Starting phenix.real_space_refine on Sat Sep 28 11:13:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/09_2024/8ec6_28013.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/09_2024/8ec6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/09_2024/8ec6_28013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/09_2024/8ec6_28013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/09_2024/8ec6_28013.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/09_2024/8ec6_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.13, per 1000 atoms: 0.63 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: 4.38 Conformation dependent library (CDL) restraints added in 2.5 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: 2.11 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: 5.81 Time building geometry restraints manager: 5.21 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: 20.100 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 43.550 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.080 ------------------------------------------------------------------------------- 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= 0.224 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 2.178 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: 0.3056 time to fit residues: 109.0706 Evaluate side-chains 229 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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= 0.185 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 *********************** 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 fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 2.300 Fit side-chains REVERT: C 230 MET cc_start: 0.7482 (ttt) cc_final: 0.7282 (mtp) REVERT: C 232 PHE cc_start: 0.7673 (t80) cc_final: 0.7444 (t80) REVERT: C 512 LYS cc_start: 0.8425 (ptpp) cc_final: 0.8144 (ptmt) REVERT: D 387 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7688 (mtm110) REVERT: F 386 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7997 (mt-10) REVERT: G 503 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8003 (mtm) outliers start: 33 outliers final: 16 residues processed: 273 average time/residue: 0.2908 time to fit residues: 123.1944 Evaluate side-chains 257 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 chunk 242 optimal weight: 0.0050 chunk 200 optimal weight: 0.1980 chunk 222 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0791 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= 0.173 Angle : 0.472 6.506 26504 Z= 0.249 Chirality : 0.042 0.168 2863 Planarity : 0.004 0.064 3438 Dihedral : 3.566 19.150 2615 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 2.19 % Allowed : 10.89 % Favored : 86.92 % 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: 2.16 (0.15), residues: 1275 sheet: 0.61 (0.33), residues: 241 loop : -0.46 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 266 HIS 0.004 0.000 HIS A 521 PHE 0.025 0.001 PHE D 473 TYR 0.012 0.001 TYR C 240 ARG 0.005 0.000 ARG B 387 *********************** 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 301 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 2.120 Fit side-chains revert: symmetry clash REVERT: B 495 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8246 (tt) REVERT: C 230 MET cc_start: 0.7512 (ttt) cc_final: 0.7304 (mtp) REVERT: C 512 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8136 (ptmt) REVERT: C 525 ASP cc_start: 0.7794 (m-30) cc_final: 0.7239 (m-30) REVERT: D 387 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7745 (mtm110) REVERT: F 351 LYS cc_start: 0.7137 (mttm) cc_final: 0.6929 (mttm) REVERT: F 386 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7976 (mt-10) outliers start: 46 outliers final: 29 residues processed: 288 average time/residue: 0.3125 time to fit residues: 139.9236 Evaluate side-chains 273 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 2.269 ------------------------------------------------------------------------------- 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 495 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain H residue 274 ASP 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 222 optimal weight: 0.7980 chunk 168 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 chunk 225 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN F 515 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0926 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= 0.201 Angle : 0.486 6.385 26504 Z= 0.256 Chirality : 0.042 0.166 2863 Planarity : 0.004 0.045 3438 Dihedral : 3.614 18.686 2615 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 2.52 % Allowed : 11.51 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.18 (0.15), residues: 1275 sheet: 0.53 (0.33), residues: 241 loop : -0.44 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 266 HIS 0.004 0.001 HIS G 235 PHE 0.018 0.001 PHE D 473 TYR 0.011 0.001 TYR H 240 ARG 0.005 0.000 ARG B 387 *********************** 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 313 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 260 time to evaluate : 2.241 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8381 (mp) REVERT: C 230 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7309 (mtp) REVERT: C 512 