Starting phenix.real_space_refine on Thu Aug 6 18:20:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zq0_74539/08_2026/9zq0_74539.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zq0_74539/08_2026/9zq0_74539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zq0_74539/08_2026/9zq0_74539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zq0_74539/08_2026/9zq0_74539.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zq0_74539/08_2026/9zq0_74539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zq0_74539/08_2026/9zq0_74539.map" } resolution = 2.11 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= 0.001 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: 6 Type Number sf(0) Gaussians K 5 8.98 5 P 36 5.49 5 S 76 5.16 5 C 10685 2.51 5 N 2388 2.21 5 O 2948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16138 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "D" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "A" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 396 Unusual residues: {' K': 5, 'CLR': 1, 'PCW': 7, 'PIO': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'PCW:plan-4': 3, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 295 Unusual residues: {'CLR': 1, 'PCW': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'PCW:plan-2': 4, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 394 Unusual residues: {'CLR': 1, 'PCW': 7, 'PIO': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'PCW:plan-4': 3, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 297 Unusual residues: {'CLR': 1, 'PCW': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'PCW:plan-4': 2, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.25, per 1000 atoms: 0.20 Number of scatterers: 16138 At special positions: 0 Unit cell: (107.1, 107.1, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 5 19.00 S 76 16.00 P 36 15.00 O 2948 8.00 N 2388 7.00 C 10685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 656.5 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 12 sheets defined 67.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.547A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.158A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.887A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.924A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.662A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 4.008A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 404 through 424 Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 458 through 476 removed outlier: 6.141A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 588 through 605 Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.549A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.145A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.876A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.931A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 removed outlier: 3.515A pdb=" N LEU B 258 " --> pdb=" O PRO B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.681A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 4.009A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 404 through 424 Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 458 through 476 removed outlier: 6.124A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 588 through 605 Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.550A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.150A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.884A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.951A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 removed outlier: 3.516A pdb=" N LEU C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 258' Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.686A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 4.000A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 404 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 476 removed outlier: 6.118A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.548A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.162A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.881A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.954A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 removed outlier: 3.538A pdb=" N LEU D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.778A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 4.012A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 458 through 476 removed outlier: 6.147A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 588 through 605 Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 498 Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.293A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 498 Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.284A pdb=" N TYR B 505 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 567 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 536 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 498 Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.299A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 536 " --> pdb=" O VAL C 526 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 498 Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.304A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 954 hydrogen bonds defined for protein. 