Starting phenix.real_space_refine on Mon Sep 14 16:50:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7koq_22980/09_2026/7koq_22980_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7koq_22980/09_2026/7koq_22980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7koq_22980/09_2026/7koq_22980_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7koq_22980/09_2026/7koq_22980_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7koq_22980/09_2026/7koq_22980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7koq_22980/09_2026/7koq_22980.map" } resolution = 3.6 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= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 S 110 5.16 5 Cl 5 4.86 5 C 10510 2.51 5 N 2565 2.21 5 O 2925 1.98 5 H 15640 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31760 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6281 Classifications: {'peptide': 391} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "F" 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 8.13, per 1000 atoms: 0.26 Number of scatterers: 31760 At special positions: 0 Unit cell: (92.046, 93.38, 166.083, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 Cl 5 17.00 S 110 16.00 O 2925 8.00 N 2565 7.00 C 10510 6.00 H 15640 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.05 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.05 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.05 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.05 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 23 " " NAG A 502 " - " ASN A 67 " " NAG B 501 " - " ASN B 23 " " NAG B 502 " - " ASN B 67 " " NAG C 501 " - " ASN C 23 " " NAG C 502 " - " ASN C 67 " " NAG D 501 " - " ASN D 23 " " NAG D 502 " - " ASN D 67 " " NAG E 501 " - " ASN E 23 " " NAG E 502 " - " ASN E 67 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN B 110 " " NAG H 1 " - " ASN C 110 " " NAG I 1 " - " ASN D 110 " " NAG J 1 " - " ASN E 110 " Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 939.8 milliseconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3730 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 42.0% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.880A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.562A pdb=" N LEU A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 239 through 259 Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 306 through 320 Processing helix chain 'A' and resid 409 through 466 Processing helix chain 'A' and resid 469 through 477 removed outlier: 3.658A pdb=" N SER A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.702A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.562A pdb=" N LEU B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 239 through 259 Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'B' and resid 409 through 466 Processing helix chain 'B' and resid 469 through 477 removed outlier: 3.658A pdb=" N SER B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.702A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.561A pdb=" N LEU C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 239 through 259 Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 306 through 320 Processing helix chain 'C' and resid 409 through 466 Processing helix chain 'C' and resid 469 through 477 removed outlier: 3.658A pdb=" N SER C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.702A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 removed outlier: 3.562A pdb=" N LEU D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 239 through 259 Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 306 through 320 Processing helix chain 'D' and resid 409 through 466 Processing helix chain 'D' and resid 469 through 477 removed outlier: 3.658A pdb=" N SER D 475 " --> pdb=" O VAL D 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.702A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 removed outlier: 3.562A pdb=" N LEU E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 239 through 259 Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 306 through 320 Processing helix chain 'E' and resid 409 through 466 Processing helix chain 'E' and resid 469 through 477 removed outlier: 3.658A pdb=" N SER E 475 " --> pdb=" O VAL E 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.730A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.730A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.741A pdb=" N GLY A 146 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.741A pdb=" N GLY A 146 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.730A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.730A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.740A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.740A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.729A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.729A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.740A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.740A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.729A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.729A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.740A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.740A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.730A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.730A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.741A