Starting phenix.real_space_refine on Sat Mar 7 00:35:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s1f_54448/03_2026/9s1f_54448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s1f_54448/03_2026/9s1f_54448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s1f_54448/03_2026/9s1f_54448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s1f_54448/03_2026/9s1f_54448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s1f_54448/03_2026/9s1f_54448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s1f_54448/03_2026/9s1f_54448.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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: 7 Type Number sf(0) Gaussians P 217 5.49 5 Mg 7 5.21 5 S 60 5.16 5 C 10948 2.51 5 N 3161 2.21 5 O 4021 1.98 5 H 16504 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34918 Number of models: 1 Model: "" Number of chains: 15 Chain: "D" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1674 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 22, 'rna3p_pyr': 14} Link IDs: {'rna2p': 16, 'rna3p': 35} Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1640 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 22, 'rna3p_pyr': 15} Link IDs: {'rna2p': 14, 'rna3p': 36} Chain: "F" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1674 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 21, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 33} Chain: "B" Number of atoms: 9328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 9328 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} Chain breaks: 3 Chain: "G" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 657 Classifications: {'DNA': 21} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 20} Chain breaks: 2 Chain: "I" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 625 Classifications: {'DNA': 20} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 19} Chain breaks: 2 Chain: "A" Number of atoms: 9328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 9328 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} Chain breaks: 3 Chain: "H" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 657 Classifications: {'DNA': 21} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 20} Chain breaks: 2 Chain: "C" Number of atoms: 9328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 9328 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} Chain breaks: 3 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.77, per 1000 atoms: 0.19 Number of scatterers: 34918 At special positions: 0 Unit cell: (137.5, 146.3, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 60 16.00 P 217 15.00 Mg 7 11.99 O 4021 8.00 N 3161 7.00 C 10948 6.00 H 16504 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 921.7 milliseconds 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 22 sheets defined 55.0% alpha, 10.9% beta 58 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 6.23 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.693A pdb=" N ALA B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.592A pdb=" N LEU B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.934A pdb=" N GLN B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 38 through 43' Processing helix chain 'B' and resid 62 through 88 removed outlier: 3.798A pdb=" N ILE B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 removed outlier: 4.011A pdb=" N HIS B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 168 through 193 removed outlier: 4.613A pdb=" N ILE B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N MET B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.508A pdb=" N SER B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 302 through 327 removed outlier: 3.933A pdb=" N LEU B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 removed outlier: 3.506A pdb=" N LYS B 344 " --> pdb=" O HIS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 428 through 446 removed outlier: 4.197A pdb=" N GLU B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 475 removed outlier: 4.404A pdb=" N LEU B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.766A pdb=" N ILE B 525 " --> pdb=" O ASP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 566 through 586 Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.575A pdb=" N ALA A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 24 removed outlier: 3.600A pdb=" N LEU A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.719A pdb=" N GLN A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 43' Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.743A pdb=" N ILE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.917A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 4.093A pdb=" N