Starting phenix.real_space_refine on Wed Sep 17 19:09:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vt2_43516/09_2025/8vt2_43516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vt2_43516/09_2025/8vt2_43516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vt2_43516/09_2025/8vt2_43516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vt2_43516/09_2025/8vt2_43516.map" model { file = "/net/cci-nas-00/data/ceres_data/8vt2_43516/09_2025/8vt2_43516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vt2_43516/09_2025/8vt2_43516.cif" } resolution = 3.14 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= 0.055 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6678 2.51 5 N 1818 2.21 5 O 2115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10674 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3477 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3477 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain breaks: 1 Chain: "C" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3477 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.49, per 1000 atoms: 0.23 Number of scatterers: 10674 At special positions: 0 Unit cell: (83.424, 87.216, 133.668, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2115 8.00 N 1818 7.00 C 6678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 353 " " NAG B 501 " - " ASN B 353 " " NAG D 1 " - " ASN A 172 " " NAG E 1 " - " ASN A 57 " " NAG F 1 " - " ASN B 172 " " NAG G 1 " - " ASN B 57 " " NAG H 1 " - " ASN C 172 " " NAG I 1 " - " ASN C 57 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 442.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 36.7% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.653A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.734A pdb=" N ALA A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.846A pdb=" N THR A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.558A pdb=" N ASP A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.521A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.638A pdb=" N ASN A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.720A pdb=" N CYS A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.899A pdb=" N GLY A 340 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.871A pdb=" N LYS A 348 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 460 through 480 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.653A pdb=" N THR B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.836A pdb=" N ALA B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.840A pdb=" N THR B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.645A pdb=" N ASP B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.536A pdb=" N ALA B 176 " --> pdb=" O ASN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 removed outlier: 3.535A pdb=" N VAL B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 210 removed outlier: 3.639A pdb=" N ASN B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 344 through 350 removed outlier: 3.885A pdb=" N LYS B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS B 350 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 480 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 66 through 81 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.916A pdb=" N ALA C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.663A pdb=" N ALA C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.676A pdb=" N ASN C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 344 through 350 removed outlier: 3.898A pdb=" N CYS C 350 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.766A pdb=" N PHE C 446 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 480 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 removed outlier: 7.138A pdb=" N SER A 29 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 288 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 31 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 286 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU A 33 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TRP A 284 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR A 35 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER A 37 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 320 current: chain 'A' and resid 332 through 334 Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 150 removed outlier: 9.421A pdb=" N TRP A 43 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N LEU A 158 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR A 45 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR A 160 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL A 162 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 49 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 257 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AA5, first strand: chain 'A' and resid 399 through 402 