Starting phenix.real_space_refine on Sun Aug 24 10:23:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ec6_28013/08_2025/8ec6_28013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ec6_28013/08_2025/8ec6_28013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ec6_28013/08_2025/8ec6_28013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ec6_28013/08_2025/8ec6_28013.map" model { file = "/net/cci-nas-00/data/ceres_data/8ec6_28013/08_2025/8ec6_28013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ec6_28013/08_2025/8ec6_28013.cif" } resolution = 3.1 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= -0.001 sd= 0.157 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 184 5.16 5 C 12207 2.51 5 N 3159 2.21 5 O 3575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19133 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "B" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "C" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "D" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "E" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2377 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain: "F" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "G" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "H" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.87, per 1000 atoms: 0.20 Number of scatterers: 19133 At special positions: 0 Unit cell: (97.9, 124.3, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 8 15.00 O 3575 8.00 N 3159 7.00 C 12207 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: 1.66 Conformation dependent library (CDL) restraints added in 940.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4510 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 16 sheets defined 52.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.889A pdb=" N LYS A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 339 through 350 removed outlier: 3.626A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.506A pdb=" N GLU A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.684A pdb=" N PHE A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 428 through 442 Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.862A pdb=" N LYS B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 292 through 306 removed outlier: 4.523A pdb=" N LEU B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 411 through 424 Processing helix chain 'B' and resid 428 through 442 Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 516 through 530 Processing helix chain 'C' and resid 232 through 244 Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.539A pdb=" N GLU C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 403 removed outlier: 3.712A pdb=" N PHE C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 424 Processing helix chain 'C' and resid 428 through 442 Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 472 No H-bonds generated for 'chain 'C' and resid 470 through 472' Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'C' and resid 516 through 530 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 306 through 312 Processing helix chain 'D' and resid 339 through 349 Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'D' and resid 379 through 388 removed outlier: 3.768A pdb=" N GLU D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 403 Processing helix chain 'D' and resid 411 through 424 Processing helix chain 'D' and resid 428 through 442 Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'D' and resid 473 through 481 Processing helix chain 'D' and resid 516 through 530 Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.702A pdb=" N GLU E 241 " --> pdb=" O ASP E 237 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 339 through 349 Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'E' and resid 379 through 388 Processing helix chain 'E' and resid 390 through 403 Processing helix chain 'E' and resid 411 through 424 Processing helix chain 'E' and resid 428 through 442 Processing helix chain 'E' and resid 454 through 469 Processing helix chain 'E' and resid 470 through 472 No H-bonds generated for 'chain 'E' and resid 470 through 472' Processing helix chain 'E' and resid 473 through 481 Processing helix chain 'E' and resid 516 through 530 Processing helix chain 'F' and resid 230 through 245 removed outlier: 3.890A pdb=" N LYS F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 260 Processing helix chain 'F' and resid 293 through 306 Processing helix chain 'F' and resid 306 through 311 Processing helix chain 'F' and resid 339 through 350 removed outlier: 3.588A pdb=" N ILE F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'F' and resid 379 