Starting phenix.real_space_refine on Wed Apr 8 15:03:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yep_33774/04_2026/7yep_33774_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yep_33774/04_2026/7yep_33774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yep_33774/04_2026/7yep_33774_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yep_33774/04_2026/7yep_33774_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yep_33774/04_2026/7yep_33774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yep_33774/04_2026/7yep_33774.map" } resolution = 2.83 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= 0.005 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 S 108 5.16 5 B 4 2.79 5 C 13120 2.51 5 N 3376 2.21 5 O 3440 1.98 5 H 20284 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40332 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.93, per 1000 atoms: 0.17 Number of scatterers: 40332 At special positions: 0 Unit cell: (147.87, 147.87, 118.11, 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) S 108 16.00 O 3440 8.00 N 3376 7.00 C 13120 6.00 B 4 5.00 H 20284 1.00 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: 4.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 64.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.614A pdb=" N GLY A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.935A pdb=" N THR A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.956A pdb=" N ARG A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.876A pdb=" N LYS A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.763A pdb=" N THR A 222 " --> pdb=" O TRP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 370 through 408 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 453 Processing helix chain 'A' and resid 461 through 466 removed outlier: 4.390A pdb=" N SER A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 466' Processing helix chain 'A' and resid 467 through 487 Processing helix chain 'A' and resid 491 through 511 removed outlier: 3.716A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 508 " --> pdb=" O TRP A 504 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 532 removed outlier: 3.560A pdb=" N ILE A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 520 " --> pdb=" O HIS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.542A pdb=" N TRP A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.611A pdb=" N GLY B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.939A pdb=" N THR B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.906A pdb=" N ARG B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.853A pdb=" N LYS B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 217 through 227 removed outlier: 3.727A pdb=" N THR B 222 " --> pdb=" O TRP B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 350 through 357 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 370 through 408 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 454 Processing helix chain 'B' and resid 461 through 466 removed outlier: 4.495A pdb=" N SER B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 461 through 466' Processing helix chain 'B' and resid 467 through 487 Processing helix chain 'B' and resid 491 through 511 removed outlier: 3.676A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 508 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 532 removed outlier: 3.558A pdb=" N ILE B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR B 520 " --> pdb=" O HIS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 Processing helix chain 'B' and resid 587 through 600 Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 631 through 647 Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.548A pdb=" N TRP B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.594A pdb=" N GLY C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.928A pdb=" N THR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.993A pdb=" N ARG C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.871A pdb=" N LYS C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.762A pdb=" N THR C 222 " --> pdb=" O TRP C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 Processing helix chain 'C' and resid 292 through 300 Processing helix chain 'C' and resid 303 through 311 Processing helix chain 'C' and resid 350 through 357 Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 370 through 408 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 453 Processing helix