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 24 removed outlier: 7.183A pdb=" N SER B 29 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 288 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 31 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 286 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU B 33 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TRP B 284 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYR B 35 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER B 37 " --> pdb=" O ASP B 280 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 278 " --> pdb=" O LEU B 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 316 through 320 current: chain 'B' and resid 332 through 336 Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 150 removed outlier: 8.307A pdb=" N ARG B 156 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N THR B 45 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 257 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 295 Processing sheet with id=AA9, first strand: chain 'B' and resid 372 through 376 Processing sheet with id=AB1, first strand: chain 'B' and resid 399 through 402 Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 29 through 51 current: chain 'C' and resid 156 through 162 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 156 through 162 current: chain 'C' and resid 256 through 263 removed outlier: 6.702A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 320 current: chain 'C' and resid 332 through 336 Processing sheet with id=AB3, first strand: chain 'C' and resid 291 through 295 removed outlier: 7.522A pdb=" N THR C 365 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE C 456 " --> pdb=" O THR C 365 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AB5, first strand: chain 'C' and resid 399 through 402 493 hydrogen bonds defined for protein. 1290 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: 1.31 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2943 1.33 - 1.45: 1680 1.45 - 1.57: 6115 1.57 - 1.69: 2 1.69 - 1.81: 84 Bond restraints: 10824 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.59e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" CB THR C 160 " pdb=" CG2 THR C 160 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.29e+00 bond pdb=" CB THR A 160 " pdb=" CG2 THR A 160 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.98e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 ... (remaining 10819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 13767 1.77 - 3.54: 736 3.54 - 5.30: 125 5.30 - 7.07: 24 7.07 - 8.84: 9 Bond angle restraints: 14661 Sorted by residual: angle pdb=" N ILE A 420 " pdb=" CA ILE A 420 " pdb=" C ILE A 420 " ideal model delta sigma weight residual 109.46 103.74 5.72 1.38e+00 5.25e-01 1.72e+01 angle pdb=" N ILE C 352 " pdb=" CA ILE C 352 " pdb=" C ILE C 352 " ideal model delta sigma weight residual 112.12 109.00 3.12 8.40e-01 1.42e+00 1.38e+01 angle pdb=" N ARG A 248 " pdb=" CA ARG A 248 " pdb=" C ARG A 248 " ideal model delta sigma weight residual 110.80 118.22 -7.42 2.13e+00 2.20e-01 1.21e+01 angle pdb=" N ARG C 248 " pdb=" CA ARG C 248 " pdb=" C ARG C 248 " ideal model delta sigma weight residual 110.80 118.06 -7.26 2.13e+00 2.20e-01 1.16e+01 angle pdb=" C THR C 411 " pdb=" N ASN C 412 " pdb=" CA ASN C 412 " ideal model delta sigma weight residual 122.56 116.85 5.71 1.72e+00 3.38e-01 1.10e+01 ... (remaining 14656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 6360 21.72 - 43.43: 352 43.43 - 65.15: 76 65.15 - 86.86: 29 86.86 - 108.58: 14 Dihedral angle restraints: 6831 sinusoidal: 2886 harmonic: 3945 Sorted by residual: dihedral pdb=" CA ILE A 420 " pdb=" C ILE A 420 " pdb=" N ASP A 421 " pdb=" CA ASP A 421 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ILE B 420 " pdb=" C ILE B 420 " pdb=" N ASP B 421 " pdb=" CA ASP B 421 " ideal model delta harmonic sigma weight residual 180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE C 420 " pdb=" C ILE C 420 " pdb=" N ASP C 421 " pdb=" CA ASP C 421 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 6828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1753 0.140 - 0.279: 27 0.279 - 0.419: 3 0.419 - 0.558: 0 0.558 - 0.698: 1 Chirality restraints: 1784 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CB THR C 357 " pdb=" CA THR C 357 " pdb=" OG1 THR C 357 " pdb=" CG2 THR C 357 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB THR A 357 " pdb=" CA THR A 357 " pdb=" OG1 THR A 357 " pdb=" CG2 THR A 357 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1781 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 193 " 0.021 2.00e-02 2.50e+03 2.58e-02 1.16e+01 pdb=" CG PHE C 193 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE C 193 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE C 193 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 