Starting phenix.real_space_refine on Fri Jul 3 22:38:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zq0_74539/07_2026/9zq0_74539.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zq0_74539/07_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_74539/07_2026/9zq0_74539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zq0_74539/07_2026/9zq0_74539.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zq0_74539/07_2026/9zq0_74539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zq0_74539/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 391 Ad-hoc single atom residues: {' K': 5} Unusual residues: {'CLR': 1, 'PCW': 7, 'PIO': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 5 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: 3.13, per 1000 atoms: 0.19 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: 1.01 Conformation dependent library (CDL) restraints added in 618.0 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: 0.58 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: 2.08 Time building geometry restraints manager: 1.40 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: 4.710 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: 0.040 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.330 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- 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 : 0.613 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: 0.6699 time to fit residues: 92.0261 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 : 0.519 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.068205 restraints weight = 23903.074| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.74 r_work: 0.2781 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9247 moved from start: 0.0438 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= 0.111 Angle : 0.429 7.246 22105 Z= 0.228 Chirality : 0.038 0.154 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.549 157.897 3237 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.87 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: 1.05 (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 A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (16457) covalent geometry : angle 0.42924 / 0.23 (22105) hydrogen bonds : bond 0.03801 / 2.51 ( 954) hydrogen bonds : angle 3.47015 / 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 : 0.627 Fit side-chains REVERT: A 205 TYR cc_start: 0.7271 (m-10) cc_final: 0.7042 (t80) REVERT: A 583 GLU cc_start: 0.8541 (tt0) cc_final: 0.8030 (tm-30) REVERT: A 586 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.8964 (p) REVERT: B 205 TYR cc_start: 0.7294 (m-10) cc_final: 0.7037 (t80) REVERT: B 413 ARG cc_start: 0.8637 (mtm-85) cc_final: 0.8200 (mtp85) REVERT: B 521 GLU cc_start: 0.7704 (tt0) cc_final: 0.7475 (tm-30) REVERT: C 205 TYR cc_start: 0.7273 (m-10) cc_final: 0.7042 (t80) REVERT: C 451 LYS cc_start: 0.9039 (mppt) cc_final: 0.8825 (mppt) REVERT: C 583 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: D 205 TYR cc_start: 0.7266 (m-10) cc_final: 0.7027 (t80) REVERT: D 596 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8584 (mt-10) outliers start: 19 outliers final: 8 residues processed: 132 average time/residue: 0.7157 time to fit residues: 103.6939 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 : 0.517 ------------------------------------------------------------------------------- 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: 5.9990 chunk 171 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 127 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.092448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.069129 restraints weight = 24071.771| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.74 r_work: 0.2797 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9243 moved from start: 0.0517 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= 0.098 Angle : 0.414 8.272 22105 Z= 0.218 Chirality : 0.038 0.154 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.157 158.331 3217 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.72 % Allowed : 15.15 % Favored : 83.13 % 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: 3.17 (0.20), residues: 1792 helix: 2.74 (0.15), residues: 1228 sheet: 1.21 (0.83), residues: 44 loop : 0.66 (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 349 PHE 0.013 0.001 PHE A 423 TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (16457) covalent geometry : angle 0.41374 / 0.22 (22105) hydrogen bonds : bond 0.03533 / 2.33 ( 954) hydrogen bonds : angle 3.31520 / 2.37 ( 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 142 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.651 Fit side-chains REVERT: A 299 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8206 (mtp180) REVERT: A 583 GLU cc_start: 0.8526 (tt0) cc_final: 0.8007 (tm-30) REVERT: A 586 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.8949 (p) REVERT: B 205 TYR cc_start: 0.7283 (m-10) cc_final: 0.7063 (t80) REVERT: B 413 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8203 (mtp85) REVERT: B 521 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: C 205 TYR cc_start: 0.7286 (m-10) cc_final: 0.7065 (t80) REVERT: C 583 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7768 (pp20) REVERT: D 205 TYR cc_start: 0.7249 (m-10) cc_final: 0.7048 (t80) REVERT: D 596 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8591 (mt-10) outliers start: 28 outliers final: 7 residues processed: 139 average time/residue: 0.6959 time to fit residues: 106.1579 Evaluate side-chains 121 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 427 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.090314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.066749 restraints weight = 24008.526| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.75 r_work: 0.2747 