PHE A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 169 through 193 removed outlier: 4.789A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.581A pdb=" N SER A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 302 through 327 removed outlier: 3.973A pdb=" N LEU A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 428 through 446 removed outlier: 3.712A pdb=" N GLU A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.646A pdb=" N ILE A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 566 through 586 Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.589A pdb=" N ALA C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 23 removed outlier: 3.604A pdb=" N LEU C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 38 through 43 removed outlier: 3.879A pdb=" N GLN C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 38 through 43' Processing helix chain 'C' and resid 62 through 87 removed outlier: 3.802A pdb=" N ILE C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 removed outlier: 3.937A pdb=" N HIS C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.988A pdb=" N PHE C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 169 through 193 removed outlier: 4.763A pdb=" N ILE C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 269 through 287 Processing helix chain 'C' and resid 302 through 327 removed outlier: 4.069A pdb=" N LEU C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 348 through 364 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.825A pdb=" N ALA C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 397 Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 428 through 446 removed outlier: 3.723A pdb=" N GLU C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 475 removed outlier: 4.362A pdb=" N LEU C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 489 Processing helix chain 'C' and resid 519 through 524 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 563 through 565 No H-bonds generated for 'chain 'C' and resid 563 through 565' Processing helix chain 'C' and resid 566 through 586 removed outlier: 3.614A pdb=" N PHE C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 572 " --> pdb=" O CYS C 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 44 through 48 removed outlier: 3.985A pdb=" N ILE B 48 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG B 56 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 195 through 199 removed outlier: 4.605A pdb=" N GLU B 240 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 199 Processing sheet with id=AA4, first strand: chain 'B' and resid 217 through 220 Processing sheet with id=AA5, first strand: chain 'B' and resid 256 through 257 Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 292 removed outlier: 4.830A pdb=" N TYR B 289 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 371 Processing sheet with id=AA8, first strand: chain 'B' and resid 456 through 459 Processing sheet with id=AA9, first strand: chain 'A' and resid 44 through 48 removed outlier: 3.811A pdb=" N ILE A 48 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 56 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 195 through 199 removed outlier: 4.775A pdb=" N GLU A 240 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 195 through 199 Processing sheet with id=AB3, first strand: chain 'A' and resid 217 through 220 Processing sheet with id=AB4, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AB5, first strand: chain 'A' and resid 289 through 292 removed outlier: 4.867A pdb=" N TYR A 289 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AB7, first strand: chain 'C' and resid 44 through 46 Processing sheet with id=AB8, first strand: chain 'C' and resid 195 through 199 removed outlier: 4.827A pdb=" N GLU C 240 " --> pdb=" O LYS C 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 195 through 199 Processing sheet with id=AC1, first strand: chain 'C' and resid 217 through 220 Processing sheet with id=AC2, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AC3, first strand: chain 'C' and resid 289 through 292 removed outlier: 4.645A pdb=" N TYR C 289 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 411 through 412 removed outlier: 6.322A pdb=" N VAL C 455 " --> pdb=" O TYR C 499 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 1986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 8.94 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16474 1.03 - 1.23: 118 1.23 - 1.42: 8361 1.42 - 1.62: 10643 1.62 - 1.81: 90 Bond restraints: 35686 Sorted by residual: bond pdb=" N THR B 4 " pdb=" H THR B 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR C 4 " pdb=" H THR C 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR A 4 " pdb=" H THR A 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" CD LYS C 433 " pdb=" CE LYS C 433 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CA TYR A 447 " pdb=" CB TYR A 447 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.69e-02 3.50e+03 9.36e-01 ... (remaining 35681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 63205 1.72 - 3.44: 1197 3.44 - 5.16: 64 5.16 - 6.88: 9 6.88 - 8.61: 1 Bond angle restraints: 64476 Sorted by residual: angle pdb=" CB ARG C 473 " pdb=" CG ARG C 473 " pdb=" CD ARG C 473 " ideal model delta sigma weight residual 111.30 119.91 -8.61 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CB ARG B 70 " pdb=" CG ARG B 70 " pdb=" CD ARG B 70 " ideal model delta sigma weight residual 111.30 117.84 -6.54 2.30e+00 1.89e-01 8.07e+00 angle pdb=" C ALA B 200 " pdb=" CA ALA B 200 " pdb=" CB ALA B 200 " ideal model delta sigma weight residual 110.42 116.05 -5.63 1.99e+00 2.53e-01 8.02e+00 angle pdb=" CA MET C 489 " pdb=" CB MET C 489 " pdb=" CG MET C 489 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.25e+00 angle pdb=" CA LYS C 546 " pdb=" CB LYS C 546 " pdb=" CG LYS C 546 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.88e+00 ... (remaining 64471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 15882 35.00 - 70.00: 705 70.00 - 105.01: 34 105.01 - 140.01: 0 140.01 - 175.01: 4 Dihedral angle restraints: 16625 sinusoidal: 10691 harmonic: 5934 Sorted by residual: dihedral pdb=" O4' C F 46 " pdb=" C1' C F 46 " pdb=" N1 C F 46 " pdb=" C2 C F 46 " ideal model delta sinusoidal sigma weight residual 200.00 46.63 153.37 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' U F 18 " pdb=" C1' U F 18 " pdb=" N1 U F 18 " pdb=" C2 U F 18 " ideal model delta sinusoidal sigma weight residual -128.00 47.01 -175.01 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U E 18 " pdb=" C1' U E 18 " pdb=" N1 U E 18 " pdb=" C2 U E 18 " ideal model delta sinusoidal sigma weight residual -128.00 46.15 -174.15 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 16622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2174 0.032 - 0.063: 672 0.063 - 0.095: 183 0.095 - 0.126: 101 0.126 - 0.158: 11 Chirality restraints: 3141 Sorted by residual: chirality pdb=" C1' A F 62 " pdb=" O4' A F 62 " pdb=" C2' A F 62 " pdb=" N9 A F 62 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA LYS C 546 " pdb=" N LYS C 546 " pdb=" C LYS C 546 " pdb=" CB LYS C 546 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE C 412 " pdb=" N ILE C 412 " pdb=" C ILE C 412 " pdb=" CB ILE C 412 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3138 not shown) Planarity restraints: 4401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 464 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO C 465 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 465 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 465 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 464 " -0.048 5.00e-02 4.00e+02 7.21e-02 8.32e+00 pdb=" N PRO B 465 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 465 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 465 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 453 " -0.038 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO B 454 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 454 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 454 " -0.031 5.00e-02 4.00e+02 ... (remaining 4398 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.04: 143 2.04 - 2.68: 50515 2.68 - 3.32: 102357 3.32 - 3.96: 133501 3.96 - 4.60: 205710 Nonbonded interactions: 492226 Sorted by model distance: nonbonded pdb=" O2' G E 15 " pdb=" OP1 DT H 1 " model vdw 1.394 2.800 nonbonded pdb=" O2' G F 15 " pdb=" P DT I 1 " model vdw 1.442 3.200 nonbonded pdb=" O2' G D 15 " pdb=" OP1 DT G 1 " model vdw 1.462 2.800 nonbonded pdb=" O2' G E 15 " pdb=" P DT H 1 " model vdw 1.474 3.200 nonbonded pdb=" O2' G D 15 " pdb=" P DT G 1 " model vdw 1.489 3.200 ... (remaining 492221 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' selection = (chain 'B' and resid 4 through 601) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 13 through 63) selection = chain 'E' selection = (chain 'F' and resid 13 through 63) } ncs_group { reference = (chain 'G' and (resid 1 through 25 or resid 56 through 67)) selection = (chain 'H' and (resid 1 through 25 or resid 56 through 67)) selection = (chain 'I' and resid 1 through 67) } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.150 Process input model: 39.030 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19182 Z= 0.133 Angle : 0.548 8.606 26823 Z= 0.304 Chirality : 0.037 0.158 3141 Planarity : 0.005 0.084 2611 Dihedral : 