Starting phenix.real_space_refine on Tue May 13 14:51:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vt2_43516/05_2025/8vt2_43516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vt2_43516/05_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_43516/05_2025/8vt2_43516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vt2_43516/05_2025/8vt2_43516.map" model { file = "/net/cci-nas-00/data/ceres_data/8vt2_43516/05_2025/8vt2_43516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vt2_43516/05_2025/8vt2_43516.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.30, per 1000 atoms: 0.59 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: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.21 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: 3.11 Time building geometry restraints manager: 2.94 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: 0.03 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: 0.800 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.550 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (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 TRP 0.026 0.003 TRP B 473 HIS 0.005 0.002 HIS C 435 PHE 0.059 0.003 PHE C 193 TYR 0.022 0.004 TYR C 310 ARG 0.008 0.001 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.01553 ( 8) link_NAG-ASN : angle 7.15470 ( 24) link_BETA1-4 : bond 0.01285 ( 9) link_BETA1-4 : angle 2.78815 ( 27) hydrogen bonds : bond 0.16599 ( 493) hydrogen bonds : angle 6.19945 ( 1290) SS BOND : bond 0.00041 ( 1) SS BOND : angle 1.28619 ( 2) covalent geometry : bond 0.01359 (10824) covalent geometry : angle 0.95679 (14661) *********************** 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 : 1.094 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: 0.3208 time to fit residues: 44.6521 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 : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 402 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099496 restraints weight = 11407.847| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.32 r_work: 0.2944 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10842 Z= 0.132 Angle : 0.687 15.504 14714 Z= 0.333 Chirality : 0.048 0.488 1784 Planarity : 0.005 0.047 1857 Dihedral : 12.257 94.206 1836 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.52 % Allowed : 3.70 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1350 helix: 0.69 (0.25), residues: 429 sheet: 0.16 (0.27), residues: 342 loop : -1.78 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS A 332 PHE 0.019 0.001 PHE A 193 TYR 0.011 0.001 TYR A 385 ARG 0.004 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01179 ( 8) link_NAG-ASN : angle 6.57312 ( 24) link_BETA1-4 : bond 0.00939 ( 9) link_BETA1-4 : angle 3.03332 ( 27) hydrogen bonds : bond 0.05457 ( 493) hydrogen bonds : angle 4.90312 ( 1290) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.49543 ( 2) covalent geometry : bond 0.00279 (10824) covalent geometry : angle 0.62086 (14661) *********************** 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: 6 poor density : 99 time to evaluate : 1.172 Fit side-chains REVERT: B 179 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7680 (mmtm) outliers start: 6 outliers final: 5 residues processed: 104 average time/residue: 0.2845 time to fit residues: 40.1366 Evaluate side-chains 97 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 B residue 428 SER 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 31 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 125 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.0970 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 457 ASN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN C 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098852 restraints weight = 11629.673| |-----------------------------------------------------------------------------| 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: 0.2821 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10842 Z= 0.114 Angle : 0.621 14.968 14714 Z= 0.299 Chirality : 0.047 0.539 1784 Planarity : 0.004 0.045 1857 Dihedral : 9.795 81.802 1836 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.34 % Allowed : 5.94 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1350 helix: 1.16 (0.25), residues: 435 sheet: 0.34 (0.28), residues: 345 loop : -1.54 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.001 0.001 HIS A 332 PHE 0.015 0.001 PHE C 193 TYR 0.012 0.001 TYR A 385 ARG 0.005 0.000 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01084 ( 8) link_NAG-ASN : angle 5.92817 ( 24) link_BETA1-4 : bond 0.00975 ( 9) link_BETA1-4 : angle 2.62251 ( 27) hydrogen bonds : bond 0.04402 ( 493) hydrogen bonds : angle 4.49004 ( 1290) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.52709 ( 2) covalent geometry : bond 0.00243 (10824) covalent geometry : angle 0.56313 (14661) *********************** 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 