chain 'C' and resid 461 through 466 removed outlier: 4.429A pdb=" N SER C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 466 " --> pdb=" O PHE C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 461 through 466' Processing helix chain 'C' and resid 467 through 487 Processing helix chain 'C' and resid 491 through 511 removed outlier: 3.668A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU C 508 " --> pdb=" O TRP C 504 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 532 removed outlier: 3.584A pdb=" N ILE C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR C 520 " --> pdb=" O HIS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 553 Processing helix chain 'C' and resid 587 through 600 Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 648 through 668 removed outlier: 3.542A pdb=" N TRP C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 713 removed outlier: 3.618A pdb=" N THR C 713 " --> pdb=" O TRP C 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.614A pdb=" N GLY D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.937A pdb=" N THR D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 130 through 141 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.963A pdb=" N ARG D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.856A pdb=" N LYS D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 217 through 227 removed outlier: 3.703A pdb=" N THR D 222 " --> pdb=" O TRP D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 Processing helix chain 'D' and resid 292 through 300 Processing helix chain 'D' and resid 303 through 311 Processing helix chain 'D' and resid 350 through 357 Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 370 through 408 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 453 Processing helix chain 'D' and resid 461 through 466 removed outlier: 4.668A pdb=" N SER D 465 " --> pdb=" O SER D 461 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 466 " --> pdb=" O PHE D 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 461 through 466' Processing helix chain 'D' and resid 467 through 487 Processing helix chain 'D' and resid 491 through 511 removed outlier: 3.723A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU D 508 " --> pdb=" O TRP D 504 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR D 510 " --> pdb=" O ASN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 532 removed outlier: 3.566A pdb=" N ILE D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR D 520 " --> pdb=" O HIS D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 553 Processing helix chain 'D' and resid 587 through 600 Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 631 through 647 Processing helix chain 'D' and resid 648 through 668 removed outlier: 3.547A pdb=" N TRP D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.626A pdb=" N LEU A 337 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 333 through 339 Processing sheet with id=AA3, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.585A pdb=" N LEU C 337 " --> pdb=" O PHE C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 324 through 326 removed outlier: 3.608A pdb=" N LEU D 337 " --> pdb=" O PHE D 325 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3177 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: 12.05 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 20228 1.03 - 1.22: 56 1.22 - 1.42: 8776 1.42 - 1.61: 11620 1.61 - 1.81: 160 Bond restraints: 40840 Sorted by residual: bond pdb=" C02 FZ4 B1001 " pdb=" C03 FZ4 B1001 " ideal model delta sigma weight residual 1.400 1.367 0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C02 FZ4 D1001 " pdb=" C03 FZ4 D1001 " ideal model delta sigma weight residual 1.400 1.368 0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C02 FZ4 A1001 " pdb=" C03 FZ4 A1001 " ideal model delta sigma weight residual 1.400 1.368 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" C02 FZ4 C1001 " pdb=" C03 FZ4 C1001 " ideal model delta sigma weight residual 1.400 1.368 0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" N VAL A 335 " pdb=" CA VAL A 335 " ideal model delta sigma weight residual 1.474 1.452 0.022 1.57e-02 4.06e+03 1.98e+00 ... (remaining 40835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 72357 1.67 - 3.34: 1264 3.34 - 5.01: 122 5.01 - 6.68: 6 6.68 - 8.35: 7 Bond angle restraints: 73756 Sorted by residual: angle pdb=" N VAL C 335 " pdb=" CA VAL C 335 " pdb=" C VAL C 335 " ideal model