pdb=" N GLY E 146 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.741A pdb=" N GLY E 146 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2790 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: 7.44 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15600 1.04 - 1.24: 2110 1.24 - 1.45: 5274 1.45 - 1.65: 9051 1.65 - 1.85: 170 Bond restraints: 32205 Sorted by residual: bond pdb=" C1 EPJ E 503 " pdb=" C7 EPJ E 503 " ideal model delta sigma weight residual 1.505 1.732 -0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1 EPJ B 503 " pdb=" C7 EPJ B 503 " ideal model delta sigma weight residual 1.505 1.732 -0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1 EPJ A 503 " pdb=" C7 EPJ A 503 " ideal model delta sigma weight residual 1.505 1.731 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1 EPJ C 503 " pdb=" C7 EPJ C 503 " ideal model delta sigma weight residual 1.505 1.731 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1 EPJ D 503 " pdb=" C7 EPJ D 503 " ideal model delta sigma weight residual 1.505 1.731 -0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 32200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.52: 57995 8.52 - 17.03: 35 17.03 - 25.55: 25 25.55 - 34.07: 35 34.07 - 42.58: 20 Bond angle restraints: 58110 Sorted by residual: angle pdb=" CE LYS D 5 " pdb=" CD LYS D 5 " pdb=" HD3 LYS D 5 " ideal model delta sigma weight residual 108.00 65.42 42.58 3.00e+00 1.11e-01 2.01e+02 angle pdb=" CE LYS E 5 " pdb=" CD LYS E 5 " pdb=" HD3 LYS E 5 " ideal model delta sigma weight residual 108.00 65.43 42.57 3.00e+00 1.11e-01 2.01e+02 angle pdb=" CE LYS C 5 " pdb=" CD LYS C 5 " pdb=" HD3 LYS C 5 " ideal model delta sigma weight residual 108.00 65.43 42.57 3.00e+00 1.11e-01 2.01e+02 angle pdb=" CE LYS B 5 " pdb=" CD LYS B 5 " pdb=" HD3 LYS B 5 " ideal model delta sigma weight residual 108.00 65.44 42.56 3.00e+00 1.11e-01 2.01e+02 angle pdb=" CE LYS A 5 " pdb=" CD LYS A 5 " pdb=" HD3 LYS A 5 " ideal model delta sigma weight residual 108.00 65.45 42.55 3.00e+00 1.11e-01 2.01e+02 ... (remaining 58105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 13685 14.17 - 28.35: 1301 28.35 - 42.52: 404 42.52 - 56.69: 190 56.69 - 70.87: 40 Dihedral angle restraints: 15620 sinusoidal: 8530 harmonic: 7090 Sorted by residual: dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual -180.00 -154.99 -25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 15617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 2580 0.278 - 0.556: 5 0.556 - 0.834: 5 0.834 - 1.111: 5 1.111 - 1.389: 5 Chirality restraints: 2600 Sorted by residual: chirality pdb=" CB VAL C 68 " pdb=" CA VAL C 68 " pdb=" CG1 VAL C 68 " pdb=" CG2 VAL C 68 " both_signs ideal model delta sigma weight residual False -2.63 -1.24 -1.39 2.00e-01 2.50e+01 4.82e+01 chirality pdb=" CB VAL D 68 " pdb=" CA VAL D 68 " pdb=" CG1 VAL D 68 " pdb=" CG2 VAL D 68 " both_signs ideal model delta sigma weight residual False -2.63 -1.24 -1.39 2.00e-01 2.50e+01 4.81e+01 chirality pdb=" CB VAL A 68 " pdb=" CA VAL A 68 " pdb=" CG1 VAL A 68 " pdb=" CG2 VAL A 68 " both_signs ideal model delta sigma weight residual False -2.63 -1.24 -1.39 2.00e-01 2.50e+01 4.80e+01 ... (remaining 2597 not shown) Planarity restraints: 4630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 118 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO D 119 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 118 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO C 119 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 118 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO A 119 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.025 5.00e-02 4.00e+02 ... (remaining 4627 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 919 2.14 - 2.76: 58646 2.76 - 3.37: 81313 3.37 - 3.99: 104474 3.99 - 4.60: 168016 Nonbonded interactions: 413368 Sorted by model distance: nonbonded pdb=" O ILE B 463 " pdb=" HG SER B 466 " model vdw 1.528 2.450 nonbonded pdb=" O ILE D 463 " pdb=" HG SER D 466 " model vdw 1.528 2.450 nonbonded pdb=" O ILE A 463 " pdb=" HG SER A 466 " model vdw 1.528 2.450 nonbonded pdb=" O ILE C 463 " pdb=" HG SER C 466 " model vdw 1.528 2.450 nonbonded pdb=" O ILE E 463 " pdb=" HG SER E 466 " model vdw 1.529 2.450 ... (remaining 413363 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 7.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.250 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.227 16595 Z= 0.614 Angle : 0.892 17.140 22660 Z= 0.434 Chirality : 0.093 1.389 2600 Planarity : 0.005 0.046 2775 Dihedral : 13.069 70.867 6330 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.57 % Allowed : 3.97 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: 0.04 (0.19), residues: 1935 helix: 1.74 (0.17), residues: 790 sheet: -0.21 (0.24), residues: 445 loop : -1.86 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 423 TYR 0.012 0.002 TYR E 92 PHE 0.011 0.001 PHE D 134 TRP 0.012 0.001 TRP D 437 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.01381 / 0.61 (16565) covalent geometry : angle 0.86965 / 0.43 (22580) SS BOND : bond 0.01224 / 0.66 ( 10) SS BOND : angle 4.43007 / 2.77 ( 20) hydrogen bonds : bond 0.13305 / 8.87 ( 850) hydrogen bonds : angle 5.31647 / 3.74 ( 2790) link_BETA1-4 : bond 0.00070 / 0.04 ( 5) link_BETA1-4 : angle 1.92365 / 1.18 ( 15) link_NAG-ASN : bond 0.00596 / 0.32 ( 15) link_NAG-ASN : angle 3.33439 / 2.