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8118 (ptmt) REVERT: C 525 ASP cc_start: 0.7773 (m-30) cc_final: 0.7208 (m-30) REVERT: D 279 SER cc_start: 0.9190 (p) cc_final: 0.8747 (m) REVERT: D 358 GLU cc_start: 0.7102 (mp0) cc_final: 0.6732 (mp0) REVERT: E 330 GLU cc_start: 0.7249 (pm20) cc_final: 0.7000 (pm20) REVERT: G 402 GLU cc_start: 0.8289 (tt0) cc_final: 0.8058 (tt0) outliers start: 53 outliers final: 39 residues processed: 294 average time/residue: 0.3017 time to fit residues: 137.0757 Evaluate side-chains 292 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 251 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 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 230 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 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain 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 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 203 optimal weight: 0.1980 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 H 515 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19596 Z= 0.252 Angle : 0.515 6.347 26504 Z= 0.272 Chirality : 0.044 0.162 2863 Planarity : 0.005 0.049 3438 Dihedral : 3.761 19.316 2615 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 2.57 % Allowed : 11.70 % Favored : 85.73 % 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: 1.45 (0.18), residues: 2463 helix: 2.10 (0.15), residues: 1275 sheet: 0.46 (0.34), residues: 241 loop : -0.48 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 266 HIS 0.004 0.001 HIS G 235 PHE 0.016 0.001 PHE D 473 TYR 0.012 0.001 TYR H 240 ARG 0.006 0.000 ARG B 387 *********************** 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 303 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 2.188 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8360 (mp) REVERT: C 230 MET cc_start: 0.7546 (ttt) cc_final: 0.7310 (mtp) REVERT: C 305 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8469 (mp) REVERT: C 322 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7446 (ttp-110) REVERT: C 512 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8135 (ptmt) REVERT: C 525 ASP cc_start: 0.7762 (m-30) cc_final: 0.7158 (m-30) REVERT: D 279 SER cc_start: 0.9192 (p) cc_final: 0.8751 (m) REVERT: E 330 GLU cc_start: 0.7255 (pm20) cc_final: 0.6962 (pm20) REVERT: F 386 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8067 (mt-10) REVERT: H 238 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7357 (mp0) outliers start: 54 outliers final: 47 residues processed: 285 average time/residue: 0.3033 time to fit residues: 133.5634 Evaluate side-chains 293 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 2.295 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 361 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 365 GLN G 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1157 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= 0.218 Angle : 0.498 6.213 26504 Z= 0.262 Chirality : 0.043 0.154 2863 Planarity : 0.005 0.052 3438 Dihedral : 3.729 19.072 2615 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 2.76 % Allowed : 11.84 % 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: 1.45 (0.18), residues: 2463 helix: 2.17 (0.15), residues: 1268 sheet: 0.43 (0.34), residues: 241 loop : -0.57 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 266 HIS 0.005 0.001 HIS G 235 PHE 0.018 0.001 PHE B 473 TYR 0.012 0.001 TYR H 240 ARG 0.007 0.000 ARG B 387 *********************** 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 317 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 259 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8365 (mp) REVERT: C 230 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7286 (mtp) REVERT: C 305 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8463 (mp) REVERT: C 512 LYS cc_start: 0.8450 (ptpp) cc_final: 0.8131 (ptmt) REVERT: C 525 ASP cc_start: 0.7768 (m-30) cc_final: 0.7171 (m-30) REVERT: D 232 PHE cc_start: 0.7716 (t80) cc_final: 0.7374 (t80) REVERT: D 279 SER cc_start: 0.9182 (p) cc_final: 0.8754 (m) REVERT: E 330 GLU cc_start: 0.7252 (pm20) cc_final: 0.6957 (pm20) REVERT: E 495 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8614 (pp) REVERT: F 386 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8098 (mt-10) REVERT: G 330 GLU cc_start: 0.7442 (pm20) cc_final: 0.7224 (pm20) REVERT: H 238 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: H 277 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.8132 (mmm-85) outliers start: 58 outliers final: 44 residues processed: 297 average time/residue: 0.3118 time to fit residues: 143.7051 Evaluate side-chains 297 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 248 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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 230 MET Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain 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 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 230 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 H 515 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1214 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= 0.215 Angle : 0.499 6.196 26504 Z= 0.263 Chirality : 0.043 0.148 2863 Planarity : 0.004 0.048 3438 Dihedral : 3.729 19.237 2615 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 