delta sigma weight residual 106.21 109.65 -3.44 1.07e+00 8.73e-01 1.03e+01 angle pdb=" C08 FZ4 D1001 " pdb=" B01 FZ4 D1001 " pdb=" O14 FZ4 D1001 " ideal model delta sigma weight residual 123.29 114.94 8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" C08 FZ4 A1001 " pdb=" B01 FZ4 A1001 " pdb=" O14 FZ4 A1001 " ideal model delta sigma weight residual 123.29 115.51 7.78 3.00e+00 1.11e-01 6.72e+00 angle pdb=" C SER C 465 " pdb=" N TYR C 466 " pdb=" CA TYR C 466 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.23e+00 angle pdb=" CB MET D 523 " pdb=" CG MET D 523 " pdb=" SD MET D 523 " ideal model delta sigma weight residual 112.70 105.30 7.40 3.00e+00 1.11e-01 6.09e+00 ... (remaining 73751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 17834 22.53 - 45.07: 940 45.07 - 67.60: 247 67.60 - 90.13: 16 90.13 - 112.66: 3 Dihedral angle restraints: 19040 sinusoidal: 10212 harmonic: 8828 Sorted by residual: dihedral pdb=" CA ARG B 512 " pdb=" C ARG B 512 " pdb=" N GLY B 513 " pdb=" CA GLY B 513 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU B 508 " pdb=" C LEU B 508 " pdb=" N TYR B 509 " pdb=" CA TYR B 509 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ARG A 512 " pdb=" C ARG A 512 " pdb=" N GLY A 513 " pdb=" CA GLY A 513 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 19037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1945 0.029 - 0.058: 818 0.058 - 0.087: 265 0.087 - 0.116: 99 0.116 - 0.145: 13 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA VAL D 335 " pdb=" N VAL D 335 " pdb=" C VAL D 335 " pdb=" CB VAL D 335 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL B 335 " pdb=" N VAL B 335 " pdb=" C VAL B 335 " pdb=" CB VAL B 335 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CB VAL B 483 " pdb=" CA VAL B 483 " pdb=" CG1 VAL B 483 " pdb=" CG2 VAL B 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 3137 not shown) Planarity restraints: 5808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 C1001 " 0.572 2.00e-02 2.50e+03 3.74e-01 2.45e+03 pdb=" C02 FZ4 C1001 " -0.315 2.00e-02 2.50e+03 pdb=" C03 FZ4 C1001 " -0.547 2.00e-02 2.50e+03 pdb=" C04 FZ4 C1001 " 0.128 2.00e-02 2.50e+03 pdb=" C05 FZ4 C1001 " 0.424 2.00e-02 2.50e+03 pdb=" C06 FZ4 C1001 " -0.018 2.00e-02 2.50e+03 pdb=" C07 FZ4 C1001 " -0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 D1001 " 0.554 2.00e-02 2.50e+03 3.66e-01 2.35e+03 pdb=" C02 FZ4 D1001 " -0.309 2.00e-02 2.50e+03 pdb=" C03 FZ4 D1001 " -0.549 2.00e-02 2.50e+03 pdb=" C04 FZ4 D1001 " 0.144 2.00e-02 2.50e+03 pdb=" C05 FZ4 D1001 " 0.405 2.00e-02 2.50e+03 pdb=" C06 FZ4 D1001 " -0.024 2.00e-02 2.50e+03 pdb=" C07 FZ4 D1001 " -0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 B1001 " -0.550 2.00e-02 2.50e+03 3.59e-01 2.25e+03 pdb=" C02 FZ4 B1001 " 0.319 2.00e-02 2.50e+03 pdb=" C03 FZ4 B1001 " 0.534 2.00e-02 2.50e+03 pdb=" C04 FZ4 B1001 " -0.150 2.00e-02 2.50e+03 pdb=" C05 FZ4 B1001 " -0.380 2.00e-02 2.50e+03 pdb=" C06 FZ4 B1001 " 0.016 2.00e-02 2.50e+03 pdb=" C07 FZ4 B1001 " 0.211 2.00e-02 2.50e+03 ... (remaining 5805 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 636 2.06 - 2.70: 66395 2.70 - 3.33: 122049 3.33 - 3.97: 151657 3.97 - 4.60: 242221 Nonbonded interactions: 582958 Sorted by model distance: nonbonded pdb=" O TRP C 452 " pdb="HH11 ARG C 455 " model vdw 1.426 2.450 nonbonded pdb=" O ILE C 167 " pdb="HE22 GLN C 217 " model vdw 1.523 2.450 nonbonded pdb=" O ILE A 167 " pdb="HE22 GLN A 217 " model vdw 1.532 2.450 nonbonded pdb=" OD1 ASN B 227 " pdb=" H GLN B 230 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASN D 227 " pdb=" H GLN D 230 " model vdw 1.590 2.450 ... (remaining 582953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.210 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 42.280 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20556 Z= 0.254 Angle : 0.669 8.352 27884 Z= 0.370 Chirality : 0.038 0.145 3140 Planarity : 0.015 0.374 3440 Dihedral : 14.193 112.664 7424 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.21 (0.17), residues: 2432 helix: 1.39 (0.14), residues: 1428 sheet: -1.89 (0.51), residues: 68 loop : -1.75 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 701 TYR 0.022 0.002 TYR C 492 PHE 0.015 0.002 PHE A 402 TRP 0.026 0.002 TRP A 449 HIS 0.005 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00568 (20556) covalent geometry : angle 0.66908 (27884) hydrogen bonds : bond 0.12563 ( 1098) hydrogen bonds : angle 5.57298 ( 