through 390 Processing helix chain 'F' and resid 390 through 404 removed outlier: 3.733A pdb=" N PHE F 394 " --> pdb=" O GLY F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 424 Processing helix chain 'F' and resid 428 through 442 removed outlier: 3.560A pdb=" N LEU F 439 " --> pdb=" O MET F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 469 Processing helix chain 'F' and resid 470 through 472 No H-bonds generated for 'chain 'F' and resid 470 through 472' Processing helix chain 'F' and resid 473 through 481 Processing helix chain 'F' and resid 516 through 530 Processing helix chain 'G' and resid 230 through 245 removed outlier: 3.843A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 260 Processing helix chain 'G' and resid 293 through 306 Processing helix chain 'G' and resid 306 through 311 Processing helix chain 'G' and resid 339 through 349 Processing helix chain 'G' and resid 355 through 371 Processing helix chain 'G' and resid 379 through 388 removed outlier: 3.558A pdb=" N GLU G 388 " --> pdb=" O GLN G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 403 Processing helix chain 'G' and resid 411 through 424 Processing helix chain 'G' and resid 428 through 442 Processing helix chain 'G' and resid 454 through 469 Processing helix chain 'G' and resid 470 through 472 No H-bonds generated for 'chain 'G' and resid 470 through 472' Processing helix chain 'G' and resid 473 through 481 Processing helix chain 'G' and resid 516 through 530 Processing helix chain 'H' and resid 230 through 245 removed outlier: 3.872A pdb=" N LYS H 245 " --> pdb=" O GLU H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 305 Processing helix chain 'H' and resid 306 through 311 Processing helix chain 'H' and resid 339 through 350 removed outlier: 3.587A pdb=" N ILE H 350 " --> pdb=" O VAL H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 371 Processing helix chain 'H' and resid 379 through 388 removed outlier: 3.603A pdb=" N GLU H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 403 removed outlier: 3.683A pdb=" N PHE H 394 " --> pdb=" O GLY H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 424 Processing helix chain 'H' and resid 428 through 442 removed outlier: 3.527A pdb=" N LEU H 439 " --> pdb=" O MET H 435 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 469 Processing helix chain 'H' and resid 470 through 472 No H-bonds generated for 'chain 'H' and resid 470 through 472' Processing helix chain 'H' and resid 473 through 481 Processing helix chain 'H' and resid 516 through 530 Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 281 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AA3, first strand: chain 'B' and resid 277 through 281 removed outlier: 3.956A pdb=" N GLY B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 287 through 288 Processing sheet with id=AA5, first strand: chain 'C' and resid 277 through 281 Processing sheet with id=AA6, first strand: chain 'C' and resid 287 through 288 Processing sheet with id=AA7, first strand: chain 'D' and resid 277 through 281 Processing sheet with id=AA8, first strand: chain 'D' and resid 287 through 288 Processing sheet with id=AA9, first strand: chain 'E' and resid 277 through 281 removed outlier: 3.876A pdb=" N GLY E 492 " --> pdb=" O GLY E 488 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AB2, first strand: chain 'F' and resid 277 through 281 Processing sheet with id=AB3, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AB4, first strand: chain 'G' and resid 277 through 281 removed outlier: 3.862A pdb=" N GLY G 492 " --> pdb=" O GLY G 488 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 287 through 288 Processing sheet with id=AB6, first strand: chain 'H' and resid 277 through 280 removed outlier: 3.784A pdb=" N GLY H 492 " --> pdb=" O GLY H 488 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 287 through 288 1038 hydrogen bonds defined for protein. 3042 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: 2.50 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5878 1.34 - 1.46: 3031 1.46 - 1.57: 10407 1.57 - 1.69: 0 1.69 - 1.81: 280 Bond restraints: 19596 Sorted by residual: bond pdb=" O3 PO4 F 701 " pdb=" P PO4 F 701 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" O3 PO4 B 701 " pdb=" P PO4 B 701 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" O3 PO4 C 701 " pdb=" P PO4 C 701 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" O3 PO4 H 701 " pdb=" P PO4 H 701 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O3 PO4 D 701 " pdb=" P PO4 D 701 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.84e+00 ... (remaining 19591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 26036 1.57 - 3.15: 406 3.15 - 4.72: 44 4.72 - 6.30: 15 6.30 - 7.87: 3 Bond angle restraints: 26504 Sorted by residual: angle pdb=" N MET F 501 " pdb=" CA MET F 501 " pdb=" C MET F 501 " ideal model delta sigma weight residual 107.88 114.40 -6.52 1.41e+00 5.03e-01 2.14e+01 angle pdb=" N MET C 501 " pdb=" CA MET C 501 " pdb=" C MET C 501 " ideal model delta sigma weight residual 107.88 114.05 -6.17 1.41e+00 5.03e-01 1.91e+01 angle pdb=" CA PRO E 509 " pdb=" N PRO E 509 " pdb=" CD PRO E 509 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 angle pdb=" C TYR F 471 " pdb=" CA TYR F 471 " pdb=" CB TYR F 471 " ideal model delta sigma weight residual 116.34 111.52 4.82 1.40e+00 5.10e-01 1.18e+01 angle pdb=" CA PRO F 509 " pdb=" N PRO F 509 " pdb=" CD PRO F 509 " ideal model delta sigma weight residual 112.00 107.18 4.82 1.40e+00 5.10e-01 1.18e+01 ... (remaining 26499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 10401 15.76 - 31.52: 872 31.52 - 47.28: 240 47.28 - 63.03: 43 63.03 - 78.79: 7 Dihedral angle restraints: 11563 sinusoidal: 4494 harmonic: 7069 Sorted by residual: dihedral pdb=" CA VAL A 500 " pdb=" C VAL A 500 " pdb=" N MET A 501 " pdb=" CA MET A 501 " ideal model delta harmonic sigma weight residual 180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PRO C 227 " pdb=" C PRO C 227 " pdb=" N ASP C 228 " pdb=" CA ASP C 228 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB MET F 501 " pdb=" CG MET F 501 " pdb=" SD MET F 501 " pdb=" CE MET F 501 " ideal model delta sinusoidal sigma weight residual -180.00 -122.33 -57.67 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 11560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1932 0.035 - 0.071: 672 0.071 - 0.106: 174 0.106 - 0.142: 77 0.142 - 0.177: 8 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA MET E 230 " pdb=" N MET E 230 " pdb=" C MET E 230 " pdb=" CB MET E 230 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA LEU B 510 " pdb=" N LEU B 510 " pdb=" C LEU B 510 " pdb=" CB LEU B 510 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2860 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 508 " 0.066 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO E 509 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO E 509 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 509 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 508 " -0.058 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO C 509 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 509 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 509 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 262 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO E 263 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 263 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 263 " 0.036 5.00e-02 4.00e+02 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 135 2.62 - 3.19: 17055 3.19 - 3.76: 29060 3.76 - 4.33: 40890 4.33 - 4.90: 70620 Nonbonded interactions: 157760 Sorted by model distance: nonbonded pdb=" O ASP A 274 " pdb=" OD1 ASP A 274 " model vdw 2.049 3.040 nonbonded pdb=" O VAL A 345 " pdb=" OG SER A 348 " model vdw 2.261 3.040 nonbonded pdb=" O ASP C 228 " pdb=" N MET C 230 " model vdw 2.286 3.120 nonbonded pdb=" OG SER C 262 " pdb=" OD1 ASP C 264 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASP H 228 " pdb=" N PHE H 229 " model vdw 2.301 3.120 ... (remaining 157755 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 225 through 701) selection = (chain 'B' and resid 225 through 701) selection = (chain 'C' and resid 225 through 701) selection = (chain 'D' and resid 225 through 701) selection = chain 'E' selection = (chain 'F' and resid 225 through 701) selection = (chain 'G' and resid 225 through 701) selection = (chain 'H' and resid 225 through 701) } 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.900 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.004 0.069 19596 Z= 0.180 Angle : 0.487 7.869 26504 Z= 0.269 Chirality : 0.041 0.177 2863 Planarity : 0.005 0.097 3438 Dihedral : 12.897 78.792 7053 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 0.05 % Allowed : 12.41 % Favored : 87.54 % 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 aren not related in a simple way. whole: 1.23 (0.18), residues: 2463 helix: 1.91 (0.15), residues: 1271 sheet: 0.69 (0.34), residues: 241 loop : -0.65 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 387 TYR 0.011 0.001 TYR H 240 PHE 0.030 0.001 PHE C 232 TRP 0.008 0.001 TRP E 266 HIS 0.007 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00353 (19596) covalent geometry : angle 0.48746 (26504) hydrogen bonds : bond 0.11671 ( 1038) hydrogen bonds : angle 5.13236 ( 