101 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.207 Fit side-chains REVERT: A 62 ASP cc_start: 0.7961 (m-30) cc_final: 0.7691 (m-30) REVERT: B 179 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7660 (mmtm) REVERT: B 296 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8214 (mmmm) REVERT: C 62 ASP cc_start: 0.7780 (m-30) cc_final: 0.7373 (m-30) REVERT: C 156 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.7102 (ttt-90) outliers start: 4 outliers final: 2 residues processed: 100 average time/residue: 0.2572 time to fit residues: 35.8223 Evaluate side-chains 91 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 86 optimal weight: 0.0000 chunk 16 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** 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 = 0.129875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097058 restraints weight = 11572.918| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.45 r_work: 0.2970 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10842 Z= 0.121 Angle : 0.609 14.229 14714 Z= 0.292 Chirality : 0.047 0.525 1784 Planarity : 0.004 0.043 1857 Dihedral : 8.690 72.729 1836 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.78 % Allowed : 6.72 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1350 helix: 1.32 (0.25), residues: 435 sheet: 0.40 (0.28), residues: 345 loop : -1.39 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.001 0.001 HIS C 332 PHE 0.015 0.001 PHE C 193 TYR 0.011 0.001 TYR A 385 ARG 0.005 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01087 ( 8) link_NAG-ASN : angle 5.73401 ( 24) link_BETA1-4 : bond 0.01021 ( 9) link_BETA1-4 : angle 2.67654 ( 27) hydrogen bonds : bond 0.04315 ( 493) hydrogen bonds : angle 4.36373 ( 1290) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.53190 ( 2) covalent geometry : bond 0.00271 (10824) covalent geometry : angle 0.55219 (14661) *********************** 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 104 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.121 Fit side-chains REVERT: A 62 ASP cc_start: 0.7941 (m-30) cc_final: 0.7738 (m-30) REVERT: B 197 ASN cc_start: 0.8347 (p0) cc_final: 0.8074 (p0) REVERT: B 296 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8241 (mmmm) REVERT: C 62 ASP cc_start: 0.7821 (m-30) cc_final: 0.7394 (m-30) REVERT: C 197 ASN cc_start: 0.8214 (p0) cc_final: 0.7934 (p0) outliers start: 9 outliers final: 6 residues processed: 103 average time/residue: 0.2557 time to fit residues: 36.7483 Evaluate side-chains 99 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 61 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 6 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 131 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.132589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.099808 restraints weight = 11462.464| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.44 r_work: 0.2994 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10842 Z= 0.103 Angle : 0.581 13.732 14714 Z= 0.278 Chirality : 0.046 0.522 1784 Planarity : 0.004 0.042 1857 Dihedral : 7.661 59.566 1836 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.78 % Allowed : 8.70 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1350 helix: 1.50 (0.25), residues: 438 sheet: 0.57 (0.28), residues: 345 loop : -1.31 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.001 0.001 HIS C 332 PHE 0.012 0.001 PHE C 193 TYR 0.011 0.001 TYR A 385 ARG 0.007 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01031 ( 8) link_NAG-ASN : angle 5.53383 ( 24) link_BETA1-4 : bond 0.00984 ( 9) link_BETA1-4 : angle 2.53263 ( 27) hydrogen bonds : bond 0.03847 ( 493) hydrogen bonds : angle 4.20918 ( 1290) SS BOND : bond 0.00114 ( 1) SS BOND : angle 0.55811 ( 2) covalent geometry : bond 0.00218 (10824) covalent geometry : angle 0.52657 (14661) *********************** 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 105 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.104 Fit side-chains REVERT: A 62 ASP cc_start: 0.7869 (m-30) cc_final: 0.7669 (m-30) REVERT: B 296 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8264 (mmmm) REVERT: C 62 ASP cc_start: 0.7788 (m-30) cc_final: 0.7349 (m-30) REVERT: C 466 ASN cc_start: 0.6107 (m-40) cc_final: 0.5894 (m-40) outliers start: 9 outliers final: 7 residues processed: 104 average time/residue: 0.2411 time to fit residues: 35.2435 Evaluate side-chains 100 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 58 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN C 353 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.095071 restraints weight = 11633.367| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.47 r_work: 0.2897 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10842 Z= 0.195 Angle : 0.666 15.364 14714 Z= 0.321 Chirality : 0.048 0.389 1784 Planarity : 0.004 0.043 1857 Dihedral : 7.559 59.651 1836 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.86 % Allowed : 9.65 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1350 helix: 1.37 (0.25), residues: 432 sheet: 0.39 (0.28), residues: 345 loop : -1.37 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 PHE 0.021 0.001 PHE C 193 TYR 0.011 0.002 TYR B 310 ARG 0.006 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01149 ( 8) link_NAG-ASN : angle 6.28459 ( 24) link_BETA1-4 : bond 0.00985 ( 9) link_BETA1-4 : angle 2.69301 ( 27) hydrogen bonds : bond 0.05143 ( 493) hydrogen bonds : angle 4.40945 ( 1290) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.66688 ( 2) covalent geometry : bond 0.00481 (10824) covalent geometry : angle 0.60579 (14661) *********************** 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 109 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.140 Fit side-chains REVERT: A 62 ASP cc_start: 0.7836 (m-30) cc_final: 0.7574 (m-30) REVERT: B 197 ASN cc_start: 0.8661 (p0) cc_final: 0.8337 (p0) REVERT: B 296 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8306 (mmmm) REVERT: C 62 ASP cc_start: 0.7766 (m-30) cc_final: 0.7351 (m-30) REVERT: C 197 ASN cc_start: 0.8336 (p0) cc_final: 0.8059 (p0) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 0.2949 time to fit residues: 42.6512 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 : 1.232 ------------------------------------------------------------------------------- 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 120 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 102 optimal weight: 0.0470 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.130274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.097392 restraints weight = 11679.081| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.46 r_work: 0.2978 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10842 Z= 0.109 Angle : 0.601 15.539 14714 Z= 0.287 Chirality : 0.046 0.490 1784 Planarity : 0.004 0.044 1857 Dihedral : 7.022 58.040 1836 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.78 % Allowed : 10.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1350 helix: 1.51 (0.25), residues: 438 sheet: 0.50 (0.28), residues: 345 loop : -1.34 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.001 0.001 HIS A 332 PHE 0.011 0.001 PHE C 193 TYR 0.011 0.001 TYR A 385 ARG 0.007 0.000 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01132 ( 8) link_NAG-ASN : angle 5.88216 ( 24) link_BETA1-4 : bond 0.01029 ( 9) link_BETA1-4 : angle 2.65840 ( 27) hydrogen bonds : bond 0.04042 ( 493) hydrogen bonds : angle 4.23324 ( 1290) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.52523 ( 2) covalent geometry : bond 0.00235 (10824) covalent geometry : angle 0.54061 (14661) *********************** 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 104 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.288 Fit side-chains REVERT: A 62 ASP cc_start: 0.7766 (m-30) cc_final: 0.7490 (m-30) REVERT: B 296 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8302 (mmmm) REVERT: C 62 ASP cc_start: 0.7742 (m-30) cc_final: 0.7346 (m-30) outliers start: 9 outliers final: 8 residues processed: 103 average time/residue: 0.2693 time to fit residues: 38.2543 Evaluate side-chains 102 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 44 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.132692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.100674 restraints weight = 11395.164| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.37 r_work: 0.2896 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.004 0.030 10842 Z= 0.179 Angle : 0.643 14.756 14714 Z= 0.312 Chirality : 0.048 0.501 1784 Planarity : 0.004 0.043 1857 Dihedral : 6.862 59.597 1836 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.95 % Allowed : 10.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1350 helix: 1.42 (0.25), residues: 432 sheet: 0.37 (0.28), residues: 345 loop : -1.34 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 PHE 0.018 0.001 PHE C 193 TYR 0.010 0.002 TYR A 319 ARG 0.007 0.000 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01126 ( 8) link_NAG-ASN : angle 5.78886 ( 24) link_BETA1-4 : bond 0.01043 ( 9) link_BETA1-4 : angle 2.61186 ( 27) hydrogen bonds : bond 0.04964 ( 493) hydrogen bonds : angle 4.36858 ( 1290) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.67601 ( 2) covalent geometry : bond 0.00438 (10824) covalent geometry : angle 0.58983 (14661) *********************** 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 107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.191 Fit side-chains REVERT: A 62 ASP cc_start: 0.7710 (m-30) cc_final: 0.7376 (m-30) REVERT: B 296 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8263 (mmmm) REVERT: C 62 ASP cc_start: 0.7650 (m-30) cc_final: 0.7183 (m-30) REVERT: C 197 ASN cc_start: 0.8043 (p0) cc_final: 0.7756 (p0) outliers start: 11 outliers final: 11 residues processed: 106 average time/residue: 0.2695 time to fit residues: 