Starting phenix.real_space_refine on Thu Feb 5 09:17:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lhe_63095/02_2026/9lhe_63095.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lhe_63095/02_2026/9lhe_63095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lhe_63095/02_2026/9lhe_63095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lhe_63095/02_2026/9lhe_63095.map" model { file = "/net/cci-nas-00/data/ceres_data/9lhe_63095/02_2026/9lhe_63095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lhe_63095/02_2026/9lhe_63095.cif" } resolution = 3.25 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10480 2.51 5 N 2575 2.21 5 O 2955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16125 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3183 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 19 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.36, per 1000 atoms: 0.15 Number of scatterers: 16125 At special positions: 0 Unit cell: (91.91, 93.93, 168.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 2955 8.00 N 2575 7.00 C 10480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 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 601 " - " ASN A 46 " " NAG B 601 " - " ASN B 46 " " NAG C 601 " - " ASN C 46 " " NAG D 601 " - " ASN D 46 " " NAG E 601 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 654.0 milliseconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 43.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.574A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 260 through 280 Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 431 through 490 removed outlier: 3.539A pdb=" N TRP A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 469 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.575A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 260 through 280 Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 431 through 490 removed outlier: 3.537A pdb=" N TRP B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 469 " --> pdb=" O CYS B 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.576A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 260 through 280 Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 431 through 490 removed outlier: 3.539A pdb=" N TRP C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 469 " --> pdb=" O CYS C 465 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.574A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 260 through 280 Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 431 through 490 removed outlier: 3.539A pdb=" N TRP D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG D 469 " --> pdb=" O CYS D 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.575A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 260 through 280 Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'E' and resid 337 through 344 Processing helix chain 'E' and resid 431 through 490 removed outlier: 3.538A pdb=" N TRP E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG E 469 " --> pdb=" O CYS E 465 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU E 487 " --> pdb=" O THR E 483 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA E 490 " --> pdb=" O ILE E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.704A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 83 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR A 52 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 66 removed outlier: 7.643A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 5.228A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 5.228A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 221 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 204 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.702A pdb=" N VAL B 100 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 66 removed outlier: 7.642A pdb=" N LEU B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N TRP B 77 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 5.228A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 5.228A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 221 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 204 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.703A pdb=" N VAL C 100 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR C 52 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.643A pdb=" N LEU C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N TRP C 77 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 5.228A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 5.228A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 221 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 204 " --> pdb=" O THR C 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.703A pdb=" N VAL D 100 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 66 removed outlier: 7.643A pdb=" N LEU D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N TRP D 77 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN D 75 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.228A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.228A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 221 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 204 " --> pdb=" O THR D 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.703A pdb=" N VAL E 100 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR E 83 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR E 52 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 59 through 66 removed outlier: 7.642A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 5.229A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 5.229A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR E 221 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS E 204 " --> pdb=" O THR E 221 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2613 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: 2.32 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2580 1.31 - 1.44: 4569 1.44 - 1.57: 9241 1.57 - 1.70: 0 1.70 - 1.83: 170 Bond restraints: 16560 Sorted by residual: bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.459 -0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C7 NAG I 2 " pdb=" N2 NAG I 2 " ideal model delta sigma weight residual 1.346 1.459 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C7 NAG J 2 " pdb=" N2 NAG J 2 " ideal model delta sigma weight residual 1.346 1.459 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.459 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C7 NAG D 601 " pdb=" N2 NAG D 601 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.16e+01 ... (remaining 16555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 22033 1.77 - 3.54: 441 3.54 - 5.31: 83 5.31 - 7.08: 23 7.08 - 8.85: 10 Bond angle restraints: 22590 Sorted by residual: angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" C5 NAG H 1 " ideal model delta sigma weight residual 109.38 118.23 -8.85 3.00e+00 1.11e-01 8.70e+00 angle pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" C5 NAG G 1 " ideal model delta sigma weight residual 109.38 118.22 -8.84 3.00e+00 1.11e-01 8.68e+00 angle pdb=" C3 NAG I 1 " pdb=" C4 NAG I 1 " pdb=" C5 NAG I 1 " ideal model delta sigma weight residual 109.38 118.21 -8.83 3.00e+00 1.11e-01 8.67e+00 angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" C5 NAG F 1 " ideal model delta sigma weight residual 109.38 118.17 -8.79 3.00e+00 1.11e-01 8.59e+00 angle pdb=" C3 NAG J 1 " pdb=" C4 NAG J 1 " pdb=" C5 NAG J 1 " ideal model delta sigma weight residual 109.38 118.14 -8.76 3.00e+00 1.11e-01 8.52e+00 ... (remaining 22585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 8446 15.76 - 31.51: 1054 31.51 - 47.27: 403 47.27 - 63.02: 47 63.02 - 78.78: 15 Dihedral angle restraints: 9965 sinusoidal: 4090 harmonic: 5875 Sorted by residual: dihedral pdb=" CA CYS D 212 " pdb=" C CYS D 212 " pdb=" N CYS D 213 " pdb=" CA CYS D 213 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA CYS B 212 " pdb=" C CYS B 212 " pdb=" N CYS B 213 " pdb=" CA CYS B 213 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA CYS C 212 " pdb=" C CYS C 212 " pdb=" N CYS C 213 " pdb=" CA CYS C 213 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 9962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2120 0.052 - 0.103: 398 0.103 - 0.155: 71 0.155 - 0.207: 1 0.207 - 0.258: 5 Chirality restraints: 2595 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 133 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 133 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2592 not shown) Planarity restraints: 2830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 335 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C LEU A 335 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 335 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 336 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 335 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C LEU B 335 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU B 335 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 336 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 335 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C LEU C 335 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU C 335 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 336 " 0.010 2.00e-02 2.50e+03 ... (remaining 2827 