17.156 175.010 8426 Min Nonbonded Distance : 1.394 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 0.47 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.18), residues: 1686 helix: -1.62 (0.13), residues: 816 sheet: -2.52 (0.37), residues: 159 loop : -0.18 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 473 TYR 0.035 0.001 TYR B 159 PHE 0.023 0.001 PHE C 495 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00284 (19182) covalent geometry : angle 0.54790 (26823) hydrogen bonds : bond 0.15161 ( 830) hydrogen bonds : angle 6.85417 ( 2256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7346 (mm-30) REVERT: B 431 ASP cc_start: 0.8090 (m-30) cc_final: 0.7796 (m-30) REVERT: B 446 TYR cc_start: 0.7758 (m-80) cc_final: 0.7011 (m-80) REVERT: B 486 MET cc_start: 0.8433 (mpp) cc_final: 0.7954 (mpm) REVERT: B 551 MET cc_start: 0.9096 (ttp) cc_final: 0.8873 (ttt) REVERT: B 571 ASP cc_start: 0.8423 (m-30) cc_final: 0.8180 (m-30) REVERT: A 333 TYR cc_start: 0.7391 (m-10) cc_final: 0.6920 (m-10) REVERT: A 452 LYS cc_start: 0.8524 (tptt) cc_final: 0.8214 (tptp) REVERT: A 520 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8702 (mptt) REVERT: C 271 CYS cc_start: 0.7717 (p) cc_final: 0.6631 (p) REVERT: C 318 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8209 (mtpp) REVERT: C 376 LYS cc_start: 0.7991 (mptt) cc_final: 0.7328 (pttp) REVERT: C 452 LYS cc_start: 0.9078 (mmpt) cc_final: 0.8825 (mmpt) outliers start: 0 outliers final: 1 residues processed: 188 average time/residue: 1.1979 time to fit residues: 256.9472 Evaluate side-chains 151 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 456 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 327 ASN B 441 ASN B 470 ASN A 327 ASN C 106 ASN C 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.194149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.140435 restraints weight = 79410.454| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.78 r_work: 0.3894 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19182 Z= 0.169 Angle : 0.518 7.503 26823 Z= 0.286 Chirality : 0.037 0.157 3141 Planarity : 0.004 0.054 2611 Dihedral : 19.737 178.289 4915 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Rotamer: Outliers : 0.78 % Allowed : 5.77 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1686 helix: 0.58 (0.18), residues: 780 sheet: -2.26 (0.38), residues: 159 loop : 0.24 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.010 0.001 TYR A 491 PHE 0.013 0.001 PHE A 495 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00361 (19182) covalent geometry : angle 0.51758 (26823) hydrogen bonds : bond 0.04628 ( 830) hydrogen bonds : angle 4.93846 ( 2256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 ARG cc_start: 0.8832 (tpt170) cc_final: 0.8581 (tpt170) REVERT: B 417 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7284 (mm-30) REVERT: B 431 ASP cc_start: 0.8133 (m-30) cc_final: 0.7823 (m-30) REVERT: B 486 MET cc_start: 0.8303 (mpp) cc_final: 0.7771 (mpm) REVERT: B 551 MET cc_start: 0.9230 (ttp) cc_final: 0.8931 (ppp) REVERT: B 571 ASP cc_start: 0.8463 (m-30) cc_final: 0.8229 (m-30) REVERT: A 160 ASN cc_start: 0.8307 (m-40) cc_final: 0.8077 (t0) REVERT: A 240 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 307 GLU cc_start: 0.8113 (tp30) cc_final: 0.7880 (tp30) REVERT: A 333 TYR cc_start: 0.7433 (m-10) cc_final: 0.6961 (m-10) REVERT: A 452 LYS cc_start: 0.8528 (tptt) cc_final: 0.8197 (tptp) REVERT: C 271 CYS cc_start: 0.7958 (p) cc_final: 0.7379 (p) REVERT: C 376 LYS cc_start: 0.7970 (mptt) cc_final: 0.7159 (pttp) REVERT: C 518 PHE cc_start: 0.7490 (m-80) cc_final: 0.7141 (m-80) outliers start: 12 outliers final: 6 residues processed: 166 average time/residue: 1.1692 time to fit residues: 222.1927 Evaluate side-chains 149 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 184 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.193597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.138388 restraints weight = 79088.587| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.82 r_work: 0.3822 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19182 Z= 0.132 Angle : 0.487 7.373 26823 Z= 0.267 Chirality : 0.036 0.141 3141 Planarity : 0.004 0.060 2611 Dihedral : 19.680 177.587 4913 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.91 % Favored : 96.92 % Rotamer: Outliers : 0.84 % Allowed : 7.26 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1686 helix: 1.24 (0.18), residues: 801 sheet: -2.17 (0.38), residues: 159 loop : 0.21 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 379 TYR 0.013 0.001 TYR B 159 PHE 0.011 0.001 PHE A 97 HIS 0.003 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00278 (19182) covalent