40.0552 Evaluate side-chains 105 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 61 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 29 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.128928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.095995 restraints weight = 11652.292| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.47 r_work: 0.2960 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.003 0.037 10842 Z= 0.119 Angle : 0.614 18.459 14714 Z= 0.295 Chirality : 0.047 0.552 1784 Planarity : 0.004 0.044 1857 Dihedral : 6.540 58.427 1836 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.86 % Allowed : 10.68 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1350 helix: 1.48 (0.25), residues: 441 sheet: 0.47 (0.28), residues: 345 loop : -1.32 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.001 0.001 HIS C 332 PHE 0.012 0.001 PHE C 193 TYR 0.010 0.001 TYR A 269 ARG 0.006 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01314 ( 8) link_NAG-ASN : angle 6.12818 ( 24) link_BETA1-4 : bond 0.01036 ( 9) link_BETA1-4 : angle 2.61143 ( 27) hydrogen bonds : bond 0.04212 ( 493) hydrogen bonds : angle 4.25461 ( 1290) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.53919 ( 2) covalent geometry : bond 0.00263 (10824) covalent geometry : angle 0.55193 (14661) *********************** 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 104 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.093 Fit side-chains REVERT: A 62 ASP cc_start: 0.7717 (m-30) cc_final: 0.7416 (m-30) REVERT: B 296 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8315 (mmmm) REVERT: C 62 ASP cc_start: 0.7731 (m-30) cc_final: 0.7317 (m-30) outliers start: 10 outliers final: 10 residues processed: 103 average time/residue: 0.2517 time to fit residues: 36.0940 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 : 1.082 ------------------------------------------------------------------------------- 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 61 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 118 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.129594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.096741 restraints weight = 11616.289| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.47 r_work: 0.2944 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10842 Z= 0.147 Angle : 0.622 17.516 14714 Z= 0.301 Chirality : 0.047 0.569 1784 Planarity : 0.004 0.043 1857 Dihedral : 6.327 58.892 1836 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.86 % Allowed : 10.42 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1350 helix: 1.52 (0.25), residues: 435 sheet: 0.42 (0.28), residues: 345 loop : -1.24 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS C 332 PHE 0.015 0.001 PHE C 193 TYR 0.010 0.001 TYR A 269 ARG 0.006 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01364 ( 8) link_NAG-ASN : angle 6.03102 ( 24) link_BETA1-4 : bond 0.01081 ( 9) link_BETA1-4 : angle 2.56118 ( 27) hydrogen bonds : bond 0.04522 ( 493) hydrogen bonds : angle 4.28561 ( 1290) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.60758 ( 2) covalent geometry : bond 0.00346 (10824) covalent geometry : angle 0.56219 (14661) ********************** 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 101 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7843 (m-30) cc_final: 0.7518 (m-30) REVERT: B 296 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8316 (mmmm) REVERT: C 62 ASP cc_start: 0.7720 (m-30) cc_final: 0.7310 (m-30) outliers start: 10 outliers final: 9 residues processed: 100 average time/residue: 0.2676 time to fit residues: 37.2486 Evaluate side-chains 100 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.126742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.094114 restraints weight = 11665.813| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.47 r_work: 0.2855 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 10842 Z= 0.262 Angle : 0.709 17.042 14714 Z= 0.349 Chirality : 0.051 0.568 1784 Planarity : 0.005 0.044 1857 Dihedral : 6.514 59.834 1836 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.03 % Allowed : 10.42 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1350 helix: 1.17 (0.25), residues: 429 sheet: 0.18 (0.27), residues: 345 loop : -1.47 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.003 0.001 HIS A 332 PHE 0.024 0.002 PHE C 193 TYR 0.013 0.002 TYR B 310 ARG 0.006 0.001 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01403 ( 8) link_NAG-ASN : angle 6.02598 ( 24) link_BETA1-4 : bond 0.01124 ( 9) link_BETA1-4 : angle 2.51348 ( 27) hydrogen bonds : bond 0.05887 ( 493) hydrogen bonds : angle 4.56452 ( 1290) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.74977 ( 2) covalent geometry : bond 0.00658 (10824) covalent geometry : angle 0.65873 (14661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5174.35 seconds wall clock time: 90 minutes 25.23 seconds (5425.23 seconds total)