3177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ILE cc_start: 0.8635 (tp) cc_final: 0.8416 (tp) REVERT: C 272 MET cc_start: 0.4960 (mtt) cc_final: 0.4674 (ttm) REVERT: C 305 ILE cc_start: 0.8634 (tp) cc_final: 0.8389 (tp) REVERT: D 305 ILE cc_start: 0.8580 (tp) cc_final: 0.8375 (tp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 1.0831 time to fit residues: 442.9714 Evaluate side-chains 219 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 258 ASN C 258 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.210969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152923 restraints weight = 79282.567| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.43 r_work: 0.3664 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20556 Z= 0.191 Angle : 0.625 6.915 27884 Z= 0.321 Chirality : 0.038 0.137 3140 Planarity : 0.005 0.055 3440 Dihedral : 5.072 57.205 2720 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.29 % Allowed : 8.55 % Favored : 90.17 % 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: 0.00 (0.17), residues: 2432 helix: 1.23 (0.13), residues: 1452 sheet: -1.60 (0.50), residues: 68 loop : -1.96 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 455 TYR 0.019 0.002 TYR A 466 PHE 0.015 0.002 PHE B 402 TRP 0.010 0.001 TRP A 449 HIS 0.006 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00424 (20556) covalent geometry : angle 0.62492 (27884) hydrogen bonds : bond 0.04453 ( 1098) hydrogen bonds : angle 4.65435 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 281 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.7531 (p90) cc_final: 0.7266 (p90) REVERT: A 602 MET cc_start: 0.9142 (mmp) cc_final: 0.8890 (mmm) REVERT: B 217 GLN cc_start: 0.6922 (mt0) cc_final: 0.6460 (mt0) REVERT: B 334 ARG cc_start: 0.5773 (mmt180) cc_final: 0.5121 (mmp-170) REVERT: C 204 PHE cc_start: 0.7238 (p90) cc_final: 0.6988 (p90) REVERT: C 272 MET cc_start: 0.5411 (mtt) cc_final: 0.5015 (ttm) REVERT: C 299 LYS cc_start: 0.7820 (tttm) cc_final: 0.7600 (ttmt) outliers start: 28 outliers final: 6 residues processed: 296 average time/residue: 1.0182 time to fit residues: 357.3354 Evaluate side-chains 226 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 499 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 187 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 231 optimal weight: 0.0470 chunk 202 optimal weight: 0.2980 chunk 162 optimal weight: 3.9990 overall best weight: 2.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.194701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128573 restraints weight = 74147.655| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.87 r_work: 0.3340 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20556 Z= 0.207 Angle : 0.588 6.547 27884 Z= 0.307 Chirality : 0.038 0.150 3140 Planarity : 0.005 0.071 3440 Dihedral : 4.764 59.317 2720 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.29 % Allowed : 12.87 % Favored : 85.85 % 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: 0.04 (0.17), residues: 2432 helix: 1.25 (0.13), residues: 1448 sheet: -1.27 (0.53), residues: 68 loop : -1.94 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 454 TYR 0.022 0.002 TYR A 492 PHE 0.013 0.001 PHE D 596 TRP 0.015 0.002 TRP A 671 HIS 0.005 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00469 (20556) covalent geometry : angle 0.58776 (27884) hydrogen bonds : bond 0.04758 ( 1098) hydrogen bonds : angle 4.57412 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.5418 (mmp) cc_final: 0.4639 (tpp) REVERT: A 217 GLN cc_start: 0.7623 (mt0) cc_final: 0.7142 (mt0) REVERT: A 346 TRP cc_start: 0.7775 (OUTLIER) cc_final: 0.6723 (t60) REVERT: A 360 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8198 (mptt) REVERT: A 456 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6997 (pp) REVERT: A 492 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 117 MET cc_start: 0.5376 (mmp) cc_final: 0.4548 (tpp) REVERT: B 334 ARG cc_start: 0.5893 (mmt180) cc_final: 0.5313 (mmp-170) REVERT: B 360 LYS cc_start: 0.8516 (ptpp) cc_final: 0.8215 (mptt) REVERT: B 456 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7208 (pp) REVERT: C 117 MET cc_start: 0.5349 (mmp) cc_final: 0.4329 (tpp) REVERT: C 217 GLN cc_start: 0.7466 (mt0) cc_final: 0.7067 (mt0) REVERT: C 272 MET cc_start: 0.6055 (mtt) cc_final: 0.5792 (ttm) REVERT: C 299 LYS cc_start: 0.8214 (tttm) cc_final: 0.7917 (ttmt) REVERT: C 360 LYS cc_start: 0.8548 (ptpp) cc_final: 0.8188 (mptt) REVERT: D 117 