Starting phenix.real_space_refine on Mon Jul 6 14:01:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s1f_54448/07_2026/9s1f_54448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s1f_54448/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9s1f_54448/07_2026/9s1f_54448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s1f_54448/07_2026/9s1f_54448.map" model { file = "/net/cci-nas-00/data/ceres_data/9s1f_54448/07_2026/9s1f_54448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s1f_54448/07_2026/9s1f_54448.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.54, per 1000 atoms: 0.16 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: 3.20 Conformation dependent library (CDL) restraints added in 856.8 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: 6.38 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: 8.68 Time building geometry restraints manager: 4.27 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=" C1' DT H 26 " pdb=" N1 DT H 26 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.60e+00 bond pdb=" C3' DC I 6 " pdb=" C2' DC I 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 ... (remaining 35681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 63070 1.72 - 3.44: 1333 3.44 - 5.16: 63 5.16 - 6.88: 9 6.88 - 8.61: 1 Bond angle restraints: 64476 Sorted by residual: angle pdb=" N3 DT G 64 " pdb=" C4 DT G 64 " pdb=" O4 DT G 64 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT I 64 " pdb=" C4 DT I 64 " pdb=" O4 DT I 64 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" O4' DC I 63 " pdb=" C4' DC I 63 " pdb=" C3' DC I 63 " ideal model delta sigma weight residual 106.00 103.47 2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" O4 DT G 64 " pdb=" C4 DT G 64 " pdb=" C5 DT G 64 " ideal model delta sigma weight residual 124.90 121.97 2.93 7.00e-01 2.04e+00 1.76e+01 angle pdb=" O4' DC H 67 " pdb=" C4' DC H 67 " pdb=" C3' DC H 67 " ideal model delta sigma weight residual 106.00 103.49 2.51 6.00e-01 2.78e+00 1.74e+01 ... (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 - 0.041: 2515 0.041 - 0.082: 426 0.082 - 0.124: 128 0.124 - 0.165: 58 0.165 - 0.206: 14 Chirality restraints: 3141 Sorted by residual: chirality pdb=" C3' DC G 66 " pdb=" C4' DC G 66 " pdb=" O3' DC G 66 " pdb=" C2' DC G 66 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DC I 66 " pdb=" C4' DC I 66 " pdb=" O3' DC I 66 " pdb=" C2' DC I 66 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C3' DC I 63 " pdb=" C4' DC I 63 " pdb=" O3' DC I 63 " pdb=" C2' DC I 63 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.88e-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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.330 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 0.043 19182 Z= 0.235 Angle : 0.585 8.606 26823 Z= 0.425 Chirality : 0.041 0.206 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/Z covalent geometry : bond 0.00331 / 0.24 (19182) covalent geometry : angle 0.58541 / 0.43 (26823) hydrogen bonds : bond 0.15161 / 14.58 ( 830) hydrogen bonds : angle 6.85417 / 8.41 ( 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 : 0.821 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: 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: 1.0238 time to fit residues: 223.2416 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 : 0.927 ------------------------------------------------------------------------------- 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: 0.0070 chunk 10 optimal weight: 10.0000 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: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 ASN B 441 ASN B 470 ASN A 327 ASN C 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.194673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.140009 restraints weight = 79482.902| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.84 r_work: 0.3894 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19182 Z= 0.166 Angle : 0.518 6.909 26823 Z= 0.303 Chirality : 0.038 0.236 3141 Planarity : 0.004 0.053 2611 Dihedral : 19.765 176.821 4915 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.74 % Rotamer: Outliers : 0.91 % Allowed : 5.71 % Favored : 93.39 % 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: -0.23 (0.21), residues: 1686 helix: 0.24 (0.17), residues: 801 sheet: -2.28 (0.38), residues: 159 loop : 0.16 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.011 0.001 TYR A 491 PHE 0.010 0.001 PHE A 97 HIS 0.004 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (19182) covalent geometry : angle 0.51755 / 0.30 (26823) hydrogen bonds : bond 0.05873 / 5.44 ( 830) hydrogen bonds : angle 5.29628 / 6.59 ( 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 167 