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 293 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7400 (ttmm) REVERT: A 83 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7832 (mt0) REVERT: A 160 GLN cc_start: 0.7614 (mt0) cc_final: 0.7344 (mt0) REVERT: A 234 ASP cc_start: 0.6969 (t0) cc_final: 0.6723 (t0) REVERT: B 5 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7383 (tttp) REVERT: B 83 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7831 (mt0) REVERT: B 142 LYS cc_start: 0.8205 (pttp) cc_final: 0.7982 (pttp) REVERT: C 5 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7198 (tttp) REVERT: C 83 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7859 (mt0) REVERT: C 93 ASN cc_start: 0.8478 (p0) cc_final: 0.8177 (p0) REVERT: D 5 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6987 (ttmm) REVERT: D 293 GLN cc_start: 0.7617 (tp40) cc_final: 0.7379 (tp40) REVERT: E 5 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7169 (tttt) REVERT: E 142 LYS cc_start: 0.8112 (pttp) cc_final: 0.7863 (pttp) REVERT: E 293 GLN cc_start: 0.7486 (tp40) cc_final: 0.7232 (tp40) REVERT: E 465 MET cc_start: 0.6602 (mmt) cc_final: 0.6258 (mmt) outliers start: 10 outliers final: 0 residues processed: 298 average time/residue: 0.2769 time to fit residues: 125.8151 Evaluate side-chains 261 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 256 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain E residue 5 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 293 GLN E 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.149305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.119348 restraints weight = 53422.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.125407 restraints weight = 21213.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.129232 restraints weight = 11467.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.131546 restraints weight = 7532.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.133008 restraints weight = 5668.878| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 16595 Z= 0.154 Angle : 0.660 12.962 22660 Z= 0.340 Chirality : 0.074 1.430 2600 Planarity : 0.005 0.055 2775 Dihedral : 8.638 52.118 2650 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.47 % Allowed : 7.31 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1935 helix: 2.30 (0.17), residues: 805 sheet: 0.14 (0.24), residues: 450 loop : -1.70 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 205 TYR 0.009 0.001 TYR C 187 PHE 0.007 0.001 PHE B 2 TRP 0.010 0.001 TRP D 437 HIS 0.002 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (16565) covalent geometry : angle 0.63146 / 0.33 (22580) SS BOND : bond 0.02093 / 1.09 ( 10) SS BOND : angle 5.51325 / 3.04 ( 20) hydrogen bonds : bond 0.06405 / 4.22 ( 850) hydrogen bonds : angle 4.55917 / 3.23 ( 2790) link_BETA1-4 : bond 0.00455 / 0.23 ( 5) link_BETA1-4 : angle 0.73638 / 0.40 ( 15) link_NAG-ASN : bond 0.00220 / 0.12 ( 15) link_NAG-ASN : angle 2.41433 / 1.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7306 (ttmm) REVERT: A 160 GLN cc_start: 0.7491 (mt0) cc_final: 0.7278 (mt0) REVERT: A 234 ASP cc_start: 0.6931 (t0) cc_final: 0.6723 (t0) REVERT: B 5 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7384 (ttmm) REVERT: B 83 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7793 (mt0) REVERT: B 476 LYS cc_start: 0.7640 (mttt) cc_final: 0.7255 (ttmt) REVERT: C 5 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7166 (tttp) REVERT: C 83 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7853 (mt0) REVERT: C 184 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7610 (mt-10) REVERT: D 5 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6923 (ttmm) REVERT: D 13 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8032 (m-40) REVERT: D 83 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7720 (mt0) REVERT: D 184 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7535 (mt-10) REVERT: D 293 GLN cc_start: 0.7629 (tp-100) cc_final: 0.7343 (tp40) REVERT: E 5 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7029 (ttmt) REVERT: E 13 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: E 83 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7731 (mt0) REVERT: E 293 GLN cc_start: 0.7441 (tp-100) cc_final: 0.7172 (tp40) REVERT: E 465 MET cc_start: 0.6335 (mmt) cc_final: 0.6054 (mmt) outliers start: 26 outliers final: 16 residues processed: 298 average time/residue: 0.2811 time to fit residues: 127.8070 Evaluate side-chains 293 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 459 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 22 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.147757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.118010 restraints weight = 53686.