MET cc_start: 0.5368 (mmp) cc_final: 0.4543 (tpp) REVERT: D 360 LYS cc_start: 0.8514 (ptpp) cc_final: 0.8196 (mptt) REVERT: D 456 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7136 (pp) REVERT: D 492 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8278 (t80) REVERT: D 666 MET cc_start: 0.8897 (mtm) cc_final: 0.8641 (mtm) REVERT: D 703 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6725 (mm-30) outliers start: 28 outliers final: 4 residues processed: 253 average time/residue: 1.0746 time to fit residues: 319.5529 Evaluate side-chains 214 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 703 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 222 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.190920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126173 restraints weight = 73710.089| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.92 r_work: 0.3276 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20556 Z= 0.172 Angle : 0.551 6.915 27884 Z= 0.283 Chirality : 0.037 0.135 3140 Planarity : 0.004 0.036 3440 Dihedral : 4.647 50.050 2720 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.88 % Allowed : 14.80 % Favored : 83.32 % 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: 0.24 (0.17), residues: 2432 helix: 1.52 (0.13), residues: 1432 sheet: -1.51 (0.53), residues: 68 loop : -1.97 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 454 TYR 0.015 0.002 TYR A 466 PHE 0.015 0.001 PHE C 204 TRP 0.019 0.001 TRP C 218 HIS 0.007 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00384 (20556) covalent geometry : angle 0.55115 (27884) hydrogen bonds : bond 0.04239 ( 1098) hydrogen bonds : angle 4.40376 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.949 Fit side-chains REVERT: A 117 MET cc_start: 0.5346 (mmp) cc_final: 0.4553 (tpp) REVERT: A 360 LYS cc_start: 0.8695 (ptpp) cc_final: 0.8297 (mptt) REVERT: A 367 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8781 (mtm) REVERT: A 666 MET cc_start: 0.9081 (mtm) cc_final: 0.8813 (mtm) REVERT: B 117 MET cc_start: 0.5481 (mmp) cc_final: 0.4588 (tpp) REVERT: B 360 LYS cc_start: 0.8639 (ptpp) cc_final: 0.8293 (mptt) REVERT: B 367 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8794 (mtm) REVERT: B 383 ARG cc_start: 0.8529 (tpp-160) cc_final: 0.8239 (ttp80) REVERT: C 117 MET cc_start: 0.5324 (mmp) cc_final: 0.4246 (tpp) REVERT: D 117 MET cc_start: 0.5382 (mmp) cc_final: 0.4420 (tpp) REVERT: D 346 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.6253 (t60) REVERT: D 360 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8299 (mptt) REVERT: D 703 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7093 (mm-30) outliers start: 41 outliers final: 2 residues processed: 213 average time/residue: 0.9513 time to fit residues: 243.3512 Evaluate side-chains 169 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 703 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 60 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN D 246 HIS D 668 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.189428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122184 restraints weight = 73508.236| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.84 r_work: 0.3268 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20556 Z= 0.149 Angle : 0.514 5.609 27884 Z= 0.267 Chirality : 0.035 0.126 3140 Planarity : 0.004 0.053 3440 Dihedral : 4.489 55.440 2720 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.93 % Allowed : 15.67 % Favored : 82.40 % 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: 0.44 (0.17), residues: 2432 helix: 1.70 (0.14), residues: 1432 sheet: -1.56 (0.52), residues: 68 loop : -1.90 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 383 TYR 0.013 0.001 TYR C 466 PHE 0.009 0.001 PHE C 457 TRP 0.017 0.001 TRP A 328 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00327 (20556) covalent geometry : angle 0.51413 (27884) hydrogen bonds : bond 0.04090 ( 1098) hydrogen bonds : angle 4.32626 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.038 Fit side-chains REVERT: A 117 MET cc_start: 0.5516 (mmp) cc_final: 0.4714 (tpp) REVERT: A 367 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8800 (mtm) REVERT: B 117 MET cc_start: 0.5539 (mmp) cc_final: 0.4740 (tpp) REVERT: B 360 LYS cc_start: 0.8641 (ptpp) cc_final: 0.8353 (mptt) REVERT: C 117 MET cc_start: 0.5493 (mmp) cc_final: 0.4525 (tpp) REVERT: C 272 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6027 (ttm) REVERT: C 360 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8490 (ptpp) REVERT: D 117 MET cc_start: 0.5468 (mmp) cc_final: 0.4625 (tpp) REVERT: D 346 TRP cc_start: 0.7610 (OUTLIER) cc_final: 0.6399 (t60) REVERT: D 360 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8349 (mptt) REVERT: D 456 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7249 (pp) outliers start: 42 outliers final: 14 residues processed: 196 average time/residue: 0.9914 time to fit residues: 232.3185 Evaluate side-chains 186 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 87 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.183934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116035 restraints weight = 73686.336| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.46 r_work: 0.3220 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20556 Z= 0.226 Angle : 0.572 6.931 27884 Z= 0.299 Chirality : 0.037 0.135 3140 Planarity : 0.005 0.045 3440 Dihedral : 4.632 47.888 2720 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.02 % Allowed : 16.13 % Favored : 81.85 % 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: 0.19 (0.17), residues: 2432 helix: 1.44 (0.13), residues: 1440 sheet: -1.57 (0.52), residues: 68 loop : -1.95 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 454 TYR 0.014 0.002 TYR C 510 PHE 0.020 0.001 PHE C 457 TRP 0.011 0.001 TRP A 449 HIS 0.005 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00512 (20556) covalent geometry : angle 0.57205 (27884) hydrogen bonds : bond 0.04742 ( 1098) hydrogen bonds : angle 4.48010 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 1.059 Fit side-chains REVERT: A 117 MET cc_start: 0.5587 (mmp) cc_final: 0.4892 (tpp) REVERT: A 360 LYS cc_start: 0.8913 (ptpp) cc_final: 0.8184 (mptt) REVERT: A 375 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8671 (mmtt) REVERT: B 117 MET cc_start: 0.5601 (mmp) cc_final: 0.5045 (tpp) REVERT: C 117 MET cc_start: 0.5608 (mmp) cc_final: 0.4840 (tpp) REVERT: C 272 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6421 (ttm) REVERT: D 117 MET cc_start: 0.5605 (mmp) cc_final: 0.5049 (tpp) REVERT: D 250 MET cc_start: 0.8736 (mmt) cc_final: 0.8423 (mmt) REVERT: D 346 TRP cc_start: 0.7902 (OUTLIER) cc_final: 0.6787 (t60) REVERT: D 703 GLU cc_start: 0.7429 (tt0) cc_final: 0.7167 (tt0) outliers start: 44 outliers final: 10 residues processed: 199 average time/residue: 0.9931 time to fit residues: 236.8213 Evaluate side-chains 181 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 191 optimal weight: 10.0000 chunk 65 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN B 409 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.181241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116494 restraints weight = 73509.818| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.82 r_work: 0.3174 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20556 Z= 0.254 Angle : 0.587 7.294 27884 Z= 0.306 Chirality : 0.038 0.127 3140 Planarity : 0.005 0.051 3440 Dihedral : 4.768 56.540 2720 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.16 % Allowed : 17.14 % Favored : 80.70 % 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: 0.08 (0.17), residues: 2432 helix: 1.35 (0.13), residues: 1456 sheet: -1.63 (0.50), residues: 68 loop : -2.03 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 383 TYR 0.018 0.002 TYR C 510 PHE 0.014 0.001 PHE A 325 TRP 0.022 0.002 TRP C 328 HIS 0.006 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00574 (20556) covalent geometry : angle 0.58734 (27884) hydrogen bonds : bond 0.04830 ( 1098) hydrogen bonds : angle 4.55102 ( 3177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7259 (mtm) cc_final: 0.6835 (ttm) REVERT: A 375 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8712 (mmtt) REVERT: A 456 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7295 (pp) REVERT: B 360 LYS cc_start: 0.9000 (ptpp) cc_final: 0.8277 (mttp) REVERT: C 117 MET cc_start: 0.5738 (mmp) cc_final: 0.5450 (mpp) REVERT: C 272 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6513 (ttm) REVERT: C 360 LYS cc_start: 0.9007 (ptpp) cc_final: 0.8269 (mptt) REVERT: C 428 MET cc_start: 0.6679 (tpp) cc_final: 0.6401 (ttm) REVERT: D 343 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8508 (p) REVERT: D 346 TRP cc_start: 0.8049 (OUTLIER) cc_final: 0.6999 (t60) REVERT: D 360 LYS cc_start: 0.9016 (ptpp) cc_final: 0.8302 (mptt) REVERT: D 703 GLU cc_start: 0.7519 (tt0) cc_final: 