2754 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: 2.66 Time building geometry restraints manager: 1.78 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: 2424 1.31 - 1.43: 4371 1.43 - 1.56: 9470 1.56 - 1.68: 64 1.68 - 1.81: 128 Bond restraints: 16457 Sorted by residual: bond pdb=" C1B PIO A 707 " pdb=" O3C PIO A 707 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1A PIO C 710 " pdb=" O2C PIO C 710 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1B PIO C 708 " pdb=" O3C PIO C 708 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1B PIO A 709 " pdb=" O3C PIO A 709 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1B PIO C 710 " pdb=" O3C PIO C 710 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 16452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 21869 2.50 - 5.01: 169 5.01 - 7.51: 45 7.51 - 10.01: 13 10.01 - 12.52: 9 Bond angle restraints: 22105 Sorted by residual: angle pdb=" O11 PIO C 710 " pdb=" P1 PIO C 710 " pdb=" O12 PIO C 710 " ideal model delta sigma weight residual 121.09 108.57 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O11 PIO A 707 " pdb=" P1 PIO A 707 " pdb=" O12 PIO A 707 " ideal model delta sigma weight residual 121.09 108.62 12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" O1 PIO A 707 " pdb=" P1 PIO A 707 " pdb=" O13 PIO A 707 " ideal model delta sigma weight residual 97.64 109.76 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O1 PIO C 710 " pdb=" P1 PIO C 710 " pdb=" O13 PIO C 710 " ideal model delta sigma weight residual 97.64 109.63 -11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O11 PIO C 708 " pdb=" P1 PIO C 708 " pdb=" O12 PIO C 708 " ideal model delta sigma weight residual 121.09 109.33 11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 22100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.54: 9596 31.54 - 63.09: 569 63.09 - 94.63: 33 94.63 - 126.17: 2 126.17 - 157.72: 2 Dihedral angle restraints: 10202 sinusoidal: 4878 harmonic: 5324 Sorted by residual: dihedral pdb=" N PCW B 703 " pdb=" C4 PCW B 703 " pdb=" C5 PCW B 703 " pdb=" O4P PCW B 703 " ideal model delta sinusoidal sigma weight residual -66.66 91.06 -157.72 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C33 PCW D 701 " pdb=" C31 PCW D 701 " pdb=" C32 PCW D 701 " pdb=" O2 PCW D 701 " ideal model delta sinusoidal sigma weight residual 191.83 48.56 143.27 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C33 PCW A 703 " pdb=" C31 PCW A 703 " pdb=" C32 PCW A 703 " pdb=" O2 PCW A 703 " ideal model delta sinusoidal sigma weight residual 191.83 84.97 106.86 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 10199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1612 0.031 - 0.061: 521 0.061 - 0.092: 179 0.092 - 0.122: 64 0.122 - 0.153: 8 Chirality restraints: 2384 Sorted by residual: chirality pdb=" CA ASN C 559 " pdb=" N ASN C 559 " pdb=" C ASN C 559 " pdb=" CB ASN C 559 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ASN A 559 " pdb=" N ASN A 559 " pdb=" C ASN A 559 " pdb=" CB ASN A 559 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ASN B 559 " pdb=" N ASN B 559 " pdb=" C ASN B 559 " pdb=" CB ASN B 559 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 2381 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 572 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ASP A 572 " 0.026 2.00e-02 2.50e+03 pdb=" O ASP A 572 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 573 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 572 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C ASP C 572 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP C 572 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU C 573 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 572 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C ASP B 572 " -0.024 2.00e-02 2.50e+03 pdb=" O ASP B 572 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 573 " 0.008 2.00e-02 2.50e+03 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 3725 2.80 - 3.38: 17605 3.38 - 3.97: 31937 3.97 - 4.55: 45380 4.55 - 5.14: 64611 Nonbonded interactions: 163258 Sorted by model distance: nonbonded pdb=" OG SER A 427 " pdb=" OD1 ASP A 429 " model vdw 2.213 3.040 nonbonded pdb=" OG SER D 427 " pdb=" OD1 ASP D 429 " model vdw 2.224 3.040 nonbonded pdb=" O THR D 357 " pdb=" OG1 THR D 361 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 427 " pdb=" OD1 ASP B 429 " model vdw 2.233 3.040 