193 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 193 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 193 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 193 " 0.021 2.00e-02 2.50e+03 2.57e-02 1.15e+01 pdb=" CG PHE A 193 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 193 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 193 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 193 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 193 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 193 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 63 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO C 64 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.028 5.00e-02 4.00e+02 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 439 2.70 - 3.25: 9958 3.25 - 3.80: 15146 3.80 - 4.35: 20625 4.35 - 4.90: 36543 Nonbonded interactions: 82711 Sorted by model distance: nonbonded pdb=" OG1 THR C 45 " pdb=" OE1 GLN C 272 " model vdw 2.144 3.040 nonbonded pdb=" O ASP C 62 " pdb=" O6 BMA F 3 " model vdw 2.145 3.040 nonbonded pdb=" OE2 GLU B 305 " pdb=" OG SER B 364 " model vdw 2.149 3.040 nonbonded pdb=" OE2 GLU A 305 " pdb=" OG SER A 364 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR B 45 " pdb=" OE1 GLN B 272 " model vdw 2.162 3.040 ... (remaining 82706 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 1.100 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: 0.030 Set scattering table: 0.030 Process input model: 10.820 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.014 0.086 10842 Z= 0.541 Angle : 1.005 16.152 14714 Z= 0.521 Chirality : 0.064 0.698 1784 Planarity : 0.006 0.049 1857 Dihedral : 15.923 108.580 4278 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.22), residues: 1350 helix: 0.14 (0.25), residues: 408 sheet: -0.02 (0.28), residues: 345 loop : -2.13 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 205 TYR 0.022 0.004 TYR C 310 PHE 0.059 0.003 PHE C 193 TRP 0.026 0.003 TRP B 473 HIS 0.005 0.002 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.01359 (10824) covalent geometry : angle 0.95679 (14661) SS BOND : bond 0.00041 ( 1) SS BOND : angle 1.28619 ( 2) hydrogen bonds : bond 0.16599 ( 493) hydrogen bonds : angle 6.19945 ( 1290) link_BETA1-4 : bond 0.01285 ( 9) link_BETA1-4 : angle 2.78815 ( 27) link_NAG-ASN : bond 0.01553 ( 8) link_NAG-ASN : angle 7.15470 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.7987 (p0) cc_final: 0.7681 (p0) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1567 time to fit residues: 21.7740 Evaluate side-chains 92 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN B 206 GLN B 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.093928 restraints weight = 11740.801| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.41 r_work: 0.2937 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10842 Z= 0.140 Angle : 0.685 16.409 14714 Z= 0.332 Chirality : 0.048 0.424 1784 Planarity : 0.004 0.046 1857 Dihedral : 11.894 93.162 1836 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.43 % Allowed : 4.13 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.23), residues: 1350 helix: 0.63 (0.25), residues: 432 sheet: 0.16 (0.27), residues: 342 loop : -1.78 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 175 TYR 0.012 0.001 TYR A 385 PHE 0.020 0.001 PHE A 193 TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00305 (10824) covalent geometry : angle 0.62082 (14661) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.50822 ( 2) hydrogen bonds : bond 0.05386 ( 493) hydrogen bonds : angle 4.86260 ( 1290) link_BETA1-4 : bond 0.01015 ( 9) link_BETA1-4 : angle 2.94105 ( 27) link_NAG-ASN : bond 0.01172 ( 8) link_NAG-ASN : angle 6.51514 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.431 Fit side-chains REVERT: B 179 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7699 (mmtm) REVERT: B 296 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8209 (mmmm) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.1455 time to fit residues: 20.2861 Evaluate side-chains 97 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 15 optimal weight: 0.0870 chunk 132 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 127 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 206 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN C 422 ASN C 466 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098047 restraints weight = 11584.968| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.46 r_work: 0.2961 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10842 Z= 0.124 Angle : 0.627 14.831 14714 Z= 0.303 Chirality : 0.047 0.554 1784 Planarity : 0.004 0.044 1857 Dihedral : 9.752 81.633 1836 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.43 % Allowed : 6.20 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.23), residues: 1350 helix: 1.10 (0.25), residues: 