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.124003 restraints weight = 21505.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.127696 restraints weight = 11601.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.129936 restraints weight = 7655.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.131341 restraints weight = 5817.059| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 16595 Z= 0.154 Angle : 0.638 20.574 22660 Z= 0.326 Chirality : 0.074 1.440 2600 Planarity : 0.004 0.044 2775 Dihedral : 7.728 67.190 2650 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.87 % Allowed : 7.48 % Favored : 90.65 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1935 helix: 2.54 (0.17), residues: 815 sheet: 0.24 (0.24), residues: 455 loop : -1.70 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 423 TYR 0.007 0.001 TYR C 128 PHE 0.007 0.001 PHE A 134 TRP 0.009 0.001 TRP D 437 HIS 0.001 0.000 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (16565) covalent geometry : angle 0.61456 / 0.32 (22580) SS BOND : bond 0.01951 / 0.82 ( 10) SS BOND : angle 4.81117 / 3.06 ( 20) hydrogen bonds : bond 0.05957 / 3.92 ( 850) hydrogen bonds : angle 4.39145 / 3.12 ( 2790) link_BETA1-4 : bond 0.00355 / 0.20 ( 5) link_BETA1-4 : angle 1.17144 / 0.69 ( 15) link_NAG-ASN : bond 0.00142 / 0.09 ( 15) link_NAG-ASN : angle 2.23413 / 1.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7343 (ttmm) REVERT: A 160 GLN cc_start: 0.7549 (mt0) cc_final: 0.7334 (mt0) REVERT: A 234 ASP cc_start: 0.7035 (t0) cc_final: 0.6811 (t0) REVERT: B 5 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7330 (tttp) REVERT: B 184 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 476 LYS cc_start: 0.7398 (mttt) cc_final: 0.7114 (ttmm) REVERT: C 5 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7184 (tttp) REVERT: C 83 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8199 (mm-40) REVERT: C 184 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 227 LEU cc_start: 0.8033 (tp) cc_final: 0.7772 (tt) REVERT: C 476 LYS cc_start: 0.7614 (mttt) cc_final: 0.7339 (mttt) REVERT: D 5 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6976 (ttmm) REVERT: D 13 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8110 (m-40) REVERT: D 83 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7786 (mt0) REVERT: D 184 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7732 (mt-10) REVERT: D 227 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7760 (tt) REVERT: D 293 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7338 (tp40) REVERT: E 5 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7050 (ttmt) REVERT: E 13 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8187 (m-40) REVERT: E 83 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7737 (mt0) REVERT: E 293 GLN cc_start: 0.7442 (tp-100) cc_final: 0.7192 (tp40) REVERT: E 465 MET cc_start: 0.6439 (mmt) cc_final: 0.6093 (mmt) outliers start: 33 outliers final: 20 residues processed: 300 average time/residue: 0.2715 time to fit residues: 126.4504 Evaluate side-chains 307 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 459 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 122 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.0170 chunk 124 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.152234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.122867 restraints weight = 53432.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.128707 restraints weight = 21955.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.132332 restraints weight = 12090.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.134428 restraints weight = 8068.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.135818 restraints weight = 6205.163| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 16595 Z= 0.145 Angle : 0.635 23.159 22660 Z= 0.321 Chirality : 0.074 1.438 2600 Planarity : 0.004 0.043 2775 Dihedral : 7.159 69.240 2650 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.98 % Allowed : 9.18 % Favored : 88.84 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1935 helix: 2.72 (0.17), residues: 815 sheet: 0.38 (0.25), residues: 455 loop : -1.56 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 423 TYR 0.011 0.001 TYR A 128 PHE 0.006 0.001 PHE A 134 TRP 0.008 0.001 TRP B 437 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.14 (16565) covalent geometry : angle 0.60530 / 0.31 (22580) SS BOND : bond 0.01939 / 1.05 ( 10) SS BOND : angle 5.65348 / 3.63 ( 20) hydrogen bonds : bond 0.05642 / 3.70 ( 850) hydrogen bonds : angle 4.27142 / 3.03 ( 2790) link_BETA1-4 : bond 0.00297 / 0.15 ( 5) link_BETA1-4 : angle 1.07518 / 0.62 ( 15) link_NAG-ASN : bond 0.00100 / 0.06 ( 15) link_NAG-ASN : angle 2.13558 / 1.