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.237 3.040 ... (remaining 163253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 605 or (resid 704 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name O \ 11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name \ O4P or name P )) or (resid 705 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37)) or (resid 706 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name O3 or name \ O31 or name O3P)))) selection = (chain 'B' and (resid 156 through 605 or (resid 704 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name O \ 11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name \ O4P or name P )) or (resid 705 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37)) or (resid 706 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name O3 or name \ O31 or name O3P)))) selection = (chain 'C' and (resid 156 through 605 or (resid 704 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name O \ 11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name \ O4P or name P )) or (resid 705 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37)) or (resid 706 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name O3 or name \ O31 or name O3P)))) selection = (chain 'D' and (resid 156 through 605 or (resid 704 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name O \ 11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name \ O4P or name P )) or (resid 705 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or name C \ 34 or name C35 or name C36 or name C37)) or (resid 706 and (name C1 or name C11 \ or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name O3 or name \ O31 or name O3P)))) } 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: 3.150 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.430 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9252 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 : 0.003 0.068 16457 Z= 0.154 Angle : 0.625 12.515 22105 Z= 0.272 Chirality : 0.037 0.153 2384 Planarity : 0.003 0.027 2635 Dihedral : 17.529 157.717 6786 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.86 % Allowed : 16.38 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.43 (0.20), residues: 1792 helix: 3.01 (0.15), residues: 1184 sheet: 0.89 (0.80), residues: 44 loop : 0.82 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 220 TYR 0.010 0.001 TYR C 354 PHE 0.011 0.001 PHE A 423 TRP 0.017 0.001 TRP B 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (16457) covalent geometry : angle 0.62530 / 0.27 (22105) hydrogen bonds : bond 0.08497 / 5.60 ( 954) hydrogen bonds : angle 3.90103 / 2.78 ( 2754) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.619 Fit side-chains REVERT: A 205 TYR cc_start: 0.7281 (m-10) cc_final: 0.7024 (t80) REVERT: A 329 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8670 (t0) REVERT: A 451 LYS cc_start: 0.9007 (mppt) cc_final: 0.8784 (mppt) REVERT: A 583 GLU cc_start: 0.8520 (tt0) cc_final: 0.8217 (tm-30) REVERT: B 205 TYR cc_start: 0.7381 (m-10) cc_final: 0.7094 (t80) REVERT: B 329 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8661 (t0) REVERT: B 413 ARG cc_start: 0.8631 (mtm-85) cc_final: 0.8215 (mtp85) REVERT: B 521 GLU cc_start: 0.7725 (tt0) cc_final: 0.7507 (tm-30) REVERT: B 583 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7552 (pp20) REVERT: C 205 TYR cc_start: 0.7269 (m-10) cc_final: 0.7029 (t80) REVERT: C 329 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8648 (t0) REVERT: C 451 LYS cc_start: 0.9041 (mppt) cc_final: 0.8829 (mppt) REVERT: C 583 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7783 (pp20) REVERT: D 205 TYR cc_start: 0.7361 (m-10) cc_final: 0.7082 (t80) outliers start: 14 outliers final: 12 residues processed: 125 average time/residue: 0.7257 time to fit residues: 99.4990 Evaluate side-chains 127 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 423 PHE Chi-restraints excluded: chain D residue 492 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.068222 restraints weight = 23902.693| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.74 r_work: 0.2782 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9246 moved from start: 0.0431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16457 Z= 0.112 Angle : 0.430 7.259 22105 Z= 0.228 Chirality : 0.038 0.154 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.550 157.886 3237 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.17 % Allowed : 15.15 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.20), residues: 1792 helix: 2.71 (0.15), residues: 1228 sheet: 1.04 (0.83), residues: 44 loop : 0.64 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 424 TYR 0.012 0.001 TYR A 349 PHE 0.014 0.001 PHE A 423 TRP 0.016 0.001 TRP B 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16457) covalent geometry : angle 0.42967 / 0.23 (22105) hydrogen bonds : bond 0.03792 / 