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2961 2.77 - 3.30: 15019 3.30 - 3.84: 27197 3.84 - 4.37: 29368 4.37 - 4.90: 51794 Nonbonded interactions: 126339 Sorted by model distance: nonbonded pdb=" N GLU C 120 " pdb=" OE1 GLU C 120 " model vdw 2.239 3.120 nonbonded pdb=" N GLU E 120 " pdb=" OE1 GLU E 120 " model vdw 2.239 3.120 nonbonded pdb=" N GLU A 120 " pdb=" OE1 GLU A 120 " model vdw 2.239 3.120 nonbonded pdb=" N GLU D 120 " pdb=" OE1 GLU D 120 " model vdw 2.240 3.120 nonbonded pdb=" N GLU B 120 " pdb=" OE1 GLU B 120 " model vdw 2.240 3.120 ... (remaining 126334 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: 0.05 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.006 0.113 16585 Z= 0.316 Angle : 0.641 8.848 22655 Z= 0.297 Chirality : 0.042 0.258 2595 Planarity : 0.003 0.024 2820 Dihedral : 15.737 78.776 6135 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 19.32 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.62 (0.18), residues: 1980 helix: 1.61 (0.17), residues: 830 sheet: -0.51 (0.28), residues: 310 loop : -0.37 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 441 TYR 0.006 0.001 TYR B 296 PHE 0.011 0.001 PHE E 297 TRP 0.020 0.001 TRP B 176 HIS 0.002 0.000 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00636 (16560) covalent geometry : angle 0.62640 (22590) SS BOND : bond 0.00738 ( 10) SS BOND : angle 1.28937 ( 20) hydrogen bonds : bond 0.16524 ( 851) hydrogen bonds : angle 5.84662 ( 2613) link_BETA1-4 : bond 0.00049 ( 5) link_BETA1-4 : angle 0.53341 ( 15) link_NAG-ASN : bond 0.00120 ( 10) link_NAG-ASN : angle 3.71716 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.618 Fit side-chains REVERT: B 296 TYR cc_start: 0.8482 (t80) cc_final: 0.8140 (t80) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.0840 time to fit residues: 30.9489 Evaluate side-chains 201 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.065841 restraints weight = 43246.891| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.06 r_work: 0.2737 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16585 Z= 0.186 Angle : 0.596 9.072 22655 Z= 0.295 Chirality : 0.043 0.403 2595 Planarity : 0.003 0.025 2820 Dihedral : 6.797 56.121 2465 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.88 % Allowed : 17.33 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.68 (0.18), residues: 1980 helix: 1.61 (0.17), residues: 835 sheet: -0.01 (0.28), residues: 300 loop : -0.49 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 208 TYR 0.008 0.001 TYR C 296 PHE 0.010 0.001 PHE A 297 TRP 0.012 0.001 TRP A 176 HIS 0.003 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00429 (16560) covalent geometry : angle 0.57020 (22590) SS BOND : bond 0.00843 ( 10) SS BOND : angle 1.87852 ( 20) hydrogen bonds : bond 0.05367 ( 851) hydrogen bonds : angle 4.81505 ( 2613) link_BETA1-4 : bond 0.00343 ( 5) link_BETA1-4 : angle 2.24825 ( 15) link_NAG-ASN : bond 0.00335 ( 10) link_NAG-ASN : angle 4.33638 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 TYR cc_start: 0.8643 (t80) cc_final: 0.8335 (t80) REVERT: B 296 TYR cc_start: 0.8642 (t80) cc_final: 0.8369 (t80) REVERT: C 275 PHE cc_start: 0.8973 (t80) cc_final: 0.8695 (t80) REVERT: C 297 PHE cc_start: 0.9136 (m-80) cc_final: 0.8903 (m-80) REVERT: D 69 ASN cc_start: 0.8947 (t0) cc_final: 0.8686 (t0) REVERT: E 69 ASN cc_start: 0.8900 (t0) cc_final: 0.8618 (t0) outliers start: 33 outliers final: 24 residues processed: 235 average time/residue: 0.0870 time to fit residues: 34.0190 Evaluate side-chains 215 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 ILE Chi-restraints excluded: chain E residue 484 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 74 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.079034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.066430 restraints weight = 43284.510| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.27 r_work: 0.2751 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16585 Z= 0.131 Angle : 0.556 9.553 22655 Z= 0.271 Chirality : 0.043 0.423 2595 Planarity : 0.003 0.023 2820 Dihedral : 6.309 53.983 2465 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.99 % Allowed : 18.07 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.75 (0.18), residues: 1980 helix: 1.68 (0.17), residues: 835 sheet: 0.13 (0.29), residues: 300 loop : -0.52 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 229 TYR 0.009 0.001 TYR E 140 PHE 0.009 0.001 PHE B 297 TRP 0.011 0.001 TRP A 176 HIS 0.004 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00293 (16560) covalent geometry : angle 0.52628 (22590) SS BOND : bond 0.00803 ( 10) SS BOND : angle 1.60020 ( 20) hydrogen bonds : bond 0.04764 ( 851) hydrogen bonds : angle 4.48475 ( 2613) link_BETA1-4 : bond 0.00331 ( 5) link_BETA1-4 : angle 1.79470 ( 15) link_NAG-ASN : bond 0.00137 ( 10) link_NAG-ASN : angle 4.65552 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8532 (mp0) REVERT: B 93 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: B 296 TYR cc_start: 0.8625 (t80) cc_final: 0.8420 (t80) REVERT: C 93 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8681 (mp0) REVERT: C 275 PHE cc_start: 0.8880 (t80) cc_final: 0.8529 (t80) REVERT: C 297 PHE cc_start: 0.9105 (m-80) cc_final: 0.8774 (m-80) REVERT: D 69 ASN cc_start: 0.9083 (t0) cc_final: 0.8751 (t0) REVERT: D 93 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8624 (mp0) REVERT: E 120 GLU cc_start: 0.9083 (mp0) cc_final: 0.8793 (mp0) REVERT: E 296 TYR cc_start: 0.8627 (t80) cc_final: 0.7986 (t80) outliers start: 35 outliers final: 21 residues processed: 231 average time/residue: 0.0834 time to fit residues: 32.5716 Evaluate side-chains 210 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 51 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 111 optimal weight: 0.0270 chunk 96 optimal weight: 0.0060 chunk 84 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 337 ASN C 337 ASN D 337 ASN E 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.080141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.067485 restraints weight = 42692.034| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.27 r_work: 0.2771 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16585 Z= 0.112 Angle : 0.538 9.326 22655 Z= 0.260 Chirality : 0.043 0.421 2595 Planarity : 0.003 0.023 2820 Dihedral : 5.777 49.510 2465 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.82 % Allowed : 18.81 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.96 (0.18), residues: 1980 helix: 1.99 (0.18), residues: 805 sheet: 0.24 (0.27), residues: 350 loop : -0.51 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 229 TYR 0.009 0.001 TYR B 296 PHE 0.007 0.001 PHE B 297 TRP 0.010 0.001 TRP C 341 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00245 (16560) covalent geometry : angle 0.50805 (22590) SS BOND : bond 0.00803 ( 10) SS BOND : angle 1.51434 ( 20) hydrogen bonds : bond 0.04389 ( 851) hydrogen bonds : angle 4.27681 ( 2613) link_BETA1-4 : bond 0.00215 ( 5) link_BETA1-4 : angle 1.77576 ( 15) link_NAG-ASN : bond 0.00179 ( 10) link_NAG-ASN : angle 4.58659 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: A 195 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8562 (tm-30) REVERT: A 276 MET cc_start: 0.9153 (mmm) cc_final: 0.8948 (tpp) REVERT: B 93 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: B 296 TYR cc_start: 0.8633 (t80) cc_final: 0.8422 (t80) REVERT: C 93 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8695 (mp0) REVERT: C 195 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: C 275 PHE cc_start: 0.8903 (t80) cc_final: 0.8540 (t80) REVERT: C 297 PHE cc_start: 0.9095 (m-80) cc_final: 0.8794 (m-80) REVERT: D 69 ASN cc_start: 0.9075 (t0) cc_final: 0.8871 (t0) REVERT: D 93 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8649 (mp0) REVERT: D 195 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8262 (tm-30) REVERT: D 276 MET cc_start: 0.9194 (mmm) cc_final: 0.8804 (tpt) REVERT: D 438 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8385 (tm-30) REVERT: E 120 GLU cc_start: 0.9055 (mp0) cc_final: 0.8744 (mp0) REVERT: E 195 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: E 296 TYR cc_start: 0.8652 (t80) cc_final: 0.8107 (t80) outliers start: 32 outliers final: 16 residues processed: 225 average time/residue: 0.0856 time to fit residues: 32.7006 Evaluate side-chains 206 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 195 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.079549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.066982 restraints weight = 42784.893| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.14 r_work: 0.2788 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16585 Z= 0.107 Angle : 0.540 9.232 22655 Z= 0.258 Chirality : 0.042 0.423 2595 Planarity : 0.003 0.024 2820 Dihedral : 5.389 42.642 2465 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.05 % Allowed : 19.77 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.09 (0.19), residues: 1980 helix: 2.08 (0.18), residues: 805 sheet: 0.36 (0.28), residues: 350 loop : -0.45 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 229 TYR 0.008 0.001 TYR A 296 PHE 0.006 0.001 PHE B 297 TRP 0.009 0.001 TRP A 341 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00234 (16560) covalent geometry : angle 0.51097 (22590) SS BOND : bond 0.00800 ( 10) SS BOND : angle 1.49329 ( 20) hydrogen bonds : bond 