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7340 (ttmm) REVERT: A 160 GLN cc_start: 0.7525 (mt0) cc_final: 0.7296 (mt0) REVERT: A 192 GLU cc_start: 0.7941 (pt0) cc_final: 0.7648 (pt0) REVERT: A 234 ASP cc_start: 0.7010 (t0) cc_final: 0.6806 (t0) REVERT: B 5 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7334 (tttp) REVERT: B 184 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 439 PHE cc_start: 0.7795 (t80) cc_final: 0.7532 (t80) REVERT: B 476 LYS cc_start: 0.7421 (mttt) cc_final: 0.7193 (ttmt) REVERT: C 5 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7204 (tttp) REVERT: C 83 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8225 (mm-40) REVERT: C 184 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7717 (mt-10) REVERT: C 227 LEU cc_start: 0.8113 (tp) cc_final: 0.7862 (tt) REVERT: D 5 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6975 (ttmm) REVERT: D 13 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8130 (m-40) REVERT: D 184 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7696 (mt-10) REVERT: D 227 LEU cc_start: 0.8125 (tp) cc_final: 0.7872 (tt) REVERT: D 293 GLN cc_start: 0.7575 (tp-100) cc_final: 0.7323 (tp40) REVERT: D 439 PHE cc_start: 0.7806 (t80) cc_final: 0.7445 (t80) REVERT: D 476 LYS cc_start: 0.7790 (mttt) cc_final: 0.7556 (mttt) REVERT: E 5 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7104 (tttp) REVERT: E 13 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8197 (m-40) REVERT: E 227 LEU cc_start: 0.8110 (tp) cc_final: 0.7739 (tt) REVERT: E 293 GLN cc_start: 0.7457 (tp-100) cc_final: 0.7219 (tp40) REVERT: E 465 MET cc_start: 0.6369 (mmt) cc_final: 0.6057 (mmt) outliers start: 35 outliers final: 17 residues processed: 307 average time/residue: 0.2594 time to fit residues: 123.3349 Evaluate side-chains 303 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 459 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 140 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.143298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.113379 restraints weight = 54132.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.119165 restraints weight = 21977.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.122801 restraints weight = 12014.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.125105 restraints weight = 7969.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.126528 restraints weight = 6016.304| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 16595 Z= 0.214 Angle : 0.682 20.036 22660 Z= 0.349 Chirality : 0.074 1.441 2600 Planarity : 0.004 0.043 2775 Dihedral : 7.285 66.704 2650 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.15 % Allowed : 9.97 % Favored : 87.88 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1935 helix: 2.64 (0.17), residues: 810 sheet: 0.20 (0.25), residues: 465 loop : -1.49 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 423 TYR 0.009 0.001 TYR C 63 PHE 0.010 0.001 PHE A 134 TRP 0.009 0.001 TRP D 437 HIS 0.002 0.001 HIS E 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.21 (16565) covalent geometry : angle 0.64545 / 0.33 (22580) SS BOND : bond 0.02217 / 1.22 ( 10) SS BOND : angle 6.69901 / 4.45 ( 20) hydrogen bonds : bond 0.06028 / 3.96 ( 850) hydrogen bonds : angle 4.47169 / 3.17 ( 2790) link_BETA1-4 : bond 0.00086 / 0.05 ( 5) link_BETA1-4 : angle 1.21467 / 0.68 ( 15) link_NAG-ASN : bond 0.00350 / 0.19 ( 15) link_NAG-ASN : angle 2.17062 / 1.36 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 317 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7456 (ttmm) REVERT: A 160 GLN cc_start: 0.7523 (mt0) cc_final: 0.7318 (mt0) REVERT: A 192 GLU cc_start: 0.7983 (pt0) cc_final: 0.7679 (pt0) REVERT: A 234 ASP cc_start: 0.7045 (t0) cc_final: 0.6827 (t0) REVERT: B 5 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7398 (tttp) REVERT: B 439 PHE cc_start: 0.7882 (t80) cc_final: 0.7615 (t80) REVERT: C 5 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7296 (tttp) REVERT: C 184 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7701 (mt-10) REVERT: C 227 LEU cc_start: 0.8164 (tp) cc_final: 0.7879 (tt) REVERT: D 5 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7193 (ttmm) REVERT: D 13 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8237 (m-40) REVERT: D 83 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7930 (mt0) REVERT: D 184 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7772 (mt-10) REVERT: D 293 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7373 (tp40) REVERT: E 5 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7314 (tttp) REVERT: E 13 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8275 (m-40) REVERT: E 227 LEU cc_start: 0.8132 (tp) cc_final: 0.7760 (tt) REVERT: E 293 GLN cc_start: 0.7490 (tp-100) cc_final: 0.7277 (tp40) REVERT: E 439 PHE cc_start: 0.7899 (t80) cc_final: 0.7490 (t80) REVERT: E 465 MET cc_start: 0.6528 (mmt) cc_final: 0.6190 (mmt) outliers start: 38 outliers final: 25 residues processed: 333 average time/residue: 0.2749 time to fit residues: 142.2927 Evaluate side-chains 332 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 186 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN B 106 ASN E 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.144948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.114899 restraints weight = 53628.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.120759 restraints weight = 21786.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.124451 restraints weight = 11878.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.126719 restraints weight = 7855.