3042) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.434 Fit side-chains REVERT: F 386 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8109 (mt-10) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1189 time to fit residues: 43.0695 Evaluate side-chains 229 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 355 ASN E 365 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117939 restraints weight = 22300.089| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.60 r_work: 0.3173 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19596 Z= 0.141 Angle : 0.506 6.814 26504 Z= 0.268 Chirality : 0.043 0.172 2863 Planarity : 0.005 0.070 3438 Dihedral : 3.678 18.725 2615 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 1.95 % Allowed : 10.75 % Favored : 87.30 % 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 aren not related in a simple way. whole: 1.41 (0.18), residues: 2463 helix: 2.07 (0.15), residues: 1275 sheet: 0.58 (0.34), residues: 241 loop : -0.54 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 387 TYR 0.011 0.001 TYR H 240 PHE 0.014 0.001 PHE G 473 TRP 0.011 0.001 TRP F 266 HIS 0.005 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00347 (19596) covalent geometry : angle 0.50571 (26504) hydrogen bonds : bond 0.03761 ( 1038) hydrogen bonds : angle 4.22762 ( 3042) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.856 Fit side-chains REVERT: C 232 PHE cc_start: 0.8093 (t80) cc_final: 0.7786 (t80) REVERT: C 512 LYS cc_start: 0.8648 (ptpp) cc_final: 0.8420 (ptmt) REVERT: F 386 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7958 (mt-10) REVERT: G 503 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8305 (mtm) outliers start: 41 outliers final: 23 residues processed: 275 average time/residue: 0.1395 time to fit residues: 59.8124 Evaluate side-chains 263 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 489 VAL Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 2 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN F 515 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117453 restraints weight = 22451.106| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.60 r_work: 0.3164 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19596 Z= 0.135 Angle : 0.496 6.559 26504 Z= 0.262 Chirality : 0.043 0.168 2863 Planarity : 0.005 0.064 3438 Dihedral : 3.708 19.043 2615 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 2.43 % Allowed : 11.17 % Favored : 86.40 % 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 aren not related in a simple way. whole: 1.42 (0.18), residues: 2463 helix: 2.07 (0.15), residues: 1275 sheet: 0.52 (0.33), residues: 241 loop : -0.51 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 387 TYR 0.012 0.001 TYR C 240 PHE 0.025 0.001 PHE D 473 TRP 0.012 0.001 TRP F 266 HIS 0.004 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00334 (19596) covalent geometry : angle 0.49573 (26504) hydrogen bonds : bond 0.03545 ( 1038) hydrogen bonds : angle 4.15587 ( 3042) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: C 512 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8389 (ptmt) REVERT: G 503 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8317 (mtm) outliers start: 51 outliers final: 32 residues processed: 281 average time/residue: 0.1466 time to fit residues: 64.1506 Evaluate side-chains 272 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 243 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 211 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118273 restraints weight = 21876.189| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.33 r_work: 0.3191 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19596 Z= 0.128 Angle : 0.489 6.363 26504 Z= 0.258 Chirality : 0.042 0.162 2863 Planarity : 0.005 0.060 3438 Dihedral : 3.691 18.926 2615 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 2.81 % Allowed : 11.22 % Favored : 85.97 % 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 aren not related in a simple way. whole: 1.44 (0.18), residues: 2463 helix: 2.08 (0.15), residues: 1281 sheet: 0.50 (0.34), residues: 241 loop : -0.48 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 322 TYR 0.012 0.001 TYR C 240 PHE 0.017 0.001 PHE D 473 TRP 0.012 0.001 TRP H 266 HIS 0.004 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00316 (19596) covalent geometry : angle 0.48916 (26504) hydrogen bonds : bond 0.03359 ( 1038) hydrogen bonds : angle 4.08395 ( 3042) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 232 PHE cc_start: 0.8052 (t80) cc_final: 0.7714 (t80) REVERT: C 512 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8388 (ptmt) REVERT: E 330 GLU cc_start: 0.7308 (pm20) cc_final: 0.7068 (pm20) REVERT: G 503 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8297 (mtm) outliers start: 59 outliers final: 45 residues processed: 293 average time/residue: 0.1428 time to fit residues: 65.3475 Evaluate side-chains 289 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 489 VAL Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 48 optimal weight: 0.8980 chunk 159 optimal weight: 0.3980 chunk 178 optimal weight: 0.0970 chunk 81 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 211 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121310 restraints weight = 21726.109| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.31 r_work: 0.3228 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19596 Z= 0.096 Angle : 0.460 6.223 26504 Z= 0.243 Chirality : 0.041 0.157 2863 Planarity : 0.004 0.057 3438 Dihedral : 3.534 18.404 2615 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 2.00 % Allowed : 12.17 % Favored : 85.83 % 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 aren not related in a simple way. whole: 1.61 (0.18), residues: 2463 helix: 2.26 (0.15), residues: 1275 sheet: 0.54 (0.33), residues: 241 loop : -0.44 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 387 TYR 0.010 0.001 TYR H 240 PHE 0.013 0.001 PHE D 473 TRP 0.010 0.001 TRP H 266 HIS 0.004 0.000 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00222 (19596) covalent geometry : angle 0.46040 (26504) hydrogen bonds : bond 0.02743 ( 1038) hydrogen bonds : angle 3.95729 ( 3042) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.796 Fit side-chains REVERT: A 230 MET cc_start: 0.7136 (mmt) cc_final: 0.6900 (mmp) REVERT: A 305 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8612 (mp) REVERT: B 495 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 512 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8351 (ptmt) REVERT: C 525 ASP cc_start: 0.8158 (m-30) cc_final: 0.7664 (m-30) REVERT: D 232 PHE cc_start: 0.8081 (t80) cc_final: 0.7800 (t80) REVERT: E 330 GLU cc_start: 0.7337 (pm20) cc_final: 0.7101 (pm20) REVERT: E 495 LEU cc_start: 0.8627 (pp) cc_final: 0.8395 (tt) REVERT: G 503 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8294 (mtm) outliers start: 42 outliers final: 31 residues processed: 289 average time/residue: 0.1431 time to fit residues: 64.2157 Evaluate side-chains 288 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 193 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 203 optimal weight: 0.0770 chunk 109 optimal weight: 0.1980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN F 290 GLN F 499 ASN G 235 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119873 restraints weight = 21731.478| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.32 r_work: 0.3212 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19596 Z= 0.110 Angle : 0.475 6.185 26504 Z= 0.250 Chirality : 0.042 0.156 2863 Planarity : 0.004 0.056 3438 Dihedral : 3.550 18.602 2615 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 2.33 % Allowed : 12.27 % Favored : 85.40 % 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 aren not related in a simple way. whole: 1.62 (0.18), residues: 2463 helix: 2.33 (0.15), residues: 1268 sheet: 0.48 (0.33), residues: 241 loop : -0.49 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 387 TYR 0.011 0.001 TYR H 240 PHE 0.012 0.001 PHE E 473 TRP 0.011 0.001 TRP C 266 HIS 0.005 0.000 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00264 (19596) covalent geometry : angle 0.47490 (26504) hydrogen bonds : bond 0.02982 ( 1038) hydrogen bonds : angle 3.96419 ( 3042) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 0.809 Fit side-chains REVERT: A 305 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8623 (mp) REVERT: B 495 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8414 (tt) REVERT: C 232 PHE cc_start: 0.8038 (t80) cc_final: 0.7837 (t80) REVERT: C 512 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8352 (ptmt) REVERT: C 525 ASP cc_start: 0.8159 (m-30) cc_final: 0.7660 (m-30) REVERT: D 232 PHE cc_start: 0.8060 (t80) cc_final: 0.7798 (t80) REVERT: E 330 GLU cc_start: 0.7363 (pm20) cc_final: 0.7124 (pm20) REVERT: E 495 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8495 (pp) REVERT: G 305 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 49 outliers final: 40 residues processed: 296 average time/residue: 0.1456 time to fit residues: 67.1978 Evaluate side-chains 294 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 158 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 217 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN F 515 ASN F 521 HIS G 235 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118560 restraints weight = 