2.66 % Allowed : 12.32 % Favored : 85.02 % 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: 1.44 (0.18), residues: 2463 helix: 2.18 (0.15), residues: 1268 sheet: 0.41 (0.34), residues: 241 loop : -0.59 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 266 HIS 0.006 0.001 HIS G 235 PHE 0.015 0.001 PHE B 473 TYR 0.012 0.001 TYR H 240 ARG 0.007 0.000 ARG B 387 *********************** 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 311 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 255 time to evaluate : 2.285 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8368 (mp) REVERT: B 388 GLU cc_start: 0.7616 (mp0) cc_final: 0.7394 (mp0) REVERT: C 230 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7318 (mtp) REVERT: C 305 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8458 (mp) REVERT: C 512 LYS cc_start: 0.8455 (ptpp) cc_final: 0.8110 (ptmt) REVERT: D 232 PHE cc_start: 0.7685 (t80) cc_final: 0.7359 (t80) REVERT: D 279 SER cc_start: 0.9186 (p) cc_final: 0.8738 (m) REVERT: D 358 GLU cc_start: 0.7076 (mp0) cc_final: 0.6842 (mp0) REVERT: E 330 GLU cc_start: 0.7255 (pm20) cc_final: 0.6958 (pm20) REVERT: E 495 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8598 (pp) REVERT: F 386 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8088 (mt-10) REVERT: H 238 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7349 (mp0) outliers start: 56 outliers final: 49 residues processed: 291 average time/residue: 0.3167 time to fit residues: 142.7289 Evaluate side-chains 304 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 250 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 230 MET Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 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 361 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 0.0980 chunk 71 optimal weight: 0.0270 chunk 46 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 chunk 162 optimal weight: 0.2980 chunk 117 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 187 optimal weight: 0.3980 chunk 216 optimal weight: 6.9990 overall best weight: 0.2438 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19596 Z= 0.127 Angle : 0.456 6.071 26504 Z= 0.240 Chirality : 0.040 0.146 2863 Planarity : 0.004 0.044 3438 Dihedral : 3.487 18.512 2615 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 2.09 % Allowed : 13.22 % Favored : 84.69 % 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: 2.37 (0.15), residues: 1268 sheet: 0.48 (0.33), residues: 241 loop : -0.54 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 266 HIS 0.006 0.000 HIS G 235 PHE 0.016 0.001 PHE C 232 TYR 0.011 0.001 TYR E 254 ARG 0.006 0.000 ARG B 387 *********************** 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 314 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 2.245 Fit side-chains REVERT: A 305 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8409 (mp) REVERT: B 386 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7866 (mt-10) REVERT: B 388 GLU cc_start: 0.7534 (mp0) cc_final: 0.7312 (mp0) REVERT: B 495 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8245 (tt) REVERT: C 230 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7318 (mtp) REVERT: C 305 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8450 (mp) REVERT: C 512 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8086 (ptmt) REVERT: C 525 ASP cc_start: 0.7711 (m-30) cc_final: 0.7116 (m-30) REVERT: D 279 SER cc_start: 0.9150 (p) cc_final: 0.8729 (m) REVERT: D 358 GLU cc_start: 0.7013 (mp0) cc_final: 0.6743 (mp0) REVERT: E 330 GLU cc_start: 0.7252 (pm20) cc_final: 0.6952 (pm20) REVERT: E 495 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8389 (tt) REVERT: F 232 PHE cc_start: 0.7164 (t80) cc_final: 0.6889 (t80) REVERT: G 503 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: H 238 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7397 (mp0) outliers start: 44 outliers final: 32 residues processed: 299 average time/residue: 0.3201 time to fit residues: 148.3362 Evaluate side-chains 296 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 257 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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 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 230 MET Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 305 LEU 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 E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 495 LEU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 133 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 234 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1221 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= 0.187 Angle : 0.489 6.171 26504 Z= 0.256 Chirality : 0.042 0.146 2863 Planarity : 0.004 0.047 3438 Dihedral : 3.572 18.677 2615 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 2.00 % Allowed : 13.55 % 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: 1.59 (0.18), residues: 2463 helix: 2.34 (0.15), residues: 1268 sheet: 0.46 (0.33), residues: 241 loop : -0.56 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 266 HIS 0.007 0.001 HIS G 235 PHE 0.028 0.001 PHE C 232 TYR 0.011 0.001 TYR H 240 ARG 0.010 0.000 ARG B 387 *********************** 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 