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.128019 restraints weight = 5951.470| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 16595 Z= 0.162 Angle : 0.692 22.338 22660 Z= 0.348 Chirality : 0.074 1.431 2600 Planarity : 0.004 0.039 2775 Dihedral : 6.986 66.687 2646 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.76 % Allowed : 11.73 % Favored : 86.52 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1935 helix: 2.78 (0.17), residues: 810 sheet: 0.24 (0.25), residues: 465 loop : -1.42 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 423 TYR 0.007 0.001 TYR E 128 PHE 0.007 0.001 PHE A 134 TRP 0.011 0.001 TRP B 437 HIS 0.001 0.000 HIS E 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.16 (16565) covalent geometry : angle 0.64504 / 0.33 (22580) SS BOND : bond 0.01787 / 0.94 ( 10) SS BOND : angle 7.95034 / 5.28 ( 20) hydrogen bonds : bond 0.05643 / 3.70 ( 850) hydrogen bonds : angle 4.28347 / 3.04 ( 2790) link_BETA1-4 : bond 0.00309 / 0.17 ( 5) link_BETA1-4 : angle 1.02457 / 0.59 ( 15) link_NAG-ASN : bond 0.00122 / 0.07 ( 15) link_NAG-ASN : angle 1.94174 / 1.21 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7441 (ttmm) REVERT: A 192 GLU cc_start: 0.8023 (pt0) cc_final: 0.7629 (pt0) REVERT: A 230 LEU cc_start: 0.8844 (mt) cc_final: 0.8642 (mt) REVERT: A 234 ASP cc_start: 0.7061 (t0) cc_final: 0.6847 (t0) REVERT: B 5 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7377 (tttp) REVERT: C 5 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7266 (tttp) REVERT: C 184 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7673 (mt-10) REVERT: C 227 LEU cc_start: 0.8037 (tp) cc_final: 0.7772 (tt) REVERT: D 5 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7162 (ttmm) REVERT: D 13 ASN cc_start: 0.8415 (m110) cc_final: 0.8169 (m-40) REVERT: D 44 GLU cc_start: 0.7728 (mp0) cc_final: 0.6971 (mp0) REVERT: D 293 GLN cc_start: 0.7593 (tp-100) cc_final: 0.7339 (tp40) REVERT: E 5 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7206 (tttp) REVERT: E 13 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8266 (m-40) REVERT: E 227 LEU cc_start: 0.8020 (tp) cc_final: 0.7660 (tt) REVERT: E 293 GLN cc_start: 0.7418 (tp-100) cc_final: 0.7172 (tp40) REVERT: E 465 MET cc_start: 0.6460 (mmt) cc_final: 0.6115 (mmt) outliers start: 31 outliers final: 23 residues processed: 317 average time/residue: 0.2617 time to fit residues: 129.0003 Evaluate side-chains 305 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 113 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 GLN C 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.145101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.114955 restraints weight = 53972.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.120786 restraints weight = 21997.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.124427 restraints weight = 12073.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.126760 restraints weight = 8052.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.128208 restraints weight = 6068.674| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 16595 Z= 0.163 Angle : 0.698 22.891 22660 Z= 0.351 Chirality : 0.074 1.431 2600 Planarity : 0.004 0.038 2775 Dihedral : 6.867 88.327 2638 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.04 % Allowed : 11.61 % Favored : 86.35 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1935 helix: 2.83 (0.17), residues: 810 sheet: 0.24 (0.25), residues: 465 loop : -1.40 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.007 0.001 TYR E 128 PHE 0.007 0.001 PHE D 134 TRP 0.008 0.001 TRP B 437 HIS 0.002 0.000 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.16 (16565) covalent geometry : angle 0.65806 / 0.33 (22580) SS BOND : bond 0.01928 / 1.01 ( 10) SS BOND : angle 7.30829 / 5.05 ( 20) hydrogen bonds : bond 0.05543 / 3.63 ( 850) hydrogen bonds : angle 4.26425 / 3.02 ( 2790) link_BETA1-4 : bond 0.00197 / 0.10 ( 5) link_BETA1-4 : angle 1.11709 / 0.64 ( 15) link_NAG-ASN : bond 0.00144 / 0.08 ( 15) link_NAG-ASN : angle 1.95583 / 1.21 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.890 Fit side-chains REVERT: A 5 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7456 (ttmm) REVERT: A 192 GLU cc_start: 0.7980 (pt0) cc_final: 0.7625 (pt0) REVERT: A 230 LEU cc_start: 0.8892 (mt) cc_final: 0.8656 (mt) REVERT: A 234 ASP cc_start: 0.7049 (t0) cc_final: 0.6833 (t0) REVERT: B 5 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7386 (tttp) REVERT: B 227 LEU cc_start: 0.8122 (tp) cc_final: 0.7893 (tt) REVERT: C 5 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7277 (tttp) REVERT: C 184 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 227 LEU cc_start: 0.8077 (tp) cc_final: 0.7804 (tt) REVERT: D 5 LYS cc_start: 0.7554 (ttpt) cc_final: 0.7212 (ttmm) REVERT: D 13 ASN cc_start: 0.8422 (m110) cc_final: 0.8181 (m-40) REVERT: D 293 GLN cc_start: 0.7589 (tp-100) cc_final: 0.7330 (tp40) REVERT: E 5 LYS cc_start: 0.7622 (ttpt) cc_final: 0.7239 (tttp) REVERT: E 13 ASN cc_start: 0.8501 (m110) cc_final: 0.8249 (m-40) REVERT: E 227 LEU cc_start: 0.8054 (tp) cc_final: 0.7695 (tt) REVERT: E 293 GLN cc_start: 0.7388 (tp-100) cc_final: 0.7143 (tp40) REVERT: E 465 MET cc_start: 0.6473 (mmt) cc_final: 0.6127 (mmt) outliers start: 36 outliers final: 29 residues processed: 308 average time/residue: 0.2661 time to fit residues: 127.7733 Evaluate side-chains 303 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 273 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 2 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.145143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.114787 restraints weight = 54217.