geometry : angle 0.48683 (26823) hydrogen bonds : bond 0.04054 ( 830) hydrogen bonds : angle 4.56564 ( 2256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 431 ASP cc_start: 0.8115 (m-30) cc_final: 0.7834 (m-30) REVERT: B 446 TYR cc_start: 0.7490 (m-80) cc_final: 0.7197 (m-80) REVERT: B 486 MET cc_start: 0.8335 (mpp) cc_final: 0.7760 (mpm) REVERT: B 531 LYS cc_start: 0.7442 (tptt) cc_final: 0.6785 (tppt) REVERT: B 551 MET cc_start: 0.9216 (ttp) cc_final: 0.8683 (tpp) REVERT: A 27 LEU cc_start: 0.7791 (tt) cc_final: 0.7476 (tt) REVERT: A 240 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7964 (mt-10) REVERT: A 307 GLU cc_start: 0.8152 (tp30) cc_final: 0.7799 (tm-30) REVERT: A 333 TYR cc_start: 0.7415 (m-10) cc_final: 0.6947 (m-10) REVERT: A 452 LYS cc_start: 0.8505 (tptt) cc_final: 0.8123 (tptp) REVERT: C 269 ASP cc_start: 0.7415 (t0) cc_final: 0.7082 (t0) REVERT: C 271 CYS cc_start: 0.7935 (p) cc_final: 0.7437 (p) REVERT: C 376 LYS cc_start: 0.7961 (mptt) cc_final: 0.7130 (pttp) outliers start: 13 outliers final: 10 residues processed: 163 average time/residue: 1.1317 time to fit residues: 212.2450 Evaluate side-chains 156 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 456 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 103 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN B 327 ASN A 327 ASN C 179 ASN C 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.188003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.130964 restraints weight = 79234.793| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.82 r_work: 0.3710 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19182 Z= 0.270 Angle : 0.558 6.288 26823 Z= 0.308 Chirality : 0.040 0.201 3141 Planarity : 0.004 0.063 2611 Dihedral : 19.870 176.394 4913 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Rotamer: Outliers : 1.43 % Allowed : 8.50 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1686 helix: 1.13 (0.19), residues: 804 sheet: -2.13 (0.38), residues: 159 loop : 0.09 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 254 TYR 0.017 0.002 TYR B 446 PHE 0.018 0.002 PHE B 357 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00582 (19182) covalent geometry : angle 0.55774 (26823) hydrogen bonds : bond 0.04931 ( 830) hydrogen bonds : angle 4.73801 ( 2256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7310 (mm-30) REVERT: B 431 ASP cc_start: 0.8134 (m-30) cc_final: 0.7855 (m-30) REVERT: B 486 MET cc_start: 0.8382 (mpp) cc_final: 0.7806 (mpm) REVERT: B 531 LYS cc_start: 0.7485 (tptt) cc_final: 0.6853 (tppt) REVERT: B 551 MET cc_start: 0.9240 (ttp) cc_final: 0.8599 (tpp) REVERT: A 27 LEU cc_start: 0.7832 (tt) cc_final: 0.7504 (tt) REVERT: A 160 ASN cc_start: 0.8545 (t0) cc_final: 0.8252 (t0) REVERT: A 307 GLU cc_start: 0.8158 (tp30) cc_final: 0.7948 (tp30) REVERT: A 333 TYR cc_start: 0.7459 (m-10) cc_final: 0.7005 (m-10) REVERT: A 452 LYS cc_start: 0.8633 (tptt) cc_final: 0.8301 (tptp) REVERT: C 269 ASP cc_start: 0.7441 (t0) cc_final: 0.7041 (t0) REVERT: C 271 CYS cc_start: 0.7947 (p) cc_final: 0.7371 (p) REVERT: C 376 LYS cc_start: 0.7948 (mptt) cc_final: 0.7106 (pttp) REVERT: C 486 MET cc_start: 0.7874 (ptt) cc_final: 0.7472 (ptt) outliers start: 22 outliers final: 14 residues processed: 163 average time/residue: 1.1878 time to fit residues: 221.0691 Evaluate side-chains 154 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 92 ASN C 179 ASN C 320 ASN C 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.190134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.133609 restraints weight = 79185.679| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.83 r_work: 0.3743 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19182 Z= 0.164 Angle : 0.503 6.741 26823 Z= 0.275 Chirality : 0.037 0.142 3141 Planarity : 0.004 0.065 2611 Dihedral : 19.796 175.864 4913 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % Rotamer: Outliers : 1.43 % Allowed : 9.66 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1686 helix: 1.32 (0.19), residues: 801 sheet: -2.06 (0.38), residues: 159 loop : 0.12 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 379 TYR 0.016 0.001 TYR B 159 PHE 0.014 0.001 PHE B 495 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00348 (19182) covalent geometry : angle 0.50313 (26823) hydrogen bonds : bond 0.04043 ( 830) hydrogen bonds : angle 4.51749 ( 2256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7222 (mm-30) REVERT: B 431 ASP cc_start: 0.8117 (m-30) cc_final: 0.7850 (m-30) REVERT: B 486 MET cc_start: 0.8383 (mpp) cc_final: 0.7791 (mpm) REVERT: B 489 MET cc_start: 0.6565 (tpp) cc_final: 0.6345 (tpp) REVERT: B 531 LYS cc_start: 0.7491 (tptt) cc_final: 0.6875 (tppt) REVERT: B 551 MET cc_start: 0.9235 (ttp) cc_final: 0.8920 (ppp) REVERT: A 27 LEU cc_start: 0.7723 (tt) cc_final: 0.7392 (tt) REVERT: A 160 ASN cc_start: 0.8642 (t0) cc_final: 0.8232 (t0) REVERT: A 307 GLU cc_start: 0.8175 (tp30) cc_final: 0.7923 (tp30) REVERT: A 333 TYR cc_start: 0.7451 (m-10) cc_final: 0.6996 (m-10) REVERT: A 417 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7630 (tt0) REVERT: A 452 LYS cc_start: 0.8599 (tptt) cc_final: 0.8147 (tptp) REVERT: A 496 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6468 (p90) REVERT: C 104 ILE cc_start: 0.8964 (mm) cc_final: 0.8686 (mm) REVERT: C 269 ASP cc_start: 0.7475 (t0) cc_final: 0.7147 (t0) REVERT: C 271 CYS cc_start: 0.7973 (p) cc_final: 0.7306 (p) REVERT: C 376 LYS cc_start: 0.7921 (mptt) cc_final: 0.7012 (pttp) outliers start: 22 outliers final: 11 residues processed: 164 average time/residue: 1.1106 time to fit residues: 210.2287 Evaluate side-chains 155 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 410 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 185 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 179 ASN C 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.189367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.132481 restraints weight = 79074.887| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.83 r_work: 0.3728 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19182 Z= 0.185 Angle : 0.513 7.148 26823 Z= 0.280 Chirality : 0.037 0.149 3141 Planarity : 0.004 0.065 2611 Dihedral : 19.772 176.986 4913 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 1.43 % Allowed : 11.02 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1686 helix: 1.36 (0.19), residues: 798 sheet: -2.07 (0.37), residues: 159 loop : 0.08 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 379 TYR 0.025 0.001 TYR B 159 PHE 0.013 0.001 PHE B 357 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00394 (19182) covalent geometry : angle 0.51286 (26823) hydrogen bonds : bond 0.04131 ( 830) hydrogen bonds : angle 4.52129 ( 2256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 431 ASP cc_start: 0.8121 (m-30) cc_final: 0.7838 (m-30) REVERT: B 486 MET cc_start: 0.8394 (mpp) cc_final: 0.7794 (mpm) REVERT: B 531 LYS cc_start: 0.7471 (tptt) cc_final: 0.6844 (tppt) REVERT: B 551 MET cc_start: 0.9236 (ttp) cc_final: 0.8882 (ppp) REVERT: A 27 LEU cc_start: 0.7736 (tt) cc_final: 0.7410 (tt) REVERT: A 160 ASN cc_start: 0.8717 (t0) cc_final: 0.8282 (t0) REVERT: A 307 GLU cc_start: 0.8184 (tp30) cc_final: 0.7933 (tp30) REVERT: A 333 TYR cc_start: 0.7468 (m-80) cc_final: 0.7015 (m-10) REVERT: A 417 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7641 (tt0) REVERT: A 452 LYS cc_start: 0.8607 (tptt) cc_final: 0.8172 (tptp) REVERT: A 486 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6625 (mpp) REVERT: C 104 ILE cc_start: 0.8992 (mm) cc_final: 0.8728 (mm) REVERT: C 269 ASP cc_start: 0.7453 (t0) cc_final: 0.7087 (t0) REVERT: C 271 CYS cc_start: 0.8085 (p) cc_final: 0.7600 (p) REVERT: C 376 LYS cc_start: 0.7843 (mptt) cc_final: 0.6964 (pttp) outliers start: 22 outliers final: 13 residues processed: 160 average time/residue: 1.0799 time to fit residues: 199.1945 Evaluate side-chains 158 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 410 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 179 ASN C 327 ASN C 341 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.186892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.129642 restraints weight = 79337.188| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.81 r_work: 0.3738 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19182 Z= 0.245 Angle : 0.546 7.708 26823 Z= 0.299 Chirality : 0.039 0.173 3141 Planarity : 0.005 0.063 2611 Dihedral : 19.817 177.767 4913 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.15 % Favored : 95.73 % Rotamer: Outliers : 1.43 % Allowed : 11.87 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1686 helix: 1.20 (0.19), residues: 804 sheet: -2.11 (0.37), residues: 159 loop : -0.04 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 379 TYR 0.022 0.001 TYR B 159 PHE 0.017 0.002 PHE B 357 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00526 (19182) covalent geometry : angle 0.54592 (26823) hydrogen bonds : bond 0.04567 ( 830) hydrogen bonds : angle 4.64965 ( 2256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8765 (pt) cc_final: 0.8507 (pp) REVERT: B 431 ASP cc_start: 0.8136 (m-30) cc_final: 0.7846 (m-30) REVERT: B 486 MET cc_start: 0.8410 (mpp) cc_final: 0.7810 (mpm) REVERT: B 531 LYS cc_start: 0.7530 (tptt) cc_final: 0.6911 (tppt) REVERT: B 551 MET cc_start: 0.9246 (ttp) cc_final: 0.8897 (ppp) REVERT: A 27 LEU cc_start: 0.7798 (tt) cc_final: 0.7468 (tt) REVERT: A 160 ASN cc_start: 0.8800 (t0) cc_final: 0.8376 (t0) REVERT: A 307 GLU cc_start: 0.8191 (tp30) cc_final: 0.7975 (tp30) REVERT: A 333 TYR cc_start: 0.7497 (m-80) cc_final: 0.7096 (m-10) REVERT: A 417 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7534 (tt0) REVERT: A 452 LYS cc_start: 0.8565 (tptt) cc_final: 0.8151 (tptp) REVERT: C 104 ILE cc_start: 0.9065 (mm) cc_final: 0.8807 (mm) REVERT: C 269 ASP cc_start: 0.7457 (t0) cc_final: 0.7028 (t0) REVERT: C 271 CYS cc_start: 0.8041 (p) cc_final: 0.7511 (p) REVERT: C 376 LYS cc_start: 0.7778 (mptt) cc_final: 0.6890 (pttp) REVERT: C 486 MET cc_start: 0.7692 (ptp) cc_final: 0.7402 (pmm) outliers start: 22 outliers final: 18 residues processed: 162 average time/residue: 1.0783 time to fit residues: 202.0906 Evaluate side-chains 157 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 410 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 159 optimal weight: 0.0670 chunk 52 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 179 ASN C 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.189521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.133296 restraints weight = 78903.569| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.77 r_work: 0.3744 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19182 Z= 0.147 Angle : 0.504 8.545 26823 Z= 0.273 Chirality : 0.036 0.143 3141 Planarity : 0.004 0.064 2611 Dihedral : 19.726 176.256 4913 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.04 % Allowed : 12.45 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1686 helix: 1.35 (0.19), residues: 801 sheet: -2.05 (0.37), residues: 159 loop : 0.02 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 379 TYR 0.022 0.001 TYR B 159 PHE 0.019 0.001 PHE C 495 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00314 (19182) covalent geometry : angle 0.50357 (26823) hydrogen bonds : bond 0.03828 ( 830) hydrogen bonds : angle 4.45089 ( 2256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8776 (pt) cc_final: 0.8504 (pp) REVERT: B 431 ASP cc_start: 0.8141 (m-30) cc_final: 0.7870 (m-30) REVERT: B 486 MET cc_start: 0.8404 (mpp) cc_final: 0.7794 (mpm) REVERT: B 496 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.5669 (p90) REVERT: B 531 LYS cc_start: 0.7566 (tptt) cc_final: 0.6947 (tppt) REVERT: B 551 MET cc_start: 0.9244 (ttp) cc_final: 0.8916 (ppp) REVERT: A 27 LEU cc_start: 0.7782 (tt) cc_final: 0.7456 (tt) REVERT: A 160 ASN cc_start: 0.8798 (t0) cc_final: 0.8357 (t0) REVERT: A 307 GLU cc_start: 0.8142 (tp30) cc_final: 0.7901 (tp30) REVERT: A 333 TYR cc_start: 0.7499 (m-80) cc_final: 0.7103 (m-10) REVERT: A 417 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7576 (tt0) REVERT: A 452 LYS cc_start: 0.8536 (tptt) cc_final: 0.8090 (tptp) REVERT: A 486 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.6749 (mpp) REVERT: C 104 ILE cc_start: 0.9012 (mm) cc_final: 0.8749 (mm) REVERT: C 269 ASP cc_start: 0.7422 (t0) cc_final: 0.7045 (t0) REVERT: C 271 CYS cc_start: 0.8059 (p) cc_final: 0.7500 (p) REVERT: C 376 LYS cc_start: 0.7748 (mptt) cc_final: 0.6861 (pttp) REVERT: C 495 PHE cc_start: 0.7128 (p90) cc_final: 0.6868 (p90) outliers start: 16 outliers final: 9 residues processed: 159 average time/residue: 1.0554 time to fit residues: 194.5688 Evaluate side-chains 153 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 410 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN A 267 ASN A 327 ASN C 179 ASN C 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.186283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.128996 restraints weight = 79064.869| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.81 r_work: 0.3721 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 19182 Z= 0.256 Angle : 0.552 8.686 26823 Z= 0.301 Chirality : 0.039 0.173 3141 Planarity : 0.005 0.063 2611 Dihedral : 19.805 177.639 4913 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 1.56 % Allowed : 12.06 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1686 helix: 1.22 (0.19), residues: 801 sheet: -1.94 (0.37), residues: 165 loop : -0.06 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 379 TYR 0.029 0.002 TYR B 159 PHE 0.019 0.002 PHE B 357 HIS 0.003 0.001 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00552 (19182) covalent geometry : angle 0.55234 (26823) hydrogen bonds : bond 0.04539 ( 830) hydrogen bonds : angle 4.63992 ( 2256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 ARG cc_start: 0.8868 (tpt170) cc_final: 0.8664 (tpt170) REVERT: B 214 LEU cc_start: 0.8820 (pt) cc_final: 0.8548 (pp) REVERT: B 431 ASP cc_start: 0.8090 (m-30) cc_final: 0.7805 (m-30) REVERT: B 486 MET cc_start: 0.8423 (mpp) cc_final: 