Starting phenix.real_space_refine on Fri Aug 22 19:59:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jv5_36668/08_2025/8jv5_36668.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jv5_36668/08_2025/8jv5_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jv5_36668/08_2025/8jv5_36668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jv5_36668/08_2025/8jv5_36668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jv5_36668/08_2025/8jv5_36668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jv5_36668/08_2025/8jv5_36668.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.91, per 1000 atoms: 0.26 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: 0.44 Conformation dependent library (CDL) restraints added in 267.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.18 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: 0.90 Time building geometry restraints manager: 0.60 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: 4215 15.23 - 30.47: 341 30.47 - 45.70: 80 45.70 - 60.94: 24 60.94 - 76.17: 12 Dihedral angle restraints: 4672 sinusoidal: 1927 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 4669 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: 1.470 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.140 Find NCS groups from input model: 0.080 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 12.601 76.169 2867 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 aren 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 covalent geometry : bond 0.00486 ( 7651) covalent geometry : angle 0.62938 (10438) SS BOND : bond 0.00306 ( 15) SS BOND : angle 1.44619 ( 30) hydrogen bonds : bond 0.12802 ( 270) hydrogen bonds : angle 5.68562 ( 774) link_NAG-ASN : bond 0.00248 ( 9) link_NAG-ASN : angle 1.10061 ( 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 : 0.242 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: 0.1084 time to fit residues: 21.4288 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 : 0.273 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 247 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 270 GLN ** 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 = 0.4119 r_free = 0.4119 target = 0.189910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126322 restraints weight = 7079.948| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.68 r_work: 0.3239 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7675 Z= 0.123 Angle : 0.553 6.505 10495 Z= 0.289 Chirality : 0.045 0.153 1190 Planarity : 0.004 0.036 1354 Dihedral : 7.087 56.128 1231 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.63 % Allowed : 9.62 % Favored : 89.75 % 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 aren 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 : -0.33 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 281 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 covalent geometry : bond 0.00280 ( 7651) covalent geometry : angle 0.54630 (10438) SS BOND : bond 0.00276 ( 15) SS BOND : angle 1.52871 ( 30) hydrogen bonds : bond 0.03432 ( 270) hydrogen bonds : angle 4.92072 ( 774) link_NAG-ASN : bond 0.00314 ( 9) link_NAG-ASN : angle 0.83763 ( 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 110 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7680 (t0) cc_final: 0.7441 (t0) REVERT: A 72 LYS cc_start: 0.7548 (mtmm) cc_final: 0.7282 (mtpp) REVERT: A 200 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8220 (ttmm) REVERT: A 276 ARG cc_start: 0.6714 (mtp85) cc_final: 0.5968 (mtm-85) REVERT: B 72 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7233 (mtpp) REVERT: B 301 LYS cc_start: 0.8423 (mttm) cc_final: 0.8160 (mttm) REVERT: C 261 ARG cc_start: 0.8329 (ttt-90) cc_final: 0.8027 (ttt180) outliers start: 5 outliers final: 4 residues processed: 106 average time/residue: 0.1230 time to fit residues: 16.5336 Evaluate side-chains 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 0.0270 chunk 