0.04253 ( 851) hydrogen bonds : angle 4.18182 ( 2613) link_BETA1-4 : bond 0.00185 ( 5) link_BETA1-4 : angle 1.78416 ( 15) link_NAG-ASN : bond 0.00199 ( 10) link_NAG-ASN : angle 4.56111 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.619 Fit side-chains REVERT: A 93 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: A 195 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: A 276 MET cc_start: 0.9110 (mmm) cc_final: 0.8895 (tpp) REVERT: B 93 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: B 195 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: B 438 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8320 (tm-30) REVERT: C 195 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: C 468 ASP cc_start: 0.8659 (t0) cc_final: 0.8432 (t0) REVERT: D 69 ASN cc_start: 0.9046 (t0) cc_final: 0.8845 (t0) REVERT: D 195 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: D 276 MET cc_start: 0.9104 (mmm) cc_final: 0.8738 (tpt) REVERT: D 438 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8312 (tm-30) REVERT: E 120 GLU cc_start: 0.9001 (mp0) cc_final: 0.8715 (mp0) REVERT: E 182 MET cc_start: 0.8807 (ttp) cc_final: 0.8595 (ttt) REVERT: E 296 TYR cc_start: 0.8670 (t80) cc_final: 0.8184 (t80) outliers start: 36 outliers final: 22 residues processed: 224 average time/residue: 0.0861 time to fit residues: 32.7586 Evaluate side-chains 213 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 293 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 51 optimal weight: 8.9990 chunk 168 optimal weight: 0.0980 chunk 181 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 66 optimal weight: 0.0670 chunk 174 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.079423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.066948 restraints weight = 42960.930| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.15 r_work: 0.2784 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16585 Z= 0.112 Angle : 0.549 9.107 22655 Z= 0.264 Chirality : 0.042 0.416 2595 Planarity : 0.003 0.023 2820 Dihedral : 5.123 34.152 2465 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.88 % Allowed : 20.06 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.15 (0.19), residues: 1980 helix: 2.12 (0.18), residues: 805 sheet: 0.39 (0.28), residues: 350 loop : -0.40 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 229 TYR 0.009 0.001 TYR A 296 PHE 0.009 0.001 PHE B 297 TRP 0.009 0.001 TRP B 341 HIS 0.004 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00248 (16560) covalent geometry : angle 0.52050 (22590) SS BOND : bond 0.00783 ( 10) SS BOND : angle 1.47299 ( 20) hydrogen bonds : bond 0.04217 ( 851) hydrogen bonds : angle 4.15521 ( 2613) link_BETA1-4 : bond 0.00168 ( 5) link_BETA1-4 : angle 1.79155 ( 15) link_NAG-ASN : bond 0.00159 ( 10) link_NAG-ASN : angle 4.49537 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.528 Fit side-chains REVERT: A 93 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: A 195 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: A 276 MET cc_start: 0.9119 (mmm) cc_final: 0.8897 (tpp) REVERT: B 93 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: B 195 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: B 438 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8324 (tm-30) REVERT: C 195 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: D 69 ASN cc_start: 0.9035 (t0) cc_final: 0.8820 (t0) REVERT: D 195 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: D 276 MET cc_start: 0.9120 (mmm) cc_final: 0.8774 (tpt) REVERT: D 438 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8324 (tm-30) REVERT: E 120 GLU cc_start: 0.8990 (mp0) cc_final: 0.8699 (mp0) REVERT: E 195 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: E 296 TYR cc_start: 0.8654 (t80) cc_final: 0.8201 (t80) outliers start: 33 outliers final: 21 residues processed: 216 average time/residue: 0.0869 time to fit residues: 31.6577 Evaluate side-chains 212 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 293 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 162 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.065704 restraints weight = 42930.395| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.15 r_work: 0.2735 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16585 Z= 0.191 Angle : 0.592 9.360 22655 Z= 0.288 Chirality : 0.043 0.417 2595 Planarity : 0.003 0.026 2820 Dihedral : 5.105 27.918 2465 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.99 % Allowed : 20.11 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.96 (0.18), residues: 1980 helix: 1.96 (0.17), residues: 805 sheet: 0.24 (0.28), residues: 350 loop : -0.47 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 