2.50 ( 954) hydrogen bonds : angle 3.47118 / 2.48 ( 2754) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.405 Fit side-chains REVERT: A 205 TYR cc_start: 0.7269 (m-10) cc_final: 0.7041 (t80) REVERT: A 583 GLU cc_start: 0.8540 (tt0) cc_final: 0.8029 (tm-30) REVERT: A 586 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8965 (p) REVERT: B 205 TYR cc_start: 0.7296 (m-10) cc_final: 0.7039 (t80) REVERT: B 413 ARG cc_start: 0.8637 (mtm-85) cc_final: 0.8199 (mtp85) REVERT: B 521 GLU cc_start: 0.7703 (tt0) cc_final: 0.7474 (tm-30) REVERT: C 205 TYR cc_start: 0.7271 (m-10) cc_final: 0.7043 (t80) REVERT: C 451 LYS cc_start: 0.9038 (mppt) cc_final: 0.8825 (mppt) REVERT: C 583 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7780 (pp20) REVERT: D 205 TYR cc_start: 0.7268 (m-10) cc_final: 0.7028 (t80) REVERT: D 596 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8579 (mt-10) outliers start: 19 outliers final: 8 residues processed: 132 average time/residue: 0.6318 time to fit residues: 91.3841 Evaluate side-chains 125 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 143 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.066642 restraints weight = 24072.974| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.75 r_work: 0.2743 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16457 Z= 0.145 Angle : 0.455 8.618 22105 Z= 0.242 Chirality : 0.039 0.158 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.732 156.920 3217 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.79 % Allowed : 14.41 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.20), residues: 1792 helix: 2.62 (0.15), residues: 1228 sheet: 1.19 (0.84), residues: 44 loop : 0.65 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 218 TYR 0.014 0.001 TYR C 351 PHE 0.018 0.001 PHE A 423 TRP 0.017 0.001 TRP C 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16457) covalent geometry : angle 0.45488 / 0.24 (22105) hydrogen bonds : bond 0.04323 / 2.85 ( 954) hydrogen bonds : angle 3.54573 / 2.54 ( 2754) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.731 Fit side-chains REVERT: A 205 TYR cc_start: 0.7364 (m-10) cc_final: 0.7030 (t80) REVERT: A 299 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8219 (mtp180) REVERT: A 413 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8158 (mtp85) REVERT: A 583 GLU cc_start: 0.8561 (tt0) cc_final: 0.8173 (tm-30) REVERT: B 205 TYR cc_start: 0.7356 (m-10) cc_final: 0.7048 (t80) REVERT: B 521 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: C 205 TYR cc_start: 0.7360 (m-10) cc_final: 0.7048 (t80) REVERT: C 583 GLU cc_start: 0.8208 (pp20) cc_final: 0.7842 (pp20) REVERT: D 205 TYR cc_start: 0.7361 (m-10) cc_final: 0.7014 (t80) REVERT: D 596 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8598 (mt-10) outliers start: 29 outliers final: 13 residues processed: 144 average time/residue: 0.6843 time to fit residues: 108.5718 Evaluate side-chains 129 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.088970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.065362 restraints weight = 24099.782| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.75 r_work: 0.2714 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9296 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 16457 Z= 0.197 Angle : 0.501 9.060 22105 Z= 0.264 Chirality : 0.041 0.159 2384 Planarity : 0.003 0.027 2635 Dihedral : 14.379 154.896 3214 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.72 % Allowed : 14.35 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.20), residues: 1792 helix: 2.49 (0.15), residues: 1228 sheet: 1.23 (0.86), residues: 44 loop : 0.61 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 218 TYR 0.018 0.001 TYR C 351 PHE 0.021 0.002 PHE A 423 TRP 0.018 0.002 TRP C 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (16457) covalent geometry : angle 0.50076 / 0.26 (22105) hydrogen bonds : bond 0.04840 / 3.19 ( 954) hydrogen bonds : angle 3.70493 / 2.66 ( 2754) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.709 Fit side-chains REVERT: A 299 ARG cc_start: 0.8545 (ttm110) cc_final: 0.8195 (mtp180) REVERT: A 413 ARG cc_start: 0.8568 (mtm110) cc_final: 0.8174 (mtp85) REVERT: A 430 MET cc_start: 0.9054 (mmm) cc_final: 0.8675 (tpp) REVERT: A 583 GLU cc_start: 0.8583 (tt0) cc_final: 0.8203 (tm-30) REVERT: B 494 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9001 (mmmm) REVERT: B 521 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: C 583 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7855 (pp20) REVERT: D 583 GLU cc_start: 0.8300 (pp20) cc_final: 0.7892 (pp20) REVERT: D 596 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8557 (mt-10) outliers start: 28 outliers final: 13 residues processed: 135 average time/residue: 0.7573 time to fit residues: 112.1654 Evaluate side-chains 123 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 142 