21936.754| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.34 r_work: 0.3193 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19596 Z= 0.127 Angle : 0.495 6.150 26504 Z= 0.261 Chirality : 0.042 0.156 2863 Planarity : 0.004 0.054 3438 Dihedral : 3.630 18.568 2615 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 2.47 % Allowed : 12.55 % Favored : 84.97 % 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 aren not related in a simple way. whole: 1.58 (0.18), residues: 2463 helix: 2.29 (0.15), residues: 1268 sheet: 0.47 (0.33), residues: 241 loop : -0.51 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 387 TYR 0.012 0.001 TYR A 240 PHE 0.013 0.001 PHE B 473 TRP 0.012 0.001 TRP F 266 HIS 0.005 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00313 (19596) covalent geometry : angle 0.49535 (26504) hydrogen bonds : bond 0.03252 ( 1038) hydrogen bonds : angle 4.01665 ( 3042) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 0.802 Fit side-chains REVERT: B 388 GLU cc_start: 0.7755 (mp0) cc_final: 0.7545 (mp0) REVERT: C 232 PHE cc_start: 0.8021 (t80) cc_final: 0.7812 (t80) REVERT: C 512 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8348 (ptmt) REVERT: C 525 ASP cc_start: 0.8226 (m-30) cc_final: 0.7713 (m-30) REVERT: D 232 PHE cc_start: 0.8023 (t80) cc_final: 0.7737 (t80) REVERT: E 330 GLU cc_start: 0.7341 (pm20) cc_final: 0.7092 (pm20) REVERT: E 495 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8520 (pp) REVERT: F 232 PHE cc_start: 0.7235 (t80) cc_final: 0.6830 (t80) REVERT: F 274 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7441 (t0) REVERT: F 525 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: G 330 GLU cc_start: 0.7573 (pm20) cc_final: 0.7318 (pm20) REVERT: G 503 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8277 (mtm) outliers start: 52 outliers final: 42 residues processed: 292 average time/residue: 0.1484 time to fit residues: 67.1252 Evaluate side-chains 301 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 468 CYS Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 133 optimal weight: 2.9990 chunk 225 optimal weight: 0.0970 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 246 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 206 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN G 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121485 restraints weight = 21759.642| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.35 r_work: 0.3192 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19596 Z= 0.105 Angle : 0.475 6.104 26504 Z= 0.250 Chirality : 0.041 0.151 2863 Planarity : 0.004 0.055 3438 Dihedral : 3.571 19.652 2615 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 2.33 % Allowed : 12.74 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.18), residues: 2463 helix: 2.34 (0.15), residues: 1268 sheet: 0.49 (0.33), residues: 241 loop : -0.50 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 387 TYR 0.012 0.001 TYR A 240 PHE 0.011 0.001 PHE B 473 TRP 0.011 0.001 TRP C 266 HIS 0.006 0.000 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00251 (19596) covalent geometry : angle 0.47492 (26504) hydrogen bonds : bond 0.02860 ( 1038) hydrogen bonds : angle 3.94778 ( 3042) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 0.756 Fit side-chains REVERT: A 305 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8621 (mp) REVERT: B 495 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8408 (tt) REVERT: C 232 PHE cc_start: 0.7987 (t80) cc_final: 0.7770 (t80) REVERT: C 322 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: C 512 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8346 (ptmt) REVERT: C 525 ASP cc_start: 0.8174 (m-30) cc_final: 0.7651 (m-30) REVERT: E 330 GLU cc_start: 0.7346 (pm20) cc_final: 0.7100 (pm20) REVERT: E 495 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8404 (tt) REVERT: F 232 PHE cc_start: 0.7185 (t80) cc_final: 0.6737 (t80) REVERT: F 525 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: G 503 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8281 (mtm) outliers start: 49 outliers final: 39 residues processed: 291 average time/residue: 0.1457 time to fit residues: 65.9899 Evaluate side-chains 300 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 27 optimal weight: 0.0570 chunk 109 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 227 optimal weight: 0.4980 chunk 26 optimal weight: 0.0870 chunk 232 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN G 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.144118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121275 restraints weight = 21704.944| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.32 