Starting phenix.real_space_refine on Mon Jun 16 20:43:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ec6_28013/06_2025/8ec6_28013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ec6_28013/06_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_28013/06_2025/8ec6_28013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ec6_28013/06_2025/8ec6_28013.map" model { file = "/net/cci-nas-00/data/ceres_data/8ec6_28013/06_2025/8ec6_28013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ec6_28013/06_2025/8ec6_28013.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.54, per 1000 atoms: 0.60 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: 4.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.16 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: 6.70 Time building geometry restraints manager: 5.48 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 533 or resid 701)) selection = (chain 'B' and (resid 225 through 533 or resid 701)) selection = (chain 'C' and (resid 225 through 533 or resid 701)) selection = (chain 'D' and (resid 225 through 533 or resid 701)) selection = chain 'E' selection = (chain 'F' and (resid 225 through 533 or resid 701)) selection = (chain 'G' and (resid 225 through 533 or resid 701)) selection = (chain 'H' and (resid 225 through 533 or resid 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.470 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP E 266 HIS 0.007 0.001 HIS G 235 PHE 0.030 0.001 PHE C 232 TYR 0.011 0.001 TYR H 240 ARG 0.010 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.11671 ( 1038) hydrogen bonds : angle 5.13236 ( 3042) covalent geometry : bond 0.00353 (19596) covalent geometry : angle 0.48746 (26504) *********************** 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 : 2.122 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: 0.2964 time to fit residues: 106.1851 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 : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 126 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.144759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119569 restraints weight = 22235.077| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.60 r_work: 0.3195 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19596 Z= 0.120 Angle : 0.486 6.827 26504 Z= 0.258 Chirality : 0.042 0.172 2863 Planarity : 0.005 0.070 3438 Dihedral : 3.583 18.614 2615 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 1.57 % Allowed : 10.84 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.18), residues: 2463 helix: 2.13 (0.15), residues: 1275 sheet: 0.62 (0.34), residues: 241 loop : -0.53 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 266 HIS 0.005 0.001 HIS A 521 PHE 0.014 0.001 PHE G 473 TYR 0.011 0.001 TYR H 240 ARG 0.004 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 1038) hydrogen bonds : angle 4.18252 ( 3042) covalent geometry : bond 0.00283 (19596) covalent geometry : angle 0.48579 (26504) *********************** 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 287 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 1.988 Fit side-chains REVERT: C 232 PHE cc_start: 0.8100 (t80) cc_final: 0.7813 (t80) REVERT: C 512 LYS cc_start: 0.8585 (ptpp) cc_final: 0.8361 (ptmt) REVERT: D 387 ARG cc_start: 0.8502 (mtp-110) cc_final: 0.8229 (mtm110) REVERT: F 386 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7948 (mt-10) REVERT: G 503 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8291 (mtm) outliers start: 33 outliers final: 16 residues processed: 273 average time/residue: 0.2931 time to fit residues: 124.5087 Evaluate side-chains 257 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 527 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 65 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 160 optimal weight: 0.0070 chunk 56 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.141923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116704 restraints weight = 22227.882| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.59 r_work: 0.3151 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19596 Z= 0.152 Angle : 0.516 6.606 26504 Z= 0.272 Chirality : 0.044 0.169 2863 Planarity : 0.005 0.064 3438 Dihedral : 3.764 19.683 2615 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 2.52 % Allowed : 10.75 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2463 helix: 2.05 (0.15), residues: 1275 sheet: 0.53 (0.34), residues: 241 loop : -0.50 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 266 HIS 0.004 0.001 HIS A 521 PHE 0.028 0.001 PHE D 473 TYR 0.012 0.001 TYR C 240 ARG 0.005 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1038) hydrogen bonds : angle 4.19376 ( 3042) covalent geometry : bond 0.00380 (19596) covalent geometry : angle 0.51602 (26504) *********************** 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 306 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 232 PHE cc_start: 0.8027 (t80) cc_final: 0.7801 (t80) REVERT: C 512 LYS cc_start: 0.8648 (ptpp) cc_final: 0.8388 (ptmt) REVERT: C 525 ASP cc_start: 0.8142 (m-30) cc_final: 0.7623 (m-30) REVERT: F 386 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7958 (mt-10) REVERT: G 503 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8311 (mtm) outliers start: 53 outliers final: 34 residues processed: 290 average time/residue: 0.3135 time to fit residues: 141.0729 Evaluate side-chains 280 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 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 269 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 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 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 76 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.140948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117778 restraints weight = 21827.299| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.33 r_work: 0.3057 