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.090 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: B 417 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 431 ASP cc_start: 0.8134 (m-30) cc_final: 0.7796 (m-30) REVERT: B 446 TYR cc_start: 0.7847 (m-80) cc_final: 0.7234 (m-80) REVERT: B 486 MET cc_start: 0.8338 (mpp) cc_final: 0.7816 (mpm) REVERT: B 551 MET cc_start: 0.9194 (ttp) cc_final: 0.8488 (tpp) REVERT: B 571 ASP cc_start: 0.8454 (m-30) cc_final: 0.8241 (m-30) REVERT: A 27 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 160 ASN cc_start: 0.8243 (m-40) cc_final: 0.8008 (t0) REVERT: A 307 GLU cc_start: 0.8147 (tp30) cc_final: 0.7742 (tm-30) REVERT: A 333 TYR cc_start: 0.7409 (m-10) cc_final: 0.6932 (m-10) REVERT: A 452 LYS cc_start: 0.8493 (tptt) cc_final: 0.8129 (tptp) REVERT: C 271 CYS cc_start: 0.7772 (p) cc_final: 0.7273 (p) REVERT: C 376 LYS cc_start: 0.7977 (mptt) cc_final: 0.7239 (pttp) outliers start: 14 outliers final: 6 residues processed: 161 average time/residue: 1.0208 time to fit residues: 191.0456 Evaluate side-chains 147 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 456 ILE 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: 4.9990 chunk 184 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN B 255 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.195569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.138515 restraints weight = 81643.533| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.86 r_work: 0.3829 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 19182 Z= 0.273 Angle : 0.560 9.369 26823 Z= 0.324 Chirality : 0.040 0.210 3141 Planarity : 0.004 0.065 2611 Dihedral : 19.818 176.306 4915 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.74 % Rotamer: Outliers : 0.91 % Allowed : 7.00 % Favored : 92.09 % 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: 0.16 (0.21), residues: 1686 helix: 0.80 (0.18), residues: 801 sheet: -2.30 (0.37), residues: 159 loop : 0.08 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 379 TYR 0.014 0.002 TYR A 289 PHE 0.016 0.002 PHE B 357 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.27 (19182) covalent geometry : angle 0.55988 / 0.32 (26823) hydrogen bonds : bond 0.05640 / 5.33 ( 830) hydrogen bonds : angle 5.08035 / 6.34 ( 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 162 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 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 70 ARG cc_start: 0.8783 (tpt170) cc_final: 0.8552 (tpt170) REVERT: B 159 TYR cc_start: 0.7746 (t80) cc_final: 0.7520 (t80) REVERT: B 417 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7322 (mm-30) REVERT: B 431 ASP cc_start: 0.8165 (m-30) cc_final: 0.7840 (m-30) REVERT: B 446 TYR cc_start: 0.7895 (m-80) cc_final: 0.7444 (m-80) REVERT: B 486 MET cc_start: 0.8325 (mpp) cc_final: 0.7715 (mpm) REVERT: B 551 MET cc_start: 0.9214 (ttp) cc_final: 0.8868 (ppp) REVERT: A 27 LEU cc_start: 0.7859 (tt) cc_final: 0.7572 (tt) REVERT: A 160 ASN cc_start: 0.8371 (m-40) cc_final: 0.8140 (t0) REVERT: A 307 GLU cc_start: 0.8166 (tp30) cc_final: 0.7902 (tp30) REVERT: A 329 GLN cc_start: 0.7302 (mp10) cc_final: 0.7094 (mp10) REVERT: A 333 TYR cc_start: 0.7444 (m-10) cc_final: 0.6983 (m-10) REVERT: A 452 LYS cc_start: 0.8582 (tptt) cc_final: 0.8231 (tptp) REVERT: C 269 ASP cc_start: 0.7463 (t0) cc_final: 0.7188 (t0) REVERT: C 271 CYS cc_start: 0.7993 (p) cc_final: 0.7512 (p) REVERT: C 376 LYS cc_start: 0.7973 (mptt) cc_final: 0.7164 (pttp) outliers start: 14 outliers final: 10 residues processed: 153 average time/residue: 1.0066 time to fit residues: 179.1612 Evaluate side-chains 143 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 197 SER 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 90 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 455 VAL 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: 9.9990 chunk 38 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 ASN B 441 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 = 0.4663 r_free = 0.4663 target = 0.189391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.132627 restraints weight = 79016.498| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.84 r_work: 0.3785 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19182 Z= 0.246 Angle : 0.537 7.783 26823 Z= 0.311 Chirality : 0.039 0.184 3141 Planarity : 0.004 0.064 2611 Dihedral : 19.903 176.189 4913 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % Rotamer: Outliers : 1.36 % Allowed : 7.98 % Favored : 90.66 % 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: 0.18 (0.21), residues: 1686 helix: 0.90 (0.18), residues: 801 sheet: -2.26 (0.37), residues: 159 loop : -0.03 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 379 