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 159 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 444 ASN C 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.068049 restraints weight = 23958.738| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.74 r_work: 0.2774 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9258 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16457 Z= 0.107 Angle : 0.434 9.133 22105 Z= 0.228 Chirality : 0.038 0.154 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.620 157.119 3214 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.03 % Allowed : 14.10 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.20), residues: 1792 helix: 2.66 (0.15), residues: 1228 sheet: 1.30 (0.86), residues: 44 loop : 0.64 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 424 TYR 0.010 0.001 TYR C 354 PHE 0.013 0.001 PHE A 423 TRP 0.018 0.001 TRP C 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16457) covalent geometry : angle 0.43421 / 0.23 (22105) hydrogen bonds : bond 0.03720 / 2.45 ( 954) hydrogen bonds : angle 3.38546 / 2.43 ( 2754) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7420 (m-10) cc_final: 0.7057 (t80) REVERT: A 299 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8188 (mtp180) REVERT: A 329 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8648 (t0) REVERT: A 413 ARG cc_start: 0.8500 (mtm110) cc_final: 0.8143 (mtp85) REVERT: A 583 GLU cc_start: 0.8549 (tt0) cc_final: 0.8004 (tm-30) REVERT: A 586 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.8946 (p) REVERT: B 205 TYR cc_start: 0.7444 (m-10) cc_final: 0.7059 (t80) REVERT: B 329 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8648 (t0) REVERT: B 521 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: C 205 TYR cc_start: 0.7408 (m-10) cc_final: 0.7037 (t80) REVERT: C 329 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8651 (t0) REVERT: C 583 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7790 (pp20) REVERT: D 205 TYR cc_start: 0.7431 (m-10) cc_final: 0.7051 (t80) REVERT: D 583 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7837 (pp20) REVERT: D 596 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8600 (mt-10) outliers start: 33 outliers final: 14 residues processed: 142 average time/residue: 0.7190 time to fit residues: 112.6784 Evaluate side-chains 136 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 423 PHE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.066097 restraints weight = 23938.918| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.74 r_work: 0.2733 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9286 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16457 Z= 0.159 Angle : 0.469 7.767 22105 Z= 0.249 Chirality : 0.040 0.157 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.998 156.108 3214 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.79 % Allowed : 14.59 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.20), residues: 1792 helix: 2.56 (0.15), residues: 1228 sheet: 1.19 (0.85), residues: 44 loop : 0.61 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 218 TYR 0.015 0.001 TYR C 351 PHE 0.017 0.001 PHE A 423 TRP 0.018 0.001 TRP C 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (16457) covalent geometry : angle 0.46941 / 0.25 (22105) hydrogen bonds : bond 0.04471 / 2.95 ( 954) hydrogen bonds : angle 3.55521 / 2.56 ( 2754) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.459 Fit side-chains REVERT: A 299 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8196 (mtp180) REVERT: A 329 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8645 (t0) REVERT: A 413 ARG cc_start: 0.8550 (mtm110) cc_final: 0.8162 (mtp85) REVERT: A 583 GLU cc_start: 0.8578 (tt0) cc_final: 0.8186 (tm-30) REVERT: B 329 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8640 (t0) REVERT: B 494 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9005 (mmmm) REVERT: B 521 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: C 329 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8648 (t0) REVERT: C 583 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7843 (pp20) REVERT: D 521 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6973 (pp20) REVERT: D 583 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7855 (pp20) REVERT: D 596 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8566 (mt-10) outliers start: 29 outliers final: 13 residues processed: 133 average time/residue: 0.6690 time to fit residues: 97.2968 Evaluate side-chains 133 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.067786 restraints weight = 23739.719| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.73 r_work: 0.2770 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9259 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16457 Z= 0.114 Angle : 0.434 7.170 22105 Z= 0.230 Chirality : 0.038 0.154 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.592 