 ( 270) hydrogen bonds : angle 4.64786 / 3.15 ( 774) link_NAG-ASN : bond 0.00231 / 0.13 ( 9) link_NAG-ASN : angle 1.48360 / 1.00 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.84 seconds wall clock time: 34 minutes 54.14 seconds (2094.14 seconds total)