39 optimal weight: 30.0000 chunk 27 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** 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 = 0.4127 r_free = 0.4127 target = 0.190273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127524 restraints weight = 6960.217| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.64 r_work: 0.3253 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7675 Z= 0.110 Angle : 0.521 7.816 10495 Z= 0.271 Chirality : 0.044 0.149 1190 Planarity : 0.004 0.033 1354 Dihedral : 6.813 58.833 1231 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.28 % Allowed : 9.75 % Favored : 87.97 % 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 aren not related in a simple way. whole: 0.89 (0.27), residues: 943 helix: 1.55 (0.43), residues: 183 sheet: 1.52 (0.29), residues: 322 loop : -0.56 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.007 0.001 TYR C 318 PHE 0.007 0.001 PHE C 102 TRP 0.012 0.002 TRP B 167 HIS 0.000 0.000 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7651) covalent geometry : angle 0.51518 (10438) SS BOND : bond 0.00386 ( 15) SS BOND : angle 1.35909 ( 30) hydrogen bonds : bond 0.03083 ( 270) hydrogen bonds : angle 4.83165 ( 774) link_NAG-ASN : bond 0.00263 ( 9) link_NAG-ASN : angle 0.92278 ( 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 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7645 (t0) cc_final: 0.7404 (t0) REVERT: A 200 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8203 (ttmm) REVERT: A 276 ARG cc_start: 0.6754 (mtp85) cc_final: 0.5976 (mtm-85) REVERT: B 72 LYS cc_start: 0.7533 (mtmm) cc_final: 0.7280 (mtpp) REVERT: B 261 ARG cc_start: 0.8271 (ttt-90) cc_final: 0.7897 (ttt-90) REVERT: C 268 MET cc_start: 0.7716 (mmm) cc_final: 0.7439 (mmm) outliers start: 18 outliers final: 11 residues processed: 99 average time/residue: 0.1141 time to fit residues: 14.3163 Evaluate side-chains 95 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 227 ASP 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 168 CYS Chi-restraints excluded: chain B residue 221 VAL 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: 4.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 87 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.185385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119899 restraints weight = 6894.919| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.84 r_work: 0.3112 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7675 Z= 0.183 Angle : 0.596 10.181 10495 Z= 0.310 Chirality : 0.046 0.151 1190 Planarity : 0.004 0.033 1354 Dihedral : 6.373 52.206 1231 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.15 % Allowed : 12.15 % Favored : 85.70 % 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 aren not related in a simple way. whole: 0.57 (0.27), residues: 943 helix: 1.31 (0.43), residues: 183 sheet: 1.01 (0.29), residues: 336 loop : -0.52 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 298 TYR 0.012 0.002 TYR A 318 PHE 0.016 0.002 PHE B 103 TRP 0.020 0.002 TRP A 167 HIS 0.001 0.000 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 7651) covalent geometry : angle 0.58596 (10438) SS BOND : bond 0.00406 ( 15) SS BOND : angle 1.68039 ( 30) hydrogen bonds : bond 0.03411 ( 270) hydrogen bonds : angle 4.96294 ( 774) link_NAG-ASN : bond 0.00296 ( 9) link_NAG-ASN : angle 1.47231 ( 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 114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8063 (t0) cc_final: 0.7824 (t0) REVERT: A 108 MET cc_start: 0.8858 (ptp) cc_final: 0.8511 (ptp) REVERT: A 164 VAL cc_start: 0.6194 (m) cc_final: 0.5863 (m) REVERT: A 166 SER cc_start: 0.7449 (t) cc_final: 0.7169 (m) REVERT: A 276 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6269 (mtm-85) REVERT: B 84 GLU cc_start: 0.7562 (tp30) cc_final: 0.7333 (pm20) REVERT: B 164 VAL cc_start: 0.6728 (m) cc_final: 0.6445 (m) REVERT: B 261 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.7994 (ttt-90) REVERT: C 61 ASP cc_start: 0.8048 (t0) cc_final: 0.7823 (t0) REVERT: C 79 THR cc_start: 0.7829 (t) cc_final: 0.7386 (p) REVERT: C 268 MET cc_start: 0.7943 (mmm) cc_final: 0.7639 (mmm) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 0.1101 time to fit residues: 14.8296 Evaluate side-chains 109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 86 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4027 r_free = 0.4027 target = 0.181597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118010 restraints weight = 6743.091| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.71 r_work: 0.3144 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7675 Z= 0.154 Angle : 0.572 9.987 10495 Z= 0.298 Chirality : 0.045 0.158 1190 Planarity : 0.004 0.034 1354 Dihedral : 5.985 44.207 1231 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.16 % Allowed : 12.66 % Favored : 84.18 % 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 aren not related in a simple way. whole: 0.63 (0.27), residues: 943 helix: 1.42 (0.43), residues: 177 sheet: 1.09 (0.29), residues: 319 loop : -0.47 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 261 TYR 0.011 0.001 TYR C 318 PHE 0.011 0.001 PHE B 103 TRP 0.013 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7651) covalent geometry : angle 0.55857 (10438) SS BOND : bond 0.00446 ( 15) SS BOND : angle 1.97335 ( 30) hydrogen bonds : bond 0.03228 ( 270) hydrogen bonds : angle 4.92135 ( 774) link_NAG-ASN : bond 0.00216 ( 9) link_NAG-ASN : angle 1.45405 ( 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 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8012 (t0) cc_final: 0.7785 (t0) REVERT: A 108 MET cc_start: 0.8781 (ptp) cc_final: 0.8451 (ptp) REVERT: A 166 SER cc_start: 0.7447 (t) cc_final: 0.7124 (m) REVERT: A 276 ARG cc_start: 0.7146 (mtp85) cc_final: 0.6203 (mtm-85) REVERT: A 286 ASP cc_start: 0.7218 (t70) cc_final: 0.6823 (t0) REVERT: B 164 VAL cc_start: 0.6527 (m) cc_final: 0.6326 (m) REVERT: B 276 ARG cc_start: 0.7592 (mtm180) cc_final: 0.7386 (mtm-85) REVERT: B 286 ASP cc_start: 0.7326 (t70) cc_final: 0.6914 (t0) REVERT: C 61 ASP cc_start: 0.8030 (t0) cc_final: 0.7807 (t0) REVERT: C 79 THR cc_start: 0.7700 (t) cc_final: 0.7253 (p) REVERT: C 84 GLU cc_start: 0.7679 (tt0) cc_final: 0.7404 (pm20) REVERT: C 268 MET cc_start: 0.7938 (mmm) cc_final: 0.7684 (mmm) outliers start: 25 outliers final: 18 residues processed: 107 average time/residue: 0.1004 time to fit residues: 14.0809 Evaluate side-chains 109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 165 LEU 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 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 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: 0.0020 chunk 39 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117834 restraints weight = 6694.497| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.73 r_work: 0.3135 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7675 Z= 0.171 Angle : 0.593 9.686 10495 Z= 0.309 Chirality : 0.045 0.155 1190 Planarity : 0.004 0.033 1354 Dihedral : 5.745 37.278 1231 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.04 % Allowed : 13.42 % Favored : 83.54 % 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 aren not related in a simple way. whole: 0.59 (0.27), residues: 943 helix: 1.39 (0.43), residues: 179 sheet: 0.96 (0.29), residues: 322 loop : -0.42 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 261 TYR 0.011 0.001 TYR C 318 PHE 0.013 0.002 PHE B 103 TRP 0.013 0.002 TRP A 272 HIS 0.000 0.000 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 7651) covalent geometry : angle 0.58052 (10438) SS BOND : bond 0.00424 ( 15) SS BOND : angle 1.86884 ( 30) hydrogen bonds : bond 0.03334 ( 270) hydrogen bonds : angle 4.98242 ( 774) link_NAG-ASN : bond 0.00241 ( 9) link_NAG-ASN : angle 1.57812 ( 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 