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1048 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= 0.137 Angle : 0.498 6.372 26504 Z= 0.263 Chirality : 0.043 0.162 2863 Planarity : 0.005 0.060 3438 Dihedral : 3.739 19.148 2615 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 2.47 % Allowed : 11.46 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2463 helix: 2.03 (0.15), residues: 1281 sheet: 0.47 (0.34), residues: 241 loop : -0.50 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 266 HIS 0.004 0.001 HIS G 235 PHE 0.018 0.001 PHE D 473 TYR 0.012 0.001 TYR H 240 ARG 0.003 0.000 ARG H 387 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 1038) hydrogen bonds : angle 4.10921 ( 3042) covalent geometry : bond 0.00340 (19596) covalent geometry : angle 0.49839 (26504) *********************** 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: 52 poor density : 263 time to evaluate : 1.970 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8560 (mp) REVERT: C 512 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8337 (ptmt) REVERT: C 525 ASP cc_start: 0.8100 (m-30) cc_final: 0.7575 (m-30) REVERT: D 358 GLU cc_start: 0.7518 (mp0) cc_final: 0.7241 (mp0) REVERT: E 330 GLU cc_start: 0.7346 (pm20) cc_final: 0.7066 (pm20) REVERT: F 386 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7973 (mt-10) outliers start: 52 outliers final: 41 residues processed: 297 average time/residue: 0.3145 time to fit residues: 145.3532 Evaluate side-chains 289 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 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 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 438 THR 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 448 THR Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU 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 214 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 159 optimal weight: 0.0000 chunk 209 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 133 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.143662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120724 restraints weight = 21965.738| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.33 r_work: 0.3198 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1071 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= 0.099 Angle : 0.462 6.246 26504 Z= 0.244 Chirality : 0.041 0.155 2863 Planarity : 0.004 0.057 3438 Dihedral : 3.557 18.602 2615 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.21 % Favored : 93.71 % Rotamer: Outliers : 2.33 % Allowed : 12.22 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.18), residues: 2463 helix: 2.23 (0.15), residues: 1275 sheet: 0.48 (0.33), residues: 241 loop : -0.46 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 266 HIS 0.004 0.000 HIS G 235 PHE 0.019 0.001 PHE B 473 TYR 0.010 0.001 TYR H 240 ARG 0.003 0.000 ARG H 387 Details of bonding type rmsd hydrogen bonds : bond 0.02780 ( 1038) hydrogen bonds : angle 3.96593 ( 3042) covalent geometry : bond 0.00231 (19596) covalent geometry : angle 0.46217 (26504) *********************** 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 308 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 3.738 Fit side-chains REVERT: A 230 MET cc_start: 0.7165 (mmt) cc_final: 0.6919 (mmp) REVERT: A 305 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 495 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8415 (tt) REVERT: C 512 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8345 (ptmt) REVERT: C 525 ASP cc_start: 0.8202 (m-30) cc_final: 0.7711 (m-30) REVERT: D 232 PHE cc_start: 0.8094 (t80) cc_final: 0.7802 (t80) REVERT: E 330 GLU cc_start: 0.7348 (pm20) cc_final: 0.7108 (pm20) REVERT: E 495 LEU cc_start: 0.8617 (pp) cc_final: 0.8394 (tt) REVERT: H 238 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7722 (mp0) outliers start: 49 outliers final: 36 residues processed: 289 average time/residue: 0.4023 time to fit residues: 182.2754 Evaluate side-chains 290 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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 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 495 LEU 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 238 GLU 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 527 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 180 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 245 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.141684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118539 restraints weight = 21984.205| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.34 r_work: 0.3198 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1149 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= 0.124 Angle : 0.489 6.213 26504 Z= 0.258 Chirality : 0.042 0.155 2863 Planarity : 0.004 0.056 3438 Dihedral : 3.615 18.961 2615 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 2.57 % Allowed : 11.98 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2463 helix: 2.27 (0.15), residues: 1268 sheet: 0.42 (0.33), residues: 241 loop : -0.53 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 266 HIS 0.005 0.001 HIS G 235 PHE 0.016 0.001 PHE B 473 TYR 0.011 0.001 TYR H 240 ARG 0.004 0.000 ARG H 387 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 1038) hydrogen bonds : angle 4.01632 ( 3042) covalent geometry : bond 0.00305 (19596) covalent geometry : angle 0.48948 (26504) *********************** 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 314 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 2.283 Fit side-chains REVERT: A 305 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8615 (mp) REVERT: B 495 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8434 (tt) REVERT: C 232 PHE cc_start: 0.8048 (t80) cc_final: 0.7843 (t80) REVERT: C 322 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7963 (ttp-110) REVERT: C 512 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8358 (ptmt) REVERT: C 525 ASP cc_start: 0.8208 (m-30) cc_final: 0.7695 (m-30) REVERT: D 232 PHE cc_start: 0.8118 (t80) cc_final: 0.7855 (t80) REVERT: E 330 GLU cc_start: 0.7324 (pm20) cc_final: 0.7083 (pm20) REVERT: E 495 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8512 (pp) REVERT: F 232 PHE cc_start: 0.7131 (t80) cc_final: 0.6779 (t80) REVERT: H 238 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7679 (mp0) outliers start: 54 outliers final: 42 residues processed: 293 average time/residue: 0.3774 time to fit residues: 169.5617 Evaluate side-chains 299 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.141175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118064 restraints weight = 21773.197| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.33 r_work: 0.3188 rms_B_bonded: 2.14 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: 0.8356 moved from start: 0.1209 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= 0.132 Angle : 0.498 6.174 26504 Z= 0.263 Chirality : 0.043 0.154 2863 Planarity : 0.004 0.054 3438 Dihedral : 3.680 18.978 2615 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 2.62 % Allowed : 11.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2463 helix: 2.23 (0.15), residues: 1268 sheet: 0.41 (0.33), residues: 241 loop : -0.54 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 266 HIS 0.005 0.001 HIS G 235 PHE 0.015 0.001 PHE B 473 TYR 0.012 0.001 TYR E 254 ARG 0.004 0.000 ARG H 387 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 1038) hydrogen bonds : angle 4.05238 ( 3042) covalent geometry : bond 0.00327 (19596) covalent geometry : angle 0.49821 (26504) *********************** 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: 55 poor density : 258 time to evaluate : 1.971 Fit side-chains REVERT: A 305 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8575 (mp) REVERT: C 232 PHE cc_start: 0.8119 (t80) cc_final: 0.7915 (t80) REVERT: C 512 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8362 (ptmt) REVERT: C 525 ASP cc_start: 0.8193 (m-30) cc_final: 0.7672 (m-30) REVERT: D 232 PHE cc_start: 0.8024 (t80) cc_final: 0.7752 (t80) REVERT: E 330 GLU cc_start: 0.7320 (pm20) cc_final: 0.7074 (pm20) REVERT: E 495 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8520 (pp) REVERT: F 232 PHE cc_start: 0.7196 (t80) cc_final: 0.6978 (t80) REVERT: F 274 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7445 (t0) REVERT: H 238 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7688 (mp0) outliers start: 55 outliers final: 45 residues processed: 292 average time/residue: 0.3155 time to fit residues: 142.9230 Evaluate side-chains 301 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 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 438 THR 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 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 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU 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 Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 186 optimal weight: 0.7980 chunk 224 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.141984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118919 restraints weight = 21889.066| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.33 r_work: 0.3177 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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= 0.118 Angle : 0.487 6.148 26504 Z= 0.256 Chirality : 0.042 0.147 2863 Planarity : 0.004 0.054 3438 Dihedral : 3.642 19.031 2615 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 2.33 % Allowed : 12.46 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2463 helix: 2.26 (0.15), residues: 1268 sheet: 0.45 (0.33), residues: 241 loop : -0.55 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 266 HIS 0.006 0.001 HIS G 235 PHE 0.020 0.001 PHE B 473 TYR 0.012 0.001 TYR A 240 ARG 0.007 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 1038) hydrogen bonds : angle 4.01267 ( 3042) covalent geometry : bond 0.00288 (19596) covalent geometry : angle 0.48697 (26504) *********************** 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 308 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 2.146 Fit side-chains REVERT: A 305 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8617 (mp) REVERT: B 495 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8446 (tt) REVERT: C 232 PHE cc_start: 0.8102 (t80) cc_final: 0.7891 (t80) REVERT: C 322 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7887 (ttp-110) REVERT: C 512 LYS cc_start: 0.8652 (ptpp) cc_final: 0.8369 (ptmt) REVERT: C 525 ASP cc_start: 0.8186 (m-30) cc_final: 0.7657 (m-30) REVERT: D 232 PHE cc_start: 0.8029 (t80) cc_final: 0.7758 (t80) REVERT: E 330 GLU cc_start: 0.7320 (pm20) cc_final: 0.7076 (pm20) REVERT: E 495 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8457 (pp) REVERT: F 274 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7439 (t0) REVERT: H 238 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7694 (mp0) outliers start: 49 outliers final: 43 residues processed: 289 average time/residue: 0.3104 time to fit residues: 138.3532 Evaluate side-chains 301 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 2.255 ------------------------------------------------------------------------------- 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 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 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 438 THR 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 448 THR 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 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU 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 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 83 optimal weight: 0.4980 chunk 218 optimal weight: 0.0000 chunk 6 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 211 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 222 optimal weight: 0.0980 chunk 233 optimal weight: 0.8980 chunk 234 optimal weight: 3.