0.7184 (tt0) outliers start: 47 outliers final: 22 residues processed: 194 average time/residue: 1.0419 time to fit residues: 238.5737 Evaluate side-chains 183 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 628 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 217 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 26 optimal weight: 0.0970 chunk 240 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 289 GLN D 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.182419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115030 restraints weight = 73570.607| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.47 r_work: 0.3187 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20556 Z= 0.167 Angle : 0.529 6.292 27884 Z= 0.274 Chirality : 0.036 0.129 3140 Planarity : 0.004 0.048 3440 Dihedral : 4.618 49.163 2720 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.93 % Allowed : 17.33 % Favored : 80.74 % 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: 0.38 (0.17), residues: 2432 helix: 1.61 (0.13), residues: 1440 sheet: -1.62 (0.49), residues: 68 loop : -1.88 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 383 TYR 0.014 0.001 TYR D 466 PHE 0.007 0.001 PHE C 542 TRP 0.010 0.001 TRP C 328 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00368 (20556) covalent geometry : angle 0.52948 (27884) hydrogen bonds : bond 0.04267 ( 1098) hydrogen bonds : angle 4.41663 ( 3177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7309 (mtm) cc_final: 0.6883 (ttm) REVERT: A 360 LYS cc_start: 0.9030 (ptpp) cc_final: 0.8575 (ptpp) REVERT: A 375 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8761 (mmtt) REVERT: A 441 ILE cc_start: 0.8936 (pt) cc_final: 0.8658 (mt) REVERT: A 456 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7265 (pp) REVERT: A 466 TYR cc_start: 0.6887 (p90) cc_final: 0.6631 (p90) REVERT: B 441 ILE cc_start: 0.8922 (pt) cc_final: 0.8651 (mt) REVERT: C 117 MET cc_start: 0.5766 (mmp) cc_final: 0.5552 (mpp) REVERT: C 272 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6429 (ttm) REVERT: C 441 ILE cc_start: 0.8933 (pt) cc_final: 0.8661 (mt) REVERT: C 704 GLU cc_start: 0.7837 (tp30) cc_final: 0.7562 (pm20) REVERT: D 250 MET cc_start: 0.8722 (mmt) cc_final: 0.8392 (mmt) REVERT: D 289 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: D 343 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8396 (p) REVERT: D 346 TRP cc_start: 0.8017 (OUTLIER) cc_final: 0.7014 (t60) REVERT: D 441 ILE cc_start: 0.8938 (pt) cc_final: 0.8661 (mt) REVERT: D 703 GLU cc_start: 0.7518 (tt0) cc_final: 0.7231 (tt0) outliers start: 42 outliers final: 25 residues processed: 207 average time/residue: 0.9924 time to fit residues: 244.6549 Evaluate side-chains 203 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 346 TRP Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 136 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 161 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 143 optimal weight: 0.0670 chunk 96 optimal weight: 5.9990 overall best weight: 0.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.184145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117524 restraints weight = 73565.847| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.46 r_work: 0.3232 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20556 Z= 0.110 Angle : 0.506 7.977 27884 Z= 0.259 Chirality : 0.035 0.131 3140 Planarity : 0.004 0.049 3440 Dihedral : 4.473 48.123 2720 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.65 % Allowed : 17.88 % Favored : 80.47 % 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: 0.69 (0.17), residues: 2432 helix: 1.92 (0.14), residues: 1424 sheet: -1.64 (0.48), residues: 68 loop : -1.80 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 383 TYR 0.012 0.001 TYR D 466 PHE 0.007 0.001 PHE C 596 TRP 0.011 0.001 TRP C 218 HIS 0.010 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00233 (20556) covalent geometry : angle 0.50564 (27884) hydrogen bonds : bond 0.03844 ( 1098) hydrogen bonds : angle 4.28122 ( 3177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7183 (mtm) cc_final: 0.6794 (ttm) REVERT: A 375 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8738 (mmtt) REVERT: A 441 ILE cc_start: 0.8919 (pt) cc_final: 0.8648 (mt) REVERT: A 456 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7264 (pp) REVERT: A 466 TYR cc_start: 0.6821 (p90) cc_final: 0.6537 (p90) REVERT: B 272 MET cc_start: 0.7306 (mtm) cc_final: 