0.7831 (mpm) REVERT: B 531 LYS cc_start: 0.7709 (tptt) cc_final: 0.7093 (tppt) REVERT: B 551 MET cc_start: 0.9262 (ttp) cc_final: 0.8963 (ppp) REVERT: A 27 LEU cc_start: 0.7857 (tt) cc_final: 0.7538 (tt) REVERT: A 160 ASN cc_start: 0.8831 (t0) cc_final: 0.8378 (t0) REVERT: A 307 GLU cc_start: 0.8218 (tp30) cc_final: 0.8000 (tp30) REVERT: A 333 TYR cc_start: 0.7521 (m-80) cc_final: 0.7122 (m-10) REVERT: A 417 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7603 (tt0) REVERT: A 452 LYS cc_start: 0.8560 (tptt) cc_final: 0.8121 (tptp) REVERT: C 269 ASP cc_start: 0.7439 (t0) cc_final: 0.6992 (t0) REVERT: C 271 CYS cc_start: 0.8066 (p) cc_final: 0.7528 (p) REVERT: C 376 LYS cc_start: 0.7800 (mptt) cc_final: 0.6909 (pttp) REVERT: C 418 LYS cc_start: 0.8218 (tttt) cc_final: 0.7887 (mttt) REVERT: C 486 MET cc_start: 0.7605 (ptp) cc_final: 0.7373 (pmm) REVERT: C 495 PHE cc_start: 0.7160 (p90) cc_final: 0.6927 (p90) outliers start: 24 outliers final: 17 residues processed: 161 average time/residue: 1.0053 time to fit residues: 188.3801 Evaluate side-chains 155 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 578 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 179 ASN C 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.189880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.133509 restraints weight = 79155.935| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.84 r_work: 0.3749 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19182 Z= 0.123 Angle : 0.503 9.607 26823 Z= 0.271 Chirality : 0.036 0.140 3141 Planarity : 0.004 0.070 2611 Dihedral : 19.716 176.392 4913 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.26 % Rotamer: Outliers : 1.30 % Allowed : 12.52 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1686 helix: 1.41 (0.19), residues: 801 sheet: -1.99 (0.37), residues: 159 loop : 0.02 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 379 TYR 0.036 0.001 TYR B 159 PHE 0.017 0.001 PHE C 495 HIS 0.002 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00263 (19182) covalent geometry : angle 0.50281 (26823) hydrogen bonds : bond 0.03693 ( 830) hydrogen bonds : angle 4.39181 ( 2256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8801 (pt) cc_final: 0.8520 (pp) REVERT: B 431 ASP cc_start: 0.8072 (m-30) cc_final: 0.7808 (m-30) REVERT: B 486 MET cc_start: 0.8409 (mpp) cc_final: 0.7792 (mpm) REVERT: B 496 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.5524 (p90) REVERT: B 531 LYS cc_start: 0.7656 (tptt) cc_final: 0.7048 (tppt) REVERT: B 551 MET cc_start: 0.9252 (ttp) cc_final: 0.8962 (ppp) REVERT: A 27 LEU cc_start: 0.7771 (tt) cc_final: 0.7454 (tt) REVERT: A 160 ASN cc_start: 0.8807 (t0) cc_final: 0.8333 (t0) REVERT: A 307 GLU cc_start: 0.8127 (tp30) cc_final: 0.7865 (tp30) REVERT: A 333 TYR cc_start: 0.7510 (m-80) cc_final: 0.7110 (m-10) REVERT: A 452 LYS cc_start: 0.8488 (tptt) cc_final: 0.8070 (tptp) REVERT: C 104 ILE cc_start: 0.8917 (mm) cc_final: 0.8649 (mm) REVERT: C 269 ASP cc_start: 0.7423 (t0) cc_final: 0.7088 (t0) REVERT: C 271 CYS cc_start: 0.8035 (p) cc_final: 0.7278 (p) REVERT: C 376 LYS cc_start: 0.7774 (mptt) cc_final: 0.6893 (pttp) REVERT: C 486 MET cc_start: 0.7578 (ptp) cc_final: 0.7339 (pmm) outliers start: 20 outliers final: 10 residues processed: 155 average time/residue: 1.0504 time to fit residues: 189.7039 Evaluate side-chains 150 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 410 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 161 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 188 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN A 327 ASN C 179 ASN C 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.189845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.133823 restraints weight = 79050.507| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.79 r_work: 0.3755 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19182 Z= 0.137 Angle : 0.498 9.056 26823 Z= 0.269 Chirality : 0.036 0.140 3141 Planarity : 0.004 0.069 2611 Dihedral : 19.648 176.872 4913 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.61 % Rotamer: Outliers : 0.97 % Allowed : 13.10 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1686 helix: 1.47 (0.19), residues: 801 sheet: -1.94 (0.37), residues: 159 loop : 0.03 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 379 TYR 0.032 0.001 TYR B 159 PHE 0.017 0.001 PHE C 495 HIS 0.003 0.001 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00292 (19182) covalent geometry : angle 0.49812 (26823) hydrogen bonds : bond 0.03662 ( 830) hydrogen bonds : angle 4.36752 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12010.51 seconds wall clock time: 204 minutes 1.09 seconds (12241.09 seconds total)