300 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 258 time to evaluate : 2.388 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 388 GLU cc_start: 0.7648 (mp0) cc_final: 0.7399 (mp0) REVERT: B 495 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8300 (tt) REVERT: C 230 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7328 (mtp) REVERT: C 305 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8451 (mp) REVERT: C 512 LYS cc_start: 0.8422 (ptpp) cc_final: 0.8081 (ptmt) REVERT: D 232 PHE cc_start: 0.7675 (t80) cc_final: 0.7337 (t80) REVERT: D 279 SER cc_start: 0.9104 (p) cc_final: 0.8656 (m) REVERT: D 358 GLU cc_start: 0.7047 (mp0) cc_final: 0.6767 (mp0) REVERT: E 330 GLU cc_start: 0.7252 (pm20) cc_final: 0.6960 (pm20) REVERT: E 495 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8594 (pp) REVERT: F 232 PHE cc_start: 0.7251 (t80) cc_final: 0.7020 (t80) REVERT: G 503 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7982 (mtm) REVERT: H 238 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7314 (mp0) outliers start: 42 outliers final: 33 residues processed: 288 average time/residue: 0.3140 time to fit residues: 138.7988 Evaluate side-chains 299 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 259 time to evaluate : 2.273 ------------------------------------------------------------------------------- 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 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 230 MET Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 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 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 F residue 274 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 0.6980 chunk 111 optimal weight: 0.0870 chunk 163 optimal weight: 0.1980 chunk 246 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 151 optimal weight: 0.0980 chunk 120 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1259 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= 0.142 Angle : 0.468 6.048 26504 Z= 0.245 Chirality : 0.041 0.147 2863 Planarity : 0.004 0.045 3438 Dihedral : 3.472 18.513 2615 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.95 % Rotamer: Outliers : 1.76 % Allowed : 13.93 % Favored : 84.31 % 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: 1.65 (0.18), residues: 2463 helix: 2.38 (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 0.011 0.001 TRP H 266 HIS 0.008 0.000 HIS G 235 PHE 0.029 0.001 PHE C 232 TYR 0.017 0.001 TYR A 240 ARG 0.010 0.000 ARG B 387 ********************** 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 296 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 259 time to evaluate : 2.247 Fit side-chains REVERT: A 305 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 388 GLU cc_start: 0.7612 (mp0) cc_final: 0.7368 (mp0) REVERT: B 495 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8250 (tt) REVERT: C 230 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7347 (mtp) REVERT: C 305 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8453 (mp) REVERT: C 512 LYS cc_start: 0.8400 (ptpp) cc_final: 0.8066 (ptmt) REVERT: C 525 ASP cc_start: 0.7729 (m-30) cc_final: 0.7121 (m-30) REVERT: D 279 SER cc_start: 0.9044 (p) cc_final: 0.8598 (m) REVERT: D 358 GLU cc_start: 0.7051 (mp0) cc_final: 0.6791 (mp0) REVERT: E 330 GLU cc_start: 0.7285 (pm20) cc_final: 0.7002 (pm20) REVERT: E 495 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8380 (tt) REVERT: F 232 PHE cc_start: 0.7209 (t80) cc_final: 0.6693 (t80) REVERT: G 503 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7931 (mtm) REVERT: H 238 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7352 (mp0) outliers start: 37 outliers final: 29 residues processed: 284 average time/residue: 0.2997 time to fit residues: 132.5531 Evaluate side-chains 290 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 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 230 MET Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 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 E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 361 ASP 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 468 CYS 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 60 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 0.0770 chunk 196 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3606 r_free = 0.3606 target = 0.143422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120525 restraints weight = 21772.343| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.32 r_work: 0.3221 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1273 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= 0.167 Angle : 0.483 6.117 26504 Z= 0.253 Chirality : 0.041 0.147 2863 Planarity : 0.004 0.046 3438 Dihedral : 3.536 19.921 2615 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 2.00 % Allowed : 13.74 % Favored : 84.26 % 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: 2.38 (0.15), residues: 1268 sheet: 0.48 (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 H 266 HIS 0.008 0.000 HIS G 235 PHE 0.016 0.001 PHE H 232 TYR 0.017 0.001 TYR A 240 ARG 0.009 0.000 ARG B 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4145.17 seconds wall clock time: 76 minutes 29.67 seconds (4589.67 seconds total)