157.256 3214 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.54 % Allowed : 14.78 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.20), residues: 1792 helix: 2.66 (0.15), residues: 1228 sheet: 1.13 (0.84), residues: 44 loop : 0.63 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 271 TYR 0.011 0.001 TYR C 349 PHE 0.014 0.001 PHE A 423 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (16457) covalent geometry : angle 0.43402 / 0.23 (22105) hydrogen bonds : bond 0.03844 / 2.53 ( 954) hydrogen bonds : angle 3.38911 / 2.44 ( 2754) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.555 Fit side-chains REVERT: A 205 TYR cc_start: 0.7345 (m-10) cc_final: 0.7026 (t80) REVERT: A 299 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8181 (mtp180) REVERT: A 329 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8629 (t0) REVERT: A 413 ARG cc_start: 0.8499 (mtm110) cc_final: 0.8142 (mtp85) REVERT: A 583 GLU cc_start: 0.8545 (tt0) cc_final: 0.8002 (tm-30) REVERT: A 586 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.8941 (p) REVERT: B 205 TYR cc_start: 0.7334 (m-10) cc_final: 0.7052 (t80) REVERT: B 329 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8628 (t0) REVERT: B 521 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: C 205 TYR cc_start: 0.7354 (m-10) cc_final: 0.7061 (t80) REVERT: C 329 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8634 (t0) REVERT: C 583 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7773 (pp20) REVERT: D 205 TYR cc_start: 0.7339 (m-10) cc_final: 0.7024 (t80) REVERT: D 521 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6959 (pp20) REVERT: D 583 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7803 (pp20) REVERT: D 596 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8575 (mt-10) outliers start: 25 outliers final: 11 residues processed: 133 average time/residue: 0.6683 time to fit residues: 97.4464 Evaluate side-chains 134 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 7 optimal weight: 0.0060 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.068408 restraints weight = 23853.288| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.73 r_work: 0.2783 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9254 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16457 Z= 0.105 Angle : 0.424 6.776 22105 Z= 0.226 Chirality : 0.038 0.152 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.329 157.947 3214 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.48 % Allowed : 14.96 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.20), residues: 1792 helix: 2.69 (0.15), residues: 1228 sheet: 1.19 (0.84), residues: 44 loop : 0.65 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 271 TYR 0.010 0.001 TYR A 349 PHE 0.012 0.001 PHE A 423 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (16457) covalent geometry : angle 0.42432 / 0.23 (22105) hydrogen bonds : bond 0.03674 / 2.42 ( 954) hydrogen bonds : angle 3.32152 / 2.39 ( 2754) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.532 Fit side-chains REVERT: A 205 TYR cc_start: 0.7274 (m-10) cc_final: 0.7042 (t80) REVERT: A 299 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8201 (mtp180) REVERT: A 329 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8647 (t0) REVERT: A 413 ARG cc_start: 0.8506 (mtm110) cc_final: 0.8149 (mtp85) REVERT: A 583 GLU cc_start: 0.8543 (tt0) cc_final: 0.8007 (tm-30) REVERT: A 586 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.8938 (p) REVERT: B 205 TYR cc_start: 0.7267 (m-10) cc_final: 0.7038 (t80) REVERT: B 329 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8642 (t0) REVERT: C 205 TYR cc_start: 0.7283 (m-10) cc_final: 0.7041 (t80) REVERT: C 329 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8647 (t0) REVERT: C 583 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: D 205 TYR cc_start: 0.7263 (m-10) cc_final: 0.7036 (t80) REVERT: D 521 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: D 583 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7808 (pp20) REVERT: D 596 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8597 (mt-10) outliers start: 24 outliers final: 10 residues processed: 133 average time/residue: 0.6990 time to fit residues: 102.0637 Evaluate side-chains 130 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 0.0070 chunk 168 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 170 optimal weight: 0.2980 chunk 160 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.069580 restraints weight = 23774.210| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.73 r_work: 0.2810 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16457 Z= 0.094 Angle : 0.414 6.534 22105 Z= 0.221 Chirality : 0.038 0.201 2384 Planarity : 0.003 0.027 2635 Dihedral : 12.969 158.672 3214 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.05 % Allowed : 15.46 