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9275 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16457 Z= 0.142 Angle : 0.459 8.648 22105 Z= 0.242 Chirality : 0.039 0.157 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.564 157.316 3215 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 3.06 (0.20), residues: 1792 helix: 2.64 (0.15), residues: 1228 sheet: 1.29 (0.85), residues: 44 loop : 0.66 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 218 TYR 0.014 0.001 TYR D 351 PHE 0.016 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 0.00326 / 0.14 (16457) covalent geometry : angle 0.45949 / 0.24 (22105) hydrogen bonds : bond 0.04278 / 2.82 ( 954) hydrogen bonds : angle 3.49186 / 2.50 ( 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 148 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.649 Fit side-chains REVERT: A 299 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8232 (mtp180) REVERT: A 413 ARG cc_start: 0.8529 (mtm110) cc_final: 0.8148 (mtp85) REVERT: A 430 MET cc_start: 0.9023 (mmm) cc_final: 0.8622 (tpp) REVERT: A 583 GLU cc_start: 0.8558 (tt0) cc_final: 0.8173 (tm-30) REVERT: B 205 TYR cc_start: 0.7306 (m-10) cc_final: 0.7051 (t80) REVERT: B 521 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 594 MET cc_start: 0.8611 (ttp) cc_final: 0.8370 (ttp) REVERT: C 205 TYR cc_start: 0.7312 (m-10) cc_final: 0.7062 (t80) REVERT: C 583 GLU cc_start: 0.8174 (pp20) cc_final: 0.7820 (pp20) REVERT: D 205 TYR cc_start: 0.7315 (m-10) cc_final: 0.7056 (t80) REVERT: D 583 GLU cc_start: 0.8241 (pp20) cc_final: 0.7829 (pp20) REVERT: D 596 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8572 (mt-10) outliers start: 29 outliers final: 11 residues processed: 141 average time/residue: 0.7030 time to fit residues: 109.0192 Evaluate side-chains 130 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ARG 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 521 GLU Chi-restraints excluded: chain B residue 536 VAL 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 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: 0.0770 chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.092038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068756 restraints weight = 23928.304| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.74 r_work: 0.2791 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9247 moved from start: 0.0632 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= 0.099 Angle : 0.424 8.827 22105 Z= 0.222 Chirality : 0.038 0.153 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.142 158.205 3212 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.97 % Allowed : 14.84 % 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: 3.16 (0.20), residues: 1792 helix: 2.73 (0.15), residues: 1228 sheet: 1.38 (0.85), residues: 44 loop : 0.67 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 514 TYR 0.010 0.001 TYR C 354 PHE 0.012 0.001 PHE A 423 TRP 0.016 0.001 TRP C 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (16457) covalent geometry : angle 0.42382 / 0.22 (22105) hydrogen bonds : bond 0.03559 / 2.35 ( 954) hydrogen bonds : angle 3.28711 / 2.36 ( 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 146 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.541 Fit side-chains REVERT: A 299 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8207 (mtp180) REVERT: A 329 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8674 (t0) REVERT: A 413 ARG cc_start: 0.8493 (mtm110) cc_final: 0.8138 (mtp85) REVERT: A 583 GLU cc_start: 0.8541 (tt0) cc_final: 0.8151 (tm-30) REVERT: B 205 TYR cc_start: 0.7259 (m-10) cc_final: 0.7052 (t80) REVERT: B 329 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8670 (t0) REVERT: B 413 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8200 (mtp85) REVERT: B 521 GLU cc_start: 0.7745 (tt0) cc_final: 0.7498 (tm-30) REVERT: C 329 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8669 (t0) REVERT: C 583 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7803 (pp20) REVERT: D 205 TYR cc_start: 0.7287 (m-10) cc_final: 0.7062 (t80) REVERT: D 583 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7828 (pp20) REVERT: D 596 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8608 (mt-10) outliers start: 32 outliers final: 14 residues processed: 142 average time/residue: 0.6802 time to fit residues: 105.9257 Evaluate side-chains 131 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.090132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.066688 restraints weight = 23925.494| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.74 r_work: 0.2745 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16457 Z= 0.143 Angle : 0.456 7.609 22105 Z= 0.242 Chirality : 0.039 0.156 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.551 157.348 3212 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.66 % Allowed : 14.96 % 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: 3.07 (0.20), residues: 1792 helix: 2.64 (0.15), residues: 1228 sheet: 1.33 (0.86), residues: 44 loop : 0.66 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 407 TYR 0.014 0.001 TYR C 351 PHE 0.016 0.001 PHE A 423 TRP 0.016 0.001 TRP C 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (16457) covalent geometry : angle 0.45582 / 0.24 (22105) hydrogen bonds : bond 0.04268 / 2.81 ( 954) hydrogen bonds : angle 3.46687 / 2.49 ( 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 142 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.476 Fit side-chains REVERT: A 299 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8218 (mtp180) REVERT: A 329 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8648 (t0) REVERT: A 413 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8156 (mtp85) REVERT: A 583 GLU cc_start: 0.8546 (tt0) cc_final: 0.8170 (tm-30) REVERT: B 205 TYR cc_start: 0.7294 (m-10) cc_final: 0.7050 (t80) REVERT: B 329 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8635 (t0) REVERT: B 494 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.9004 (mmmm) REVERT: B 521 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: C 205 TYR cc_start: 0.7749 (t80) cc_final: 0.7518 (t80) REVERT: C 329 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8643 (t0) REVERT: C 583 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7819 (pp20) REVERT: D 205 TYR cc_start: 0.7310 (m-10) cc_final: 0.7054 (t80) REVERT: D 521 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6978 (pp20) REVERT: D 583 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: D 596 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8573 (mt-10) outliers start: 27 outliers final: 13 residues processed: 133 average time/residue: 0.6814 time to fit residues: 99.5785 Evaluate side-chains 137 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.0010 chunk 64 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.091748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.068516 restraints weight = 23697.022| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.73 r_work: 0.2787 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9248 moved from start: 0.0682 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= 0.102 Angle : 0.421 7.046 22105 Z= 0.223 Chirality : 0.038 0.152 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.154 158.061 3212 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.54 % Allowed : 15.27 % 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: 3.16 (0.20), residues: 1792 helix: 2.72 (0.15), residues: 1228 sheet: 1.28 (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 D 271 TYR 0.011 0.001 TYR A 205 PHE 0.012 0.001 PHE A 423 TRP 0.016 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (16457) covalent geometry : angle 0.42119 / 0.22 (22105) hydrogen bonds : bond 0.03612 / 2.38 ( 954) hydrogen bonds : angle 3.29126 / 2.37 ( 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 139 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.642 Fit side-chains REVERT: A 299 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8201 (mtp180) REVERT: A 329 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8659 (t0) REVERT: A 413 ARG cc_start: 0.8498 (mtm110) cc_final: 0.8145 (mtp85) REVERT: A 583 GLU cc_start: 0.8533 (tt0) cc_final: 0.8156 (tm-30) REVERT: B 329 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8663 (t0) REVERT: B 413 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8220 (mtp85) REVERT: B 521 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: C 205 TYR cc_start: 0.7748 (t80) cc_final: 0.7523 (t80) REVERT: C 329 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8660 (t0) REVERT: C 583 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7810 (pp20) REVERT: D 521 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6983 (pp20) REVERT: D 583 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7796 (pp20) REVERT: D 596 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8600 (mt-10) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 0.7130 time to fit residues: 104.6606 Evaluate side-chains 132 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 81 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 131 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 0.0060 chunk 147 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.091041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.067695 restraints weight = 23921.089| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.73 r_work: 0.2770 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9259 moved from start: 0.0761 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= 0.112 Angle : 0.430 6.690 22105 Z= 0.229 Chirality : 0.038 0.153 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.160 158.024 3212 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.48 % Allowed : 15.58 % Favored : 82.94 % 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: 3.16 (0.20), residues: 1792 helix: 2.72 (0.15), residues: 1228 sheet: 1.32 (0.85), 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 0.012 0.001 TYR C 349 PHE 0.014 0.001 PHE A 423 TRP 0.016 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16457) covalent geometry : angle 0.42982 / 0.23 (22105) hydrogen bonds : bond 0.03815 / 2.51 ( 954) hydrogen bonds : angle 3.32509 / 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 137 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.603 Fit side-chains REVERT: A 299 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8175 (mtp180) REVERT: A 329 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8661 (t0) REVERT: A 413 ARG cc_start: 0.8502 (mtm110) cc_final: 0.8141 (mtp85) REVERT: A 583 GLU cc_start: 0.8532 (tt0) cc_final: 0.8003 (tm-30) REVERT: A 586 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.8942 (p) REVERT: B 329 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8625 (t0) REVERT: B 413 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8216 (mtp85) REVERT: B 521 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: B 594 MET cc_start: 0.8585 (ttp) cc_final: 0.8333 (ttp) REVERT: C 205 TYR cc_start: 0.7792 (t80) cc_final: 0.7557 (t80) REVERT: C 329 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8635 (t0) REVERT: C 583 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7799 (pp20) REVERT: D 521 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6994 (pp20) REVERT: D 583 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7804 (pp20) REVERT: D 596 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8598 (mt-10) outliers start: 24 outliers final: 14 residues processed: 132 average time/residue: 0.7315 time to fit residues: 105.5921 Evaluate side-chains 135 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 0.0170 chunk 168 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 