435 sheet: 0.31 (0.28), residues: 345 loop : -1.56 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.011 0.001 TYR A 385 PHE 0.017 0.001 PHE C 193 TRP 0.011 0.001 TRP B 284 HIS 0.002 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00277 (10824) covalent geometry : angle 0.56952 (14661) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.55217 ( 2) hydrogen bonds : bond 0.04644 ( 493) hydrogen bonds : angle 4.50415 ( 1290) link_BETA1-4 : bond 0.00991 ( 9) link_BETA1-4 : angle 2.65472 ( 27) link_NAG-ASN : bond 0.01136 ( 8) link_NAG-ASN : angle 5.93968 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.474 Fit side-chains REVERT: B 179 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7670 (mmtm) REVERT: B 197 ASN cc_start: 0.8420 (p0) cc_final: 0.8157 (p0) REVERT: B 296 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8225 (mmmm) REVERT: C 62 ASP cc_start: 0.7905 (m-30) cc_final: 0.7434 (m-30) REVERT: C 156 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.7110 (ttt-90) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 0.1269 time to fit residues: 18.1668 Evaluate side-chains 91 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 0.0000 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 422 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.096393 restraints weight = 11739.790| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.47 r_work: 0.2983 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10842 Z= 0.117 Angle : 0.607 14.226 14714 Z= 0.291 Chirality : 0.047 0.524 1784 Planarity : 0.004 0.043 1857 Dihedral : 8.622 71.919 1836 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.69 % Allowed : 6.89 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.23), residues: 1350 helix: 1.29 (0.25), residues: 435 sheet: 0.41 (0.28), residues: 345 loop : -1.40 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 175 TYR 0.011 0.001 TYR A 385 PHE 0.014 0.001 PHE C 193 TRP 0.010 0.001 TRP B 284 HIS 0.001 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00258 (10824) covalent geometry : angle 0.55028 (14661) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.54032 ( 2) hydrogen bonds : bond 0.04252 ( 493) hydrogen bonds : angle 4.36213 ( 1290) link_BETA1-4 : bond 0.00968 ( 9) link_BETA1-4 : angle 2.65735 ( 27) link_NAG-ASN : bond 0.01065 ( 8) link_NAG-ASN : angle 5.72710 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.426 Fit side-chains REVERT: B 197 ASN cc_start: 0.8336 (p0) cc_final: 0.8040 (p0) REVERT: B 296 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8235 (mmmm) REVERT: C 62 ASP cc_start: 0.7822 (m-30) cc_final: 0.7379 (m-30) REVERT: C 197 ASN cc_start: 0.8203 (p0) cc_final: 0.7925 (p0) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.1306 time to fit residues: 18.4186 Evaluate side-chains 98 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 94 optimal weight: 0.0170 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.096641 restraints weight = 11655.801| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.47 r_work: 0.2962 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10842 Z= 0.149 Angle : 0.629 17.279 14714 Z= 0.301 Chirality : 0.048 0.563 1784 Planarity : 0.004 0.042 1857 Dihedral : 8.163 65.297 1836 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.86 % Allowed : 8.27 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.23), residues: 1350 helix: 1.34 (0.25), residues: 435 sheet: 0.38 (0.27), residues: 345 loop : -1.44 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 175 TYR 0.009 0.001 TYR A 385 PHE 0.017 0.001 PHE C 193 TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00356 (10824) covalent geometry : angle 0.56848 (14661) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.61542 ( 2) hydrogen bonds : bond 0.04632 ( 493) hydrogen bonds : angle 4.36650 ( 1290) link_BETA1-4 : bond 0.00998 ( 9) link_BETA1-4 : angle 2.62114 ( 27) link_NAG-ASN : bond 0.01167 ( 8) link_NAG-ASN : angle 6.09812 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.431 Fit side-chains REVERT: B 197 ASN cc_start: 0.8381 (p0) cc_final: 0.8089 (p0) REVERT: B 296 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8251 (mmmm) REVERT: C 62 ASP cc_start: 0.7822 (m-30) cc_final: 0.7392 (m-30) REVERT: C 197 ASN cc_start: 0.8256 (p0) cc_final: 0.7974 (p0) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.1281 time to fit residues: 17.8924 Evaluate side-chains 98 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 67 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100264 restraints weight = 11519.105| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.43 r_work: 0.2943 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10842 Z= 0.107 Angle : 0.590 15.722 14714 Z= 0.282 Chirality : 0.046 0.568 1784 Planarity : 0.004 0.042 1857 Dihedral : 7.361 57.500 1836 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.78 % Allowed : 8.96 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.24), residues: 1350 helix: 1.45 (0.25), residues: 438 sheet: 0.54 (0.28), residues: 345 loop : -1.34 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 175 TYR 0.012 0.001 TYR A 385 PHE 0.011 0.001 PHE C 193 TRP 0.010 0.001 TRP B 284 HIS 0.001 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00228 (10824) covalent geometry : angle 0.53065 (14661) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.50904 ( 2) hydrogen bonds : bond 0.03900 ( 493) hydrogen bonds : angle 4.21154 ( 1290) link_BETA1-4 : bond 0.01019 ( 9) link_BETA1-4 : angle 2.56838 ( 27) link_NAG-ASN : bond 0.01289 ( 8) link_NAG-ASN : angle 5.82921 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.452 Fit side-chains REVERT: A 146 GLU cc_start: 0.8128 (tt0) cc_final: 0.7674 (tt0) REVERT: B 197 ASN cc_start: 0.8245 (p0) cc_final: 0.7982 (p0) REVERT: B 296 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8296 (mmmm) REVERT: C 62 ASP cc_start: 0.7767 (m-30) cc_final: 0.7306 (m-30) REVERT: C 353 ASN cc_start: 0.7924 (t0) cc_final: 0.7620 (t0) outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 0.1333 time to fit residues: 18.8964 Evaluate side-chains 100 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 0.0270 chunk 63 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 434 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 = 0.3426 r_free = 0.3426 target = 0.129822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.097064 restraints weight = 11577.593| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.45 r_work: 0.2953 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10842 Z= 0.125 Angle : 0.601 15.300 14714 Z= 0.288 Chirality : 0.047 0.553 1784 Planarity : 0.004 0.043 1857 Dihedral : 6.986 58.220 1836 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.69 % Allowed : 9.73 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.23), residues: 1350 helix: 1.47 (0.25), residues: 438 sheet: 0.53 (0.28), residues: 345 loop : -1.32 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.010 0.001 TYR A 385 PHE 0.014 0.001 PHE C 193 TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00288 (10824) covalent geometry : angle 0.54420 (14661) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.59065 ( 2) hydrogen bonds : bond 0.04208 ( 493) hydrogen bonds : angle 4.22295 ( 1290) link_BETA1-4 : bond 0.01030 ( 9) link_BETA1-4 : angle 2.54198 ( 27) link_NAG-ASN : bond 0.01217 ( 8) link_NAG-ASN : angle 5.76442 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.426 Fit side-chains REVERT: A 146 GLU cc_start: 0.8157 (tt0) cc_final: 0.7678 (tt0) REVERT: B 197 ASN cc_start: 0.8309 (p0) cc_final: 0.8009 (p0) REVERT: B 296 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8312 (mmmm) REVERT: B 466 ASN cc_start: 0.7336 (t0) cc_final: 0.7119 (t0) REVERT: C 62 ASP cc_start: 0.7785 (m-30) cc_final: 0.7347 (m-30) outliers start: 8 outliers final: 8 residues processed: 100 average time/residue: 0.1251 time to fit residues: 17.4163 Evaluate side-chains 100 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 37 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN ** B 434 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 = 0.3458 r_free = 0.3458 target = 0.130813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098851 restraints weight = 11534.089| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.39 r_work: 0.2877 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10842 Z= 0.227 Angle : 0.683 14.728 14714 Z= 0.332 Chirality : 0.050 0.547 1784 Planarity : 0.004 0.043 1857 Dihedral : 7.032 59.418 1836 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.78 % Allowed : 9.99 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.23), residues: 1350 helix: 1.24 (0.25), residues: 429 sheet: 0.29 (0.28), residues: 345 loop : -1.44 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.012 0.002 TYR B 310 PHE 0.022 0.002 PHE C 193 TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00565 (10824) covalent geometry : angle 0.63342 (14661) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.72211 ( 2) hydrogen bonds : bond 0.05609 ( 493) hydrogen bonds : angle 4.51156 ( 1290) link_BETA1-4 : bond 0.01045 ( 9) link_BETA1-4 : angle 2.50704 ( 27) link_NAG-ASN : bond 0.01227 ( 8) link_NAG-ASN : angle 5.79416 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.442 Fit side-chains REVERT: B 197 ASN cc_start: 0.8466 (p0) cc_final: 0.8193 (p0) REVERT: B 296 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8276 (mmmm) REVERT: C 62 ASP cc_start: 0.7731 (m-30) cc_final: 0.7289 (m-30) REVERT: C 197 ASN cc_start: 0.8339 (p0) cc_final: 0.8072 (p0) outliers start: 9 outliers final: 9 residues processed: 105 average time/residue: 0.1296 time to fit residues: 18.6556 Evaluate side-chains 103 