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.20), residues: 1792 helix: 2.75 (0.15), residues: 1228 sheet: 1.24 (0.84), residues: 44 loop : 0.68 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 271 TYR 0.010 0.001 TYR C 354 PHE 0.011 0.001 PHE A 423 TRP 0.016 0.001 TRP D 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (16457) covalent geometry : angle 0.41443 / 0.22 (22105) hydrogen bonds : bond 0.03385 / 2.23 ( 954) hydrogen bonds : angle 3.21736 / 2.32 ( 2754) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.666 Fit side-chains REVERT: A 299 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8198 (mtp180) REVERT: A 329 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8649 (t0) REVERT: A 413 ARG cc_start: 0.8485 (mtm110) cc_final: 0.8137 (mtp85) REVERT: A 583 GLU cc_start: 0.8513 (tt0) cc_final: 0.8065 (tm-30) REVERT: A 586 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8970 (p) REVERT: B 329 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8650 (t0) REVERT: B 521 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: C 329 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8666 (t0) REVERT: C 583 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: D 521 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6993 (pp20) REVERT: D 583 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7781 (pp20) REVERT: D 596 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8587 (mt-10) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 0.7795 time to fit residues: 104.7651 Evaluate side-chains 127 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 423 PHE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 155 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.068038 restraints weight = 23823.406| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.73 r_work: 0.2777 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16457 Z= 0.111 Angle : 0.434 6.500 22105 Z= 0.232 Chirality : 0.038 0.184 2384 Planarity : 0.003 0.027 2635 Dihedral : 12.951 158.192 3206 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.05 % Allowed : 15.58 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.20), residues: 1792 helix: 2.70 (0.15), residues: 1228 sheet: 1.21 (0.84), residues: 44 loop : 0.67 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 271 TYR 0.011 0.001 TYR C 349 PHE 0.013 0.001 PHE A 423 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16457) covalent geometry : angle 0.43362 / 0.23 (22105) hydrogen bonds : bond 0.03747 / 2.46 ( 954) hydrogen bonds : angle 3.28411 / 2.36 ( 2754) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.510 Fit side-chains REVERT: A 299 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8200 (mtp180) REVERT: A 329 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8632 (t0) REVERT: A 413 ARG cc_start: 0.8521 (mtm110) cc_final: 0.8159 (mtp85) REVERT: A 583 GLU cc_start: 0.8538 (tt0) cc_final: 0.8168 (tm-30) REVERT: B 329 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8642 (t0) REVERT: B 521 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: C 329 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8646 (t0) REVERT: C 583 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7776 (pp20) REVERT: D 521 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7003 (pp20) REVERT: D 583 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7804 (pp20) REVERT: D 596 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8592 (mt-10) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.7462 time to fit residues: 98.7023 Evaluate side-chains 128 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 596 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 143 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 127 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 137 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.068186 restraints weight = 23993.183| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.74 r_work: 0.2781 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9251 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16457 Z= 0.105 Angle : 0.431 6.402 22105 Z= 0.231 Chirality : 0.038 0.176 2384 Planarity : 0.003 0.027 2635 Dihedral : 12.849 158.408 3206 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.29 % Allowed : 15.52 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.20), residues: 1792 helix: 2.71 (0.15), residues: 1228 sheet: 1.23 (0.84), residues: 44 loop : 0.69 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 271 TYR 0.010 0.001 TYR D 205 PHE 0.012 0.001 PHE A 423 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (16457) covalent geometry : angle 0.43130 / 0.23 (22105) hydrogen bonds : bond 0.03641 / 2.39 ( 954) hydrogen bonds : angle 3.23814 / 2.33 ( 2754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6888.08 seconds wall clock time: 117 minutes 47.37 seconds (7067.37 seconds total)