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8029 (t0) cc_final: 0.7809 (t0) REVERT: A 79 THR cc_start: 0.7755 (t) cc_final: 0.7216 (p) REVERT: A 166 SER cc_start: 0.7421 (t) cc_final: 0.7089 (m) REVERT: A 276 ARG cc_start: 0.7170 (mtp85) cc_final: 0.6260 (mtm-85) REVERT: A 286 ASP cc_start: 0.7271 (t70) cc_final: 0.6862 (t0) REVERT: B 118 LYS cc_start: 0.7470 (mtpt) cc_final: 0.7177 (ttmm) REVERT: B 164 VAL cc_start: 0.6724 (m) cc_final: 0.6506 (m) REVERT: B 286 ASP cc_start: 0.7405 (t70) cc_final: 0.6941 (t0) REVERT: C 61 ASP cc_start: 0.8102 (t0) cc_final: 0.7874 (t0) REVERT: C 79 THR cc_start: 0.7650 (t) cc_final: 0.7153 (p) REVERT: C 84 GLU cc_start: 0.7756 (tt0) cc_final: 0.7482 (pm20) REVERT: C 268 MET cc_start: 0.7977 (mmm) cc_final: 0.7678 (mtt) REVERT: C 286 ASP cc_start: 0.7181 (t70) cc_final: 0.6832 (t0) outliers start: 24 outliers final: 18 residues processed: 106 average time/residue: 0.0777 time to fit residues: 11.0920 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 : 0.201 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.184891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123422 restraints weight = 6693.143| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.55 r_work: 0.3234 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2569 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= 0.119 Angle : 0.546 9.108 10495 Z= 0.285 Chirality : 0.044 0.159 1190 Planarity : 0.004 0.034 1354 Dihedral : 5.253 27.496 1231 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.53 % Allowed : 13.92 % Favored : 83.54 % 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 aren not related in a simple way. whole: 0.86 (0.27), residues: 943 helix: 1.92 (0.45), residues: 165 sheet: 1.22 (0.29), residues: 314 loop : -0.37 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 261 TYR 0.012 0.001 TYR C 318 PHE 0.010 0.001 PHE C 103 TRP 0.015 0.002 TRP A 167 HIS 0.000 0.000 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7651) covalent geometry : angle 0.53642 (10438) SS BOND : bond 0.00366 ( 15) SS BOND : angle 1.54556 ( 30) hydrogen bonds : bond 0.03049 ( 270) hydrogen bonds : angle 4.76113 ( 774) link_NAG-ASN : bond 0.00236 ( 9) link_NAG-ASN : angle 1.41261 ( 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 114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7821 (t0) cc_final: 0.7595 (t0) REVERT: A 79 THR cc_start: 0.7784 (t) cc_final: 0.7206 (p) REVERT: A 108 MET cc_start: 0.8725 (ptp) cc_final: 0.8406 (ptp) REVERT: A 166 SER cc_start: 0.7417 (t) cc_final: 0.7090 (m) REVERT: A 276 ARG cc_start: 0.7155 (mtp85) cc_final: 0.6297 (mtm-85) REVERT: A 286 ASP cc_start: 0.7302 (t70) cc_final: 0.6931 (t0) REVERT: B 286 ASP cc_start: 0.7559 (t70) cc_final: 0.7161 (t0) REVERT: C 61 ASP cc_start: 0.7854 (t0) cc_final: 0.7649 (t0) REVERT: C 79 THR cc_start: 0.7687 (t) cc_final: 0.7178 (p) REVERT: C 84 GLU cc_start: 0.7699 (tt0) cc_final: 0.7479 (pm20) REVERT: C 268 MET cc_start: 0.8034 (mmm) cc_final: 0.7739 (mtt) REVERT: C 286 ASP cc_start: 0.7236 (t70) cc_final: 0.6907 (t0) outliers start: 20 outliers final: 17 residues processed: 103 average time/residue: 0.0971 time to fit residues: 13.3298 Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 325 MET 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 196 ILE Chi-restraints excluded: chain C residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.186983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123881 restraints weight = 6995.928| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.68 r_work: 0.3193 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7675 Z= 0.198 Angle : 0.604 9.240 10495 Z= 0.316 Chirality : 0.046 0.152 1190 Planarity : 0.004 0.034 1354 Dihedral : 5.296 24.884 1231 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.04 % Allowed : 13.67 % Favored : 83.29 % 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 aren not related in a simple way. whole: 0.52 (0.27), residues: 