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.099064 restraints weight = 11477.264| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.45 r_work: 0.2966 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10842 Z= 0.114 Angle : 0.597 14.451 14714 Z= 0.288 Chirality : 0.046 0.527 1784 Planarity : 0.004 0.044 1857 Dihedral : 6.495 57.994 1836 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.95 % Allowed : 9.91 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.23), residues: 1350 helix: 1.45 (0.25), residues: 435 sheet: 0.42 (0.28), residues: 345 loop : -1.29 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 175 TYR 0.011 0.001 TYR A 269 PHE 0.011 0.001 PHE C 193 TRP 0.012 0.001 TRP B 284 HIS 0.001 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00250 (10824) covalent geometry : angle 0.54285 (14661) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.58105 ( 2) hydrogen bonds : bond 0.04086 ( 493) hydrogen bonds : angle 4.25107 ( 1290) link_BETA1-4 : bond 0.01092 ( 9) link_BETA1-4 : angle 2.50485 ( 27) link_NAG-ASN : bond 0.01144 ( 8) link_NAG-ASN : angle 5.57716 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.413 Fit side-chains REVERT: A 146 GLU cc_start: 0.8058 (tt0) cc_final: 0.7534 (tt0) REVERT: B 296 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8311 (mmmm) REVERT: B 414 ASP cc_start: 0.7501 (t0) cc_final: 0.7238 (t0) REVERT: B 466 ASN cc_start: 0.7292 (t0) cc_final: 0.7071 (t0) REVERT: C 62 ASP cc_start: 0.7735 (m-30) cc_final: 0.7319 (m-30) outliers start: 11 outliers final: 10 residues processed: 106 average time/residue: 0.1231 time to fit residues: 18.0433 Evaluate side-chains 104 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 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 = 0.3446 r_free = 0.3446 target = 0.130774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.098289 restraints weight = 11498.184| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.41 r_work: 0.2927 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10842 Z= 0.140 Angle : 0.608 14.211 14714 Z= 0.294 Chirality : 0.047 0.524 1784 Planarity : 0.004 0.043 1857 Dihedral : 6.302 58.728 1836 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.86 % Allowed : 10.25 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.23), residues: 1350 helix: 1.42 (0.25), residues: 438 sheet: 0.40 (0.28), residues: 345 loop : -1.26 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 175 TYR 0.010 0.001 TYR A 269 PHE 0.015 0.001 PHE C 193 TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00332 (10824) covalent geometry : angle 0.55628 (14661) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.59402 ( 2) hydrogen bonds : bond 0.04469 ( 493) hydrogen bonds : angle 4.27482 ( 1290) link_BETA1-4 : bond 0.01087 ( 9) link_BETA1-4 : angle 2.45036 ( 27) link_NAG-ASN : bond 0.01168 ( 8) link_NAG-ASN : angle 5.53849 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8070 (tt0) cc_final: 0.7567 (tt0) REVERT: B 197 ASN cc_start: 0.8374 (p0) cc_final: 0.8100 (p0) REVERT: B 296 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8315 (mmmm) REVERT: B 414 ASP cc_start: 0.7581 (t0) cc_final: 0.7305 (t0) REVERT: B 466 ASN cc_start: 0.7362 (t0) cc_final: 0.7138 (t0) REVERT: C 62 ASP cc_start: 0.7720 (m-30) cc_final: 0.7312 (m-30) outliers start: 10 outliers final: 9 residues processed: 101 average time/residue: 0.1302 time to fit residues: 17.8606 Evaluate side-chains 101 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 41 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 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 = 0.3473 r_free = 0.3473 target = 0.132881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100192 restraints weight = 11575.432| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.43 r_work: 0.2981 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10842 Z= 0.107 Angle : 0.574 13.986 14714 Z= 0.278 Chirality : 0.046 0.511 1784 Planarity : 0.004 0.043 1857 Dihedral : 5.924 57.546 1836 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.78 % Allowed : 10.59 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.24), residues: 1350 helix: 1.53 (0.25), residues: 441 sheet: 0.52 (0.28), residues: 345 loop : -1.21 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 175 TYR 0.011 0.001 TYR A 269 PHE 0.010 0.001 PHE C 193 TRP 0.012 0.001 TRP B 284 HIS 0.001 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00232 (10824) covalent geometry : angle 0.52243 (14661) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.58638 ( 2) hydrogen bonds : bond 0.03821 ( 493) hydrogen bonds : angle 4.15693 ( 1290) link_BETA1-4 : bond 0.01100 ( 9) link_BETA1-4 : angle 2.39646 ( 27) link_NAG-ASN : bond 0.01105 ( 8) link_NAG-ASN : angle 5.36897 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.14 seconds wall clock time: 45 minutes 9.23 seconds (2709.23 seconds total)