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.120588 restraints weight = 22440.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.124194 restraints weight = 12449.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.126490 restraints weight = 8371.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.127952 restraints weight = 6362.344| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 16595 Z= 0.214 Angle : 0.771 25.365 22660 Z= 0.386 Chirality : 0.075 1.438 2600 Planarity : 0.004 0.039 2775 Dihedral : 7.044 91.456 2630 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.93 % Allowed : 11.56 % Favored : 86.52 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1935 helix: 2.72 (0.17), residues: 805 sheet: 0.22 (0.25), residues: 465 loop : -1.47 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.007 0.001 TYR B 128 PHE 0.008 0.001 PHE A 134 TRP 0.007 0.001 TRP B 437 HIS 0.002 0.000 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.21 (16565) covalent geometry : angle 0.71502 / 0.36 (22580) SS BOND : bond 0.01950 / 0.98 ( 10) SS BOND : angle 9.25775 / 6.15 ( 20) hydrogen bonds : bond 0.05718 / 3.75 ( 850) hydrogen bonds : angle 4.33348 / 3.07 ( 2790) link_BETA1-4 : bond 0.00143 / 0.07 ( 5) link_BETA1-4 : angle 1.11540 / 0.63 ( 15) link_NAG-ASN : bond 0.00247 / 0.14 ( 15) link_NAG-ASN : angle 2.02051 / 1.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7487 (ttmm) REVERT: A 192 GLU cc_start: 0.7972 (pt0) cc_final: 0.7629 (pt0) REVERT: A 234 ASP cc_start: 0.7082 (t0) cc_final: 0.6850 (t0) REVERT: A 439 PHE cc_start: 0.7914 (t80) cc_final: 0.7640 (t80) REVERT: A 465 MET cc_start: 0.6569 (tpp) cc_final: 0.5794 (tmm) REVERT: B 5 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7522 (ttmm) REVERT: B 227 LEU cc_start: 0.8166 (tp) cc_final: 0.7929 (tt) REVERT: C 5 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7323 (tttp) REVERT: C 184 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7700 (mt-10) REVERT: C 227 LEU cc_start: 0.8082 (tp) cc_final: 0.7821 (tt) REVERT: D 5 LYS cc_start: 0.7564 (ttpt) cc_final: 0.7223 (ttmm) REVERT: D 13 ASN cc_start: 0.8443 (m110) cc_final: 0.8198 (m-40) REVERT: D 26 GLN cc_start: 0.8186 (tp40) cc_final: 0.7907 (tp40) REVERT: D 293 GLN cc_start: 0.7614 (tp-100) cc_final: 0.7343 (tp40) REVERT: E 5 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7342 (tttp) REVERT: E 13 ASN cc_start: 0.8507 (m110) cc_final: 0.8255 (m-40) REVERT: E 227 LEU cc_start: 0.8091 (tp) cc_final: 0.7727 (tt) REVERT: E 293 GLN cc_start: 0.7428 (tp-100) cc_final: 0.7171 (tp40) REVERT: E 439 PHE cc_start: 0.7915 (t80) cc_final: 0.7480 (t80) REVERT: E 465 MET cc_start: 0.6588 (mmt) cc_final: 0.6221 (mmt) outliers start: 34 outliers final: 27 residues processed: 297 average time/residue: 0.2588 time to fit residues: 120.2461 Evaluate side-chains 307 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 123 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.145004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.114709 restraints weight = 53617.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.120522 restraints weight = 21948.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.124149 restraints weight = 12054.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.126374 restraints weight = 8039.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.127842 restraints weight = 6132.598| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.239 16595 Z= 0.188 Angle : 0.757 23.850 22660 Z= 0.377 Chirality : 0.075 1.429 2600 Planarity : 0.004 0.038 2775 Dihedral : 6.863 93.123 2630 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.76 % Allowed : 11.84 % Favored : 86.40 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1935 helix: 2.80 (0.17), residues: 805 sheet: 0.22 (0.24), residues: 465 loop : -1.41 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.007 0.001 TYR B 63 PHE 0.007 0.001 PHE C 134 TRP 0.008 0.001 TRP B 437 HIS 0.002 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.19 (16565) covalent geometry : angle 0.70099 / 0.35 (22580) SS BOND : bond 0.02379 / 1.22 ( 10) SS BOND : angle 9.23505 / 6.06 ( 20) hydrogen bonds : bond 0.05489 / 3.60 ( 850) hydrogen bonds : angle 4.21926 / 2.99 ( 2790) link_BETA1-4 : bond 0.00310 / 0.16 ( 5) link_BETA1-4 : angle 1.05775 / 0.61 ( 15) link_NAG-ASN : bond 0.00188 / 0.11 ( 15) link_NAG-ASN : angle 1.89324 / 1.17 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7767 (ttpt) cc_final: 0.7476 (ttmm) REVERT: A 192 GLU cc_start: 0.8012 (pt0) cc_final: 0.7626 (pt0) REVERT: A 234 ASP cc_start: 0.7088 (t0) cc_final: 0.6859 (t0) REVERT: A 439 PHE cc_start: 0.7887 (t80) cc_final: 0.7609 (t80) REVERT: A 465 MET cc_start: 0.6593 (tpp) cc_final: 0.5738 (tmm) REVERT: B 5 