943 helix: 1.24 (0.42), residues: 179 sheet: 0.93 (0.29), residues: 322 loop : -0.44 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.011 0.001 TYR C 318 PHE 0.016 0.002 PHE B 103 TRP 0.015 0.002 TRP C 87 HIS 0.000 0.000 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 7651) covalent geometry : angle 0.59276 (10438) SS BOND : bond 0.00405 ( 15) SS BOND : angle 1.69437 ( 30) hydrogen bonds : bond 0.03463 ( 270) hydrogen bonds : angle 4.88144 ( 774) link_NAG-ASN : bond 0.00297 ( 9) link_NAG-ASN : angle 1.68886 ( 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 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7978 (t0) cc_final: 0.7748 (t0) REVERT: A 79 THR cc_start: 0.7762 (t) cc_final: 0.7153 (p) REVERT: A 108 MET cc_start: 0.8840 (ptp) cc_final: 0.8515 (ptp) REVERT: A 166 SER cc_start: 0.7564 (t) cc_final: 0.7234 (m) REVERT: A 276 ARG cc_start: 0.7259 (mtp85) cc_final: 0.6417 (mtm-85) REVERT: A 286 ASP cc_start: 0.7423 (t70) cc_final: 0.7049 (t0) REVERT: B 191 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7913 (tp) REVERT: B 286 ASP cc_start: 0.7618 (t70) cc_final: 0.7203 (t0) REVERT: C 61 ASP cc_start: 0.8008 (t0) cc_final: 0.7790 (t0) REVERT: C 79 THR cc_start: 0.7665 (t) cc_final: 0.7125 (p) REVERT: C 84 GLU cc_start: 0.7778 (tt0) cc_final: 0.7545 (pm20) REVERT: C 191 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7862 (tp) REVERT: C 268 MET cc_start: 0.8038 (mmm) cc_final: 0.7753 (mtt) REVERT: C 286 ASP cc_start: 0.7369 (t70) cc_final: 0.7028 (t0) outliers start: 24 outliers final: 18 residues processed: 104 average time/residue: 0.1064 time to fit residues: 14.6550 Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 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 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 214 SER 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 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: 1.9990 chunk 51 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 5 optimal weight: 0.0570 chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.187905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126081 restraints weight = 6738.453| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.60 r_work: 0.3272 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7675 Z= 0.105 Angle : 0.552 10.315 10495 Z= 0.284 Chirality : 0.044 0.152 1190 Planarity : 0.004 0.035 1354 Dihedral : 4.803 24.657 1231 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.28 % Allowed : 15.19 % Favored : 82.53 % 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 aren not related in a simple way. whole: 0.94 (0.27), residues: 943 helix: 1.91 (0.45), residues: 165 sheet: 1.38 (0.29), residues: 309 loop : -0.36 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 276 TYR 0.008 0.001 TYR A 92 PHE 0.011 0.001 PHE C 103 TRP 0.016 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7651) covalent geometry : angle 0.54476 (10438) SS BOND : bond 0.00220 ( 15) SS BOND : angle 1.35922 ( 30) hydrogen bonds : bond 0.02924 ( 270) hydrogen bonds : angle 4.65612 ( 774) link_NAG-ASN : bond 0.00290 ( 9) link_NAG-ASN : angle 1.31213 ( 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 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7756 (t0) cc_final: 0.7541 (t0) REVERT: A 79 THR cc_start: 0.7737 (t) cc_final: 0.7124 (p) REVERT: A 166 SER cc_start: 0.7476 (t) cc_final: 0.7133 (m) REVERT: A 207 ASN cc_start: 0.7972 (p0) cc_final: 0.7538 (p0) REVERT: A 276 ARG cc_start: 0.7097 (mtp85) cc_final: 0.6247 (mtm-85) REVERT: A 286 ASP cc_start: 0.7367 (t70) cc_final: 0.7030 (t0) REVERT: B 286 ASP cc_start: 0.7536 (t70) cc_final: 0.7152 (t0) REVERT: C 61 ASP cc_start: 0.7785 (t0) cc_final: 0.7577 (t0) REVERT: C 79 THR cc_start: 0.7709 (t) cc_final: 0.7146 (p) REVERT: C 268 MET cc_start: 0.8010 (mmm) cc_final: 0.7729 (mtt) REVERT: C 286 ASP cc_start: 0.7283 (t70) cc_final: 0.6976 (t0) REVERT: C 288 ASP cc_start: 0.8084 (m-30) cc_final: 0.7456 (t70) outliers start: 18 outliers final: 15 residues processed: 105 average time/residue: 0.1102 time to fit residues: 15.0634 Evaluate side-chains 106 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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 C residue 129 CYS Chi-restraints excluded: chain C residue 152 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: 0.0020 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.185559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124335 restraints weight = 6580.934| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.54 r_work: 0.3255 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7675 Z= 0.117 Angle : 0.559 8.407 10495 Z= 0.289 Chirality : 0.044 0.151 1190 Planarity : 0.004 0.047 1354 Dihedral : 4.725 24.086 1231 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.28 % Allowed : 15.44 % 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 aren not related in a simple way. whole: 0.96 (0.28), residues: 943 helix: 1.92 (0.45), residues: 165 sheet: 1.35 (0.29), residues: 310 loop : -0.33 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 261 TYR 0.008 0.001 TYR C 318 PHE 0.010 0.001 PHE C 103 TRP 0.014 0.002 TRP A 167 HIS 0.000 0.000 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7651) covalent geometry : angle 0.55117 (10438) SS BOND : bond 0.00235 ( 15) SS BOND : angle 1.39663 ( 30) hydrogen bonds : bond 0.02931 ( 270) hydrogen bonds : angle 4.59338 ( 774) link_NAG-ASN : bond 0.00219 ( 9) link_NAG-ASN : angle 1.40636 ( 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 110 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7768 (t0) cc_final: 0.7546 (t0) REVERT: A 79 THR cc_start: 0.7728 (t) cc_final: 0.7109 (p) REVERT: A 166 SER cc_start: 0.7380 (t) cc_final: 0.7014 (m) REVERT: A 276 ARG cc_start: 0.7134 (mtp85) cc_final: 0.6274 (mtm-85) REVERT: A 286 ASP cc_start: 0.7389 (t70) cc_final: 0.7036 (t0) REVERT: B 286 ASP cc_start: 0.7577 (t70) cc_final: 0.7179 (t0) REVERT: C 61 ASP cc_start: 0.7819 (t0) cc_final: 0.7612 (t0) REVERT: C 79 THR cc_start: 0.7644 (t) cc_final: 0.7105 (p) REVERT: C 268 MET cc_start: 0.8004 (mmm) cc_final: 0.7790 (mmm) REVERT: C 286 ASP cc_start: 0.7302 (t70) cc_final: 0.6971 (t0) REVERT: C 288 ASP cc_start: 0.8160 (m-30) cc_final: 0.7492 (t70) outliers start: 18 outliers final: 16 residues processed: 100 average time/residue: 0.1053 time to fit residues: 13.8933 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 : 0.297 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 152 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 84 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.0000 chunk 35 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.188880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126469 restraints weight = 6878.545| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.64 r_work: 0.3255 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7675 Z= 0.125 Angle : 0.561 8.589 10495 Z= 0.289 Chirality : 0.044 0.146 1190 Planarity : 0.004 0.044 1354 Dihedral : 4.722 23.845 1231 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.53 % Allowed : 15.06 % 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 aren not related in a simple way. whole: 0.93 (0.28), residues: 943 helix: 1.89 (0.45), residues: 165 sheet: 1.21 (0.29), residues: 316 loop : -0.24 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.009 0.001 TYR C 318 PHE 0.010 0.001 PHE C 103 TRP 0.015 0.002 TRP B 262 HIS 0.000 0.000 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7651) covalent geometry : angle 0.55206 (10438) SS BOND : bond 0.00274 ( 15) SS BOND : angle 1.44398 ( 30) hydrogen bonds : bond 0.03006 ( 270) hydrogen bonds : angle 4.58032 ( 774) link_NAG-ASN : bond 0.00190 ( 9) link_NAG-ASN : angle 1.46470 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.18 seconds wall clock time: 36 minutes 26.23 seconds (2186.23 seconds total)