r_work: 0.3230 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 19596 Z= 0.099 Angle : 0.472 6.243 26504 Z= 0.249 Chirality : 0.041 0.150 2863 Planarity : 0.004 0.054 3438 Dihedral : 3.520 21.785 2615 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 2.14 % Allowed : 13.08 % Favored : 84.78 % 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 aren not related in a simple way. whole: 1.66 (0.18), residues: 2463 helix: 2.38 (0.15), residues: 1268 sheet: 0.49 (0.33), residues: 241 loop : -0.51 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 387 TYR 0.017 0.001 TYR A 240 PHE 0.014 0.001 PHE H 232 TRP 0.011 0.001 TRP F 266 HIS 0.007 0.000 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00230 (19596) covalent geometry : angle 0.47157 (26504) hydrogen bonds : bond 0.02694 ( 1038) hydrogen bonds : angle 3.91120 ( 3042) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 0.847 Fit side-chains REVERT: B 495 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8396 (tt) REVERT: C 525 ASP cc_start: 0.8187 (m-30) cc_final: 0.7654 (m-30) REVERT: E 330 GLU cc_start: 0.7361 (pm20) cc_final: 0.7128 (pm20) REVERT: E 495 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8378 (tt) REVERT: F 274 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7435 (t0) REVERT: F 525 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: G 503 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8256 (mtm) outliers start: 45 outliers final: 38 residues processed: 288 average time/residue: 0.1479 time to fit residues: 66.1881 Evaluate side-chains 300 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN F 499 ASN G 235 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118902 restraints weight = 21868.759| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.33 r_work: 0.3178 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19596 Z= 0.123 Angle : 0.500 6.115 26504 Z= 0.262 Chirality : 0.042 0.150 2863 Planarity : 0.004 0.054 3438 Dihedral : 3.625 22.211 2615 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 2.09 % Allowed : 13.17 % Favored : 84.74 % 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 aren not related in a simple way. whole: 1.59 (0.18), residues: 2463 helix: 2.31 (0.15), residues: 1268 sheet: 0.46 (0.34), residues: 241 loop : -0.53 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 387 TYR 0.016 0.001 TYR A 240 PHE 0.015 0.001 PHE B 473 TRP 0.012 0.001 TRP H 266 HIS 0.008 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00302 (19596) covalent geometry : angle 0.49965 (26504) hydrogen bonds : bond 0.03188 ( 1038) hydrogen bonds : angle 4.00787 ( 3042) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.505 Fit side-chains REVERT: B 495 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8444 (tt) REVERT: C 525 ASP cc_start: 0.8207 (m-30) cc_final: 0.7672 (m-30) REVERT: D 232 PHE cc_start: 0.7941 (t80) cc_final: 0.7675 (t80) REVERT: E 330 GLU cc_start: 0.7334 (pm20) cc_final: 0.7100 (pm20) REVERT: E 495 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8525 (pp) REVERT: F 274 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7439 (t0) REVERT: F 525 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7523 (m-30) outliers start: 44 outliers final: 39 residues processed: 287 average time/residue: 0.1364 time to fit residues: 59.7305 Evaluate side-chains 301 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 468 CYS Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 109 optimal weight: 0.0980 chunk 192 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 116 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN G 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119662 restraints weight = 21779.304| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.33 r_work: 0.3186 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19596 Z= 0.115 Angle : 0.493 7.096 26504 Z= 0.260 Chirality : 0.042 0.151 2863 Planarity : 0.004 0.055 3438 Dihedral : 3.599 19.180 2615 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 2.33 % Allowed : 13.08 % Favored : 84.59 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: 1.60 (0.18), residues: 2463 helix: 2.32 (0.15), residues: 1268 sheet: 0.47 (0.33), residues: 241 loop : -0.51 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 387 TYR 0.019 0.001 TYR A 240 PHE 0.017 0.001 PHE D 473 TRP 0.012 0.001 TRP F 266 HIS 0.008 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00278 (19596) covalent geometry : angle 0.49343 (26504) hydrogen bonds : bond 0.02993 ( 1038) hydrogen bonds : angle 3.98982 ( 3042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4712.60 seconds wall clock time: 82 minutes 2.09 seconds (4922.09 seconds total)