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7508 (ttmm) REVERT: C 5 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7336 (tttp) REVERT: D 5 LYS cc_start: 0.7575 (ttpt) cc_final: 0.7175 (ttmm) REVERT: D 13 ASN cc_start: 0.8445 (m110) cc_final: 0.8206 (m-40) REVERT: D 293 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7339 (tp40) REVERT: E 5 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7375 (ttmm) REVERT: E 13 ASN cc_start: 0.8538 (m110) cc_final: 0.8291 (m-40) REVERT: E 293 GLN cc_start: 0.7412 (tp-100) cc_final: 0.7146 (tp40) REVERT: E 465 MET cc_start: 0.6568 (mmt) cc_final: 0.6193 (mmt) outliers start: 31 outliers final: 25 residues processed: 298 average time/residue: 0.2582 time to fit residues: 122.1124 Evaluate side-chains 311 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 284 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 115 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.146276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.115846 restraints weight = 53879.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.121639 restraints weight = 22396.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.125144 restraints weight = 12417.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.127464 restraints weight = 8401.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.128902 restraints weight = 6402.444| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.239 16595 Z= 0.175 Angle : 0.733 24.274 22660 Z= 0.367 Chirality : 0.074 1.427 2600 Planarity : 0.004 0.038 2775 Dihedral : 6.729 93.190 2630 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.76 % Allowed : 12.46 % Favored : 85.78 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 1935 helix: 2.88 (0.17), residues: 805 sheet: 0.23 (0.24), residues: 465 loop : -1.39 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.006 0.001 TYR B 128 PHE 0.006 0.001 PHE A 134 TRP 0.008 0.001 TRP C 437 HIS 0.001 0.000 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.17 (16565) covalent geometry : angle 0.67871 / 0.34 (22580) SS BOND : bond 0.02293 / 1.20 ( 10) SS BOND : angle 8.98166 / 5.93 ( 20) hydrogen bonds : bond 0.05342 / 3.50 ( 850) hydrogen bonds : angle 4.16072 / 2.95 ( 2790) link_BETA1-4 : bond 0.00211 / 0.11 ( 5) link_BETA1-4 : angle 1.11510 / 0.63 ( 15) link_NAG-ASN : bond 0.00149 / 0.09 ( 15) link_NAG-ASN : angle 1.87214 / 1.16 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7467 (ttmm) REVERT: A 192 GLU cc_start: 0.7977 (pt0) cc_final: 0.7590 (pt0) REVERT: A 234 ASP cc_start: 0.7069 (t0) cc_final: 0.6855 (t0) REVERT: A 465 MET cc_start: 0.6583 (tpp) cc_final: 0.5762 (tmm) REVERT: B 5 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7486 (ttmm) REVERT: C 5 LYS cc_start: 0.7715 (ttpt) cc_final: 0.7325 (tttp) REVERT: D 5 LYS cc_start: 0.7572 (ttpt) cc_final: 0.7256 (ttmm) REVERT: D 13 ASN cc_start: 0.8447 (m110) cc_final: 0.8209 (m-40) REVERT: D 293 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7335 (tp40) REVERT: E 5 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7365 (ttmm) REVERT: E 13 ASN cc_start: 0.8537 (m110) cc_final: 0.8293 (m-40) REVERT: E 227 LEU cc_start: 0.8055 (tp) cc_final: 0.7692 (tt) REVERT: E 465 MET cc_start: 0.6523 (mmt) cc_final: 0.6140 (mmt) outliers start: 31 outliers final: 27 residues processed: 300 average time/residue: 0.2518 time to fit residues: 119.8917 Evaluate side-chains 313 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 459 CYS Chi-restraints excluded: chain E residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 65 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.144295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.114150 restraints weight = 53918.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.120022 restraints weight = 21846.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.123627 restraints weight = 11878.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.125949 restraints weight = 7913.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.127268 restraints weight = 5958.438| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 16595 Z= 0.183 Angle : 0.733 24.325 22660 Z= 0.368 Chirality : 0.074 1.431 2600 Planarity : 0.004 0.038 2775 Dihedral : 6.754 94.046 2630 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.87 % Allowed : 12.52 % Favored : 85.61 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 1935 helix: 2.92 (0.17), residues: 800 sheet: 0.20 (0.24), residues: 465 loop : -1.38 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 423 TYR 0.006 0.001 TYR B 63 PHE 0.007 0.001 PHE A 134 TRP 0.012 0.001 TRP B 437 HIS 0.002 0.000 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.18 (16565) covalent geometry : angle 0.68051 / 0.35 (22580) SS BOND : bond 0.02163 / 1.13 ( 10) SS BOND : angle 8.75595 / 5.85 ( 20) hydrogen bonds : bond 0.05388 / 3.53 ( 850) hydrogen bonds : angle 4.18979 / 2.97 ( 2790) link_BETA1-4 : bond 0.00143 / 0.07 ( 5) link_BETA1-4 : angle 1.12626 / 0.64 ( 15) link_NAG-ASN : bond 0.00186 / 0.10 ( 15) link_NAG-ASN : angle 1.91157 / 1.18 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4836.75 seconds wall clock time: 83 minutes 13.36 seconds (4993.36 seconds total)