208 TYR 0.010 0.001 TYR A 296 PHE 0.010 0.001 PHE B 297 TRP 0.010 0.001 TRP B 341 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00443 (16560) covalent geometry : angle 0.56538 (22590) SS BOND : bond 0.00734 ( 10) SS BOND : angle 1.61612 ( 20) hydrogen bonds : bond 0.04840 ( 851) hydrogen bonds : angle 4.36249 ( 2613) link_BETA1-4 : bond 0.00412 ( 5) link_BETA1-4 : angle 1.73777 ( 15) link_NAG-ASN : bond 0.00325 ( 10) link_NAG-ASN : angle 4.52435 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.496 Fit side-chains REVERT: A 93 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8540 (mp0) REVERT: A 195 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: B 195 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: C 195 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: C 276 MET cc_start: 0.9128 (mmm) cc_final: 0.8845 (tpt) REVERT: D 69 ASN cc_start: 0.9090 (t0) cc_final: 0.8885 (t0) REVERT: D 195 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: D 276 MET cc_start: 0.9155 (mmm) cc_final: 0.8833 (tpt) REVERT: E 120 GLU cc_start: 0.9019 (mp0) cc_final: 0.8745 (mp0) REVERT: E 195 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: E 296 TYR cc_start: 0.8763 (t80) cc_final: 0.8236 (t80) outliers start: 35 outliers final: 27 residues processed: 216 average time/residue: 0.0849 time to fit residues: 31.2079 Evaluate side-chains 213 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 293 ILE Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 126 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.066413 restraints weight = 42924.553| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.14 r_work: 0.2772 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16585 Z= 0.112 Angle : 0.561 9.244 22655 Z= 0.270 Chirality : 0.042 0.423 2595 Planarity : 0.003 0.025 2820 Dihedral : 4.945 27.623 2465 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.99 % Allowed : 20.34 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.05 (0.19), residues: 1980 helix: 2.05 (0.18), residues: 805 sheet: 0.29 (0.28), residues: 350 loop : -0.45 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 229 TYR 0.009 0.001 TYR C 296 PHE 0.007 0.001 PHE B 297 TRP 0.010 0.001 TRP B 341 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00249 (16560) covalent geometry : angle 0.53304 (22590) SS BOND : bond 0.00781 ( 10) SS BOND : angle 1.44919 ( 20) hydrogen bonds : bond 0.04350 ( 851) hydrogen bonds : angle 4.17345 ( 2613) link_BETA1-4 : bond 0.00155 ( 5) link_BETA1-4 : angle 1.52538 ( 15) link_NAG-ASN : bond 0.00218 ( 10) link_NAG-ASN : angle 4.55746 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.625 Fit side-chains REVERT: A 93 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: A 195 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8529 (tm-30) REVERT: B 195 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: B 247 LEU cc_start: 0.9457 (tp) cc_final: 0.9172 (tt) REVERT: C 195 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: C 468 ASP cc_start: 0.8636 (t0) cc_final: 0.8386 (t0) REVERT: D 69 ASN cc_start: 0.9070 (t0) cc_final: 0.8857 (t0) REVERT: D 195 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: D 276 MET cc_start: 0.9079 (mmm) cc_final: 0.8772 (tpt) REVERT: E 120 GLU cc_start: 0.9026 (mp0) cc_final: 0.8736 (mp0) REVERT: E 195 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: E 296 TYR cc_start: 0.8717 (t80) cc_final: 0.8205 (t80) outliers start: 35 outliers final: 27 residues processed: 220 average time/residue: 0.0822 time to fit residues: 30.6292 Evaluate side-chains 219 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 293 ILE Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 26 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.065380 restraints weight = 42811.953| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.13 r_work: 0.2727 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16585 Z= 0.203 Angle : 0.606 9.264 22655 Z= 0.297 Chirality : 0.043 0.415 2595 Planarity : 0.003 0.026 2820 Dihedral : 5.025 28.016 2465 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.88 % Allowed : 20.45 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.84 (0.18), residues: 1980 helix: 1.87 (0.17), residues: 805 sheet: 0.17 (0.28), residues: 350 loop : -0.55 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 208 TYR 0.010 0.001 TYR A 296 PHE 0.009 0.001 PHE E 252 TRP 0.011 0.001 TRP B 341 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00470 (16560) covalent geometry : angle 0.58089 (22590) SS BOND : bond 0.00687 ( 10) SS BOND : angle 1.62293 ( 20) hydrogen bonds : bond 0.05016 ( 851) hydrogen bonds : angle 4.39965 ( 2613) link_BETA1-4 : bond 0.00360 ( 5) link_BETA1-4 : angle 1.65542 ( 15) link_NAG-ASN : bond 0.00405 ( 10) link_NAG-ASN : angle 4.46775 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.513 Fit side-chains REVERT: A 93 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8561 (mp0) REVERT: A 195 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: B 195 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: C 275 PHE cc_start: 0.8980 (t80) cc_final: 0.8648 (t80) REVERT: D 69 ASN cc_start: 0.9121 (t0) cc_final: 0.8885 (t0) REVERT: D 195 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: D 276 MET cc_start: 0.9125 (mmm) cc_final: 0.8831 (tpt) REVERT: E 120 GLU cc_start: 0.9024 (mp0) cc_final: 0.8751 (mp0) REVERT: E 195 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: E 276 MET cc_start: 0.9144 (mmm) cc_final: 0.8881 (tpt) REVERT: E 296 TYR cc_start: 0.8765 (t80) cc_final: 0.8154 (t80) outliers start: 33 outliers final: 21 residues processed: 210 average time/residue: 0.0855 time to fit residues: 30.3528 Evaluate side-chains 207 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 293 ILE Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 132 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 39 optimal weight: 0.0270 chunk 47 optimal weight: 0.6980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.079442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.067004 restraints weight = 42676.443| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.17 r_work: 0.2780 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16585 Z= 0.109 Angle : 0.573 9.255 22655 Z= 0.277 Chirality : 0.043 0.422 2595 Planarity : 0.003 0.026 2820 Dihedral : 4.869 27.693 2465 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.65 % Allowed : 20.62 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1980 helix: 2.04 (0.18), residues: 805 sheet: 0.04 (0.28), residues: 360 loop : -0.42 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 441 TYR 0.009 0.001 TYR D 296 PHE 0.008 0.001 PHE A 297 TRP 0.010 0.001 TRP B 341 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00234 (16560) covalent geometry : angle 0.54594 (22590) SS BOND : bond 0.00805 ( 10) SS BOND : angle 1.37666 ( 20) hydrogen bonds : bond 0.04272 ( 851) hydrogen bonds : angle 4.14720 ( 2613) link_BETA1-4 : bond 0.00090 ( 5) link_BETA1-4 : angle 1.45208 ( 15) link_NAG-ASN : bond 0.00346 ( 10) link_NAG-ASN : angle 4.56908 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.679 Fit side-chains REVERT: A 93 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: A 195 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8542 (tm-30) REVERT: B 195 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: B 247 LEU cc_start: 0.9444 (tp) cc_final: 0.9179 (tt) REVERT: C 468 ASP cc_start: 0.8612 (t0) cc_final: 0.8347 (t0) REVERT: D 69 ASN cc_start: 0.9094 (t0) cc_final: 0.8888 (t0) REVERT: D 195 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: D 276 MET cc_start: 0.9058 (mmm) cc_final: 0.8768 (tpt) REVERT: E 120 GLU cc_start: 0.9024 (mp0) cc_final: 0.8742 (mp0) REVERT: E 195 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: E 296 TYR cc_start: 0.8725 (t80) cc_final: 0.8167 (t80) outliers start: 29 outliers final: 21 residues processed: 218 average time/residue: 0.0888 time to fit residues: 32.9675 Evaluate side-chains 216 residues out of total 1795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 293 ILE Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 30.0000 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.066384 restraints weight = 42781.857| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.16 r_work: 0.2773 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16585 Z= 0.120 Angle : 0.572 8.933 22655 Z= 0.275 Chirality : 0.042 0.409 2595 Planarity : 0.003 0.026 2820 Dihedral : 4.763 27.809 2465 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.65 % Allowed : 20.68 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.06 (0.19), residues: 1980 helix: 2.11 (0.18), residues: 805 sheet: 0.08 (0.28), residues: 360 loop : -0.41 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 441 TYR 0.008 0.001 TYR C 140 PHE 0.006 0.001 PHE B 297 TRP 0.009 0.001 TRP B 341 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00271 (16560) covalent geometry : angle 0.54660 (22590) SS BOND : bond 0.00768 ( 10) SS BOND : angle 1.43970 ( 20) hydrogen bonds : bond 0.04307 ( 851) hydrogen bonds : angle 4.13312 ( 2613) link_BETA1-4 : bond 0.00165 ( 5) link_BETA1-4 : angle 1.61772 ( 15) link_NAG-ASN : bond 0.00129 ( 10) link_NAG-ASN : angle 4.38936 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.22 seconds wall clock time: 42 minutes 13.27 seconds (2533.27 seconds total)