170 optimal weight: 0.0060 chunk 160 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.9438 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.090866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.067499 restraints weight = 23830.978| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.73 r_work: 0.2763 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9263 moved from start: 0.0781 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= 0.118 Angle : 0.435 6.500 22105 Z= 0.233 Chirality : 0.038 0.153 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.174 157.903 3212 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.60 % Allowed : 15.39 % Favored : 83.00 % 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: 1.29 (0.85), residues: 44 loop : 0.70 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 271 TYR 0.012 0.001 TYR C 349 PHE 0.014 0.001 PHE A 423 TRP 0.016 0.001 TRP C 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (16457) covalent geometry : angle 0.43510 / 0.23 (22105) hydrogen bonds : bond 0.03889 / 2.56 ( 954) hydrogen bonds : angle 3.34506 / 2.41 ( 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 140 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.626 Fit side-chains REVERT: A 299 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8168 (mtp180) REVERT: A 329 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8650 (t0) REVERT: A 413 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8148 (mtp85) REVERT: A 583 GLU cc_start: 0.8545 (tt0) cc_final: 0.8174 (tm-30) REVERT: B 329 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8644 (t0) REVERT: B 413 ARG cc_start: 0.8661 (mtm-85) cc_final: 0.8218 (mtp85) REVERT: B 521 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: C 205 TYR cc_start: 0.7821 (t80) cc_final: 0.7587 (t80) REVERT: C 329 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8650 (t0) REVERT: C 583 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7817 (pp20) REVERT: D 521 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7006 (pp20) REVERT: D 583 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7834 (pp20) REVERT: D 596 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8610 (mt-10) outliers start: 26 outliers final: 15 residues processed: 134 average time/residue: 0.7474 time to fit residues: 109.6476 Evaluate side-chains 137 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 40 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.090110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.066683 restraints weight = 23798.952| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.73 r_work: 0.2744 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16457 Z= 0.140 Angle : 0.456 6.422 22105 Z= 0.244 Chirality : 0.039 0.154 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.419 157.264 3212 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.35 % Allowed : 15.39 % Favored : 83.25 % 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: 3.09 (0.20), residues: 1792 helix: 2.66 (0.15), residues: 1228 sheet: 1.25 (0.85), residues: 44 loop : 0.70 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 218 TYR 0.016 0.001 TYR D 205 PHE 0.016 0.001 PHE A 423 TRP 0.016 0.001 TRP C 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16457) covalent geometry : angle 0.45583 / 0.24 (22105) hydrogen bonds : bond 0.04199 / 2.76 ( 954) hydrogen bonds : angle 3.43830 / 2.48 ( 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 139 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.557 Fit side-chains REVERT: A 299 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (mtp180) REVERT: A 329 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8651 (t0) REVERT: A 413 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8158 (mtp85) REVERT: A 583 GLU cc_start: 0.8556 (tt0) cc_final: 0.8183 (tm-30) REVERT: B 329 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8642 (t0) REVERT: B 521 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: C 205 TYR cc_start: 0.7861 (t80) cc_final: 0.7652 (t80) REVERT: C 329 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8650 (t0) REVERT: C 583 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7829 (pp20) REVERT: D 521 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6999 (pp20) REVERT: D 583 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7828 (pp20) REVERT: D 596 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8604 (mt-10) outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.7268 time to fit residues: 106.6823 Evaluate side-chains 139 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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 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 143 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.089842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.066427 restraints weight = 23944.774| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.73 r_work: 0.2739 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9278 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16457 Z= 0.146 Angle : 0.462 6.323 22105 Z= 0.247 Chirality : 0.039 0.154 2384 Planarity : 0.003 0.027 2635 Dihedral : 13.534 156.723 3212 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.42 % Allowed : 15.39 % 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: 3.06 (0.20), residues: 1792 helix: 2.63 (0.15), residues: 1228 sheet: 1.17 (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 C 218 TYR 0.014 0.001 TYR D 351 PHE 0.016 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 0.00336 / 0.15 (16457) covalent geometry : angle 0.46163 / 0.25 (22105) hydrogen bonds : bond 0.04252 / 2.80 ( 954) hydrogen bonds : angle 3.46114 / 2.50 ( 2754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6948.46 seconds wall clock time: 118 minutes 53.58 seconds (7133.58 seconds total)