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.144398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121494 restraints weight = 21750.420| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.33 r_work: 0.3232 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1264 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= 0.093 Angle : 0.464 6.171 26504 Z= 0.243 Chirality : 0.041 0.147 2863 Planarity : 0.004 0.055 3438 Dihedral : 3.495 18.479 2615 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 2.14 % Allowed : 13.03 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.18), residues: 2463 helix: 2.36 (0.15), residues: 1268 sheet: 0.48 (0.33), residues: 241 loop : -0.53 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 266 HIS 0.007 0.000 HIS G 235 PHE 0.018 0.001 PHE F 232 TYR 0.016 0.001 TYR A 240 ARG 0.009 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.02571 ( 1038) hydrogen bonds : angle 3.89678 ( 3042) covalent geometry : bond 0.00214 (19596) covalent geometry : angle 0.46352 (26504) *********************** 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 308 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 2.218 Fit side-chains REVERT: C 525 ASP cc_start: 0.8178 (m-30) cc_final: 0.7643 (m-30) REVERT: E 330 GLU cc_start: 0.7333 (pm20) cc_final: 0.7093 (pm20) REVERT: E 495 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8358 (tt) REVERT: E 503 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7871 (mtm) REVERT: F 274 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7408 (t0) REVERT: G 503 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8249 (mtm) REVERT: H 238 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7668 (mp0) outliers start: 45 outliers final: 33 residues processed: 291 average time/residue: 0.3019 time to fit residues: 136.7128 Evaluate side-chains 292 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 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 431 SER 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 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 448 THR 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 238 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 45 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 182 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 F 515 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 = 0.3595 r_free = 0.3595 target = 0.142399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119397 restraints weight = 21789.672| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.33 r_work: 0.3205 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1285 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= 0.117 Angle : 0.494 6.110 26504 Z= 0.259 Chirality : 0.042 0.146 2863 Planarity : 0.004 0.054 3438 Dihedral : 3.584 18.703 2615 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 2.00 % Allowed : 13.46 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2463 helix: 2.32 (0.15), residues: 1268 sheet: 0.49 (0.34), residues: 241 loop : -0.54 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 266 HIS 0.008 0.001 HIS G 235 PHE 0.018 0.001 PHE B 473 TYR 0.019 0.001 TYR A 240 ARG 0.009 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 1038) hydrogen bonds : angle 3.97567 ( 3042) covalent geometry : bond 0.00284 (19596) covalent geometry : angle 0.49425 (26504) ********************** 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 300 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 2.062 Fit side-chains REVERT: B 387 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8481 (mtp-110) REVERT: C 525 ASP cc_start: 0.8171 (m-30) cc_final: 0.7643 (m-30) REVERT: E 330 GLU cc_start: 0.7317 (pm20) cc_final: 0.7076 (pm20) REVERT: E 495 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8511 (pp) REVERT: F 274 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7440 (t0) REVERT: F 386 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8017 (mt-10) REVERT: H 238 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7645 (mp0) outliers start: 42 outliers final: 37 residues processed: 285 average time/residue: 0.3068 time to fit residues: 134.3533 Evaluate side-chains 292 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU 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 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 448 THR 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 238 GLU 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 527 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 195 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 238 optimal weight: 0.0030 chunk 112 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 244 optimal weight: 0.0770 chunk 149 optimal weight: 1.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.145552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122764 restraints weight = 21805.425| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.33 r_work: 0.3223 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19596 Z= 0.099 Angle : 0.475 6.100 26504 Z= 0.249 Chirality : 0.041 0.147 2863 Planarity : 0.004 0.054 3438 Dihedral : 3.524 18.639 2615 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 1.76 % Allowed : 13.79 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2463 helix: 2.36 (0.15), residues: 1268 sheet: 0.50 (0.33), residues: 241 loop : -0.51 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 266 HIS 0.008 0.000 HIS G 235 PHE 0.017 0.001 PHE B 473 TYR 0.013 0.001 TYR A 240 ARG 0.009 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 1038) hydrogen bonds : angle 3.92397 ( 3042) covalent geometry : bond 0.00233 (19596) covalent geometry : angle 0.47455 (26504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10829.01 seconds wall clock time: 191 minutes 6.39 seconds (11466.39 seconds total)