0.6877 (ttm) REVERT: B 360 LYS cc_start: 0.9028 (ptpp) cc_final: 0.8425 (mptt) REVERT: B 441 ILE cc_start: 0.8900 (pt) cc_final: 0.8633 (mt) REVERT: B 466 TYR cc_start: 0.6977 (p90) cc_final: 0.6703 (p90) REVERT: C 272 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6320 (ttm) REVERT: C 360 LYS cc_start: 0.9026 (ptpp) cc_final: 0.8642 (ptpp) REVERT: C 441 ILE cc_start: 0.8912 (pt) cc_final: 0.8646 (mt) REVERT: C 704 GLU cc_start: 0.7827 (tp30) cc_final: 0.7578 (pm20) REVERT: D 343 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8296 (p) REVERT: D 360 LYS cc_start: 0.9032 (ptpp) cc_final: 0.8387 (mptt) REVERT: D 441 ILE cc_start: 0.8924 (pt) cc_final: 0.8655 (mt) outliers start: 36 outliers final: 17 residues processed: 201 average time/residue: 1.0874 time to fit residues: 258.6872 Evaluate side-chains 195 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 218 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 109 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 GLN C 289 GLN D 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.184391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117995 restraints weight = 73166.804| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.46 r_work: 0.3240 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20556 Z= 0.116 Angle : 0.495 7.934 27884 Z= 0.255 Chirality : 0.035 0.139 3140 Planarity : 0.004 0.047 3440 Dihedral : 4.306 44.556 2720 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.42 % Allowed : 17.97 % Favored : 80.61 % 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: 0.83 (0.17), residues: 2432 helix: 2.08 (0.14), residues: 1420 sheet: -2.58 (0.47), residues: 64 loop : -1.71 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 383 TYR 0.026 0.001 TYR D 466 PHE 0.007 0.001 PHE B 596 TRP 0.015 0.001 TRP B 218 HIS 0.004 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00250 (20556) covalent geometry : angle 0.49515 (27884) hydrogen bonds : bond 0.03725 ( 1098) hydrogen bonds : angle 4.18449 ( 3177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7232 (mtm) cc_final: 0.6794 (ttm) REVERT: A 360 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8318 (mttp) REVERT: A 375 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8727 (mmtt) REVERT: A 441 ILE cc_start: 0.8908 (pt) cc_final: 0.8641 (mt) REVERT: A 456 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7276 (pp) REVERT: A 466 TYR cc_start: 0.6753 (p90) cc_final: 0.6464 (p90) REVERT: B 272 MET cc_start: 0.7308 (mtm) cc_final: 0.6855 (ttm) REVERT: B 360 LYS cc_start: 0.8994 (ptpp) cc_final: 0.8324 (mptt) REVERT: B 441 ILE cc_start: 0.8903 (pt) cc_final: 0.8638 (mt) REVERT: B 466 TYR cc_start: 0.6873 (p90) cc_final: 0.6610 (p90) REVERT: C 272 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6497 (ttm) REVERT: C 360 LYS cc_start: 0.8967 (ptpp) cc_final: 0.8287 (mttp) REVERT: C 441 ILE cc_start: 0.8909 (pt) cc_final: 0.8643 (mt) REVERT: D 343 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8252 (p) REVERT: D 360 LYS cc_start: 0.8995 (ptpp) cc_final: 0.8385 (mptt) REVERT: D 441 ILE cc_start: 0.8918 (pt) cc_final: 0.8662 (mt) outliers start: 31 outliers final: 14 residues processed: 201 average time/residue: 1.0308 time to fit residues: 245.7574 Evaluate side-chains 191 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 146 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.183033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117262 restraints weight = 73691.741| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.71 r_work: 0.3189 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20556 Z= 0.144 Angle : 0.504 8.098 27884 Z= 0.260 Chirality : 0.035 0.136 3140 Planarity : 0.004 0.043 3440 Dihedral : 4.302 44.249 2720 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.97 % Allowed : 18.84 % Favored : 80.19 % 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: 0.82 (0.17), residues: 2432 helix: 2.04 (0.14), residues: 1432 sheet: -2.50 (0.49), residues: 64 loop : -1.71 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 383 TYR 0.028 0.001 TYR D 466 PHE 0.008 0.001 PHE D 596 TRP 0.015 0.001 TRP C 218 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00316 (20556) covalent geometry : angle 0.50412 (27884) hydrogen bonds : bond 0.03912 ( 1098) hydrogen bonds : angle 4.21584 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15290.38 seconds wall clock time: 258 minutes 42.29 seconds (15522.29 seconds total)