TYR 0.016 0.001 TYR B 446 PHE 0.015 0.002 PHE C 124 HIS 0.004 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.25 (19182) covalent geometry : angle 0.53720 / 0.31 (26823) hydrogen bonds : bond 0.05275 / 5.06 ( 830) hydrogen bonds : angle 4.95820 / 6.20 ( 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 170 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.886 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 417 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7318 (mm-30) REVERT: B 431 ASP cc_start: 0.8151 (m-30) cc_final: 0.7826 (m-30) REVERT: B 486 MET cc_start: 0.8400 (mpp) cc_final: 0.7815 (mpm) REVERT: B 531 LYS cc_start: 0.7499 (tptt) cc_final: 0.6853 (tppt) REVERT: B 551 MET cc_start: 0.9214 (ttp) cc_final: 0.8890 (ppp) REVERT: A 27 LEU cc_start: 0.7725 (tt) cc_final: 0.7415 (tt) REVERT: A 307 GLU cc_start: 0.8158 (tp30) cc_final: 0.7912 (tp30) REVERT: A 333 TYR cc_start: 0.7420 (m-10) cc_final: 0.7003 (m-10) REVERT: A 452 LYS cc_start: 0.8581 (tptt) cc_final: 0.8237 (tptp) REVERT: C 269 ASP cc_start: 0.7450 (t0) cc_final: 0.7134 (t0) REVERT: C 271 CYS cc_start: 0.7931 (p) cc_final: 0.7360 (p) REVERT: C 359 TYR cc_start: 0.7080 (t80) cc_final: 0.6864 (t80) REVERT: C 376 LYS cc_start: 0.7976 (mptt) cc_final: 0.7160 (pttp) outliers start: 21 outliers final: 13 residues processed: 158 average time/residue: 1.0230 time to fit residues: 187.9497 Evaluate side-chains 151 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 197 SER 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 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: 0.8980 chunk 166 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 441 ASN A 327 ASN A 329 GLN 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 = 0.4679 r_free = 0.4679 target = 0.190814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.134454 restraints weight = 79091.911| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.82 r_work: 0.3761 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19182 Z= 0.155 Angle : 0.498 7.755 26823 Z= 0.287 Chirality : 0.037 0.160 3141 Planarity : 0.004 0.064 2611 Dihedral : 19.889 179.024 4913 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.32 % Favored : 96.56 % Rotamer: Outliers : 1.36 % Allowed : 8.88 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1686 helix: 1.10 (0.19), residues: 801 sheet: -2.18 (0.37), residues: 159 loop : 0.01 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 379 TYR 0.012 0.001 TYR A 446 PHE 0.017 0.001 PHE B 495 HIS 0.003 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (19182) covalent geometry : angle 0.49840 / 0.29 (26823) hydrogen bonds : bond 0.04814 / 4.63 ( 830) hydrogen bonds : angle 4.78596 / 5.98 ( 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 174 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.827 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 417 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7289 (mm-30) REVERT: B 431 ASP cc_start: 0.8118 (m-30) cc_final: 0.7810 (m-30) REVERT: B 486 MET cc_start: 0.8395 (mpp) cc_final: 0.7792 (mpm) REVERT: B 531 LYS cc_start: 0.7439 (tptt) cc_final: 0.6787 (tppt) REVERT: B 551 MET cc_start: 0.9205 (ttp) cc_final: 0.8891 (ppp) REVERT: A 27 LEU cc_start: 0.7742 (tt) cc_final: 0.7427 (tt) REVERT: A 307 GLU cc_start: 0.8167 (tp30) cc_final: 0.7904 (tp30) REVERT: A 333 TYR cc_start: 0.7410 (m-10) cc_final: 0.6951 (m-10) REVERT: A 452 LYS cc_start: 0.8580 (tptt) cc_final: 0.8259 (tptp) REVERT: C 269 ASP cc_start: 0.7519 (t0) cc_final: 0.7282 (t0) REVERT: C 271 CYS cc_start: 0.7994 (p) cc_final: 0.7241 (p) REVERT: C 359 TYR cc_start: 0.7093 (t80) cc_final: 0.6889 (t80) REVERT: C 376 LYS cc_start: 0.7939 (mptt) cc_final: 0.7116 (pttp) outliers start: 21 outliers final: 11 residues processed: 162 average time/residue: 0.9493 time to fit residues: 180.1163 Evaluate side-chains 152 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 455 VAL 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 410 LEU Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 chunk 185 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 441 ASN A 327 ASN A 329 GLN C 92 ASN C 179 ASN C 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.189196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.132289 restraints weight = 79052.134| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.83 r_work: 0.3723 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19182 Z= 0.228 Angle : 0.521 9.150 26823 Z= 0.301 Chirality : 0.038 0.171 3141 Planarity : 0.004 0.060 2611 Dihedral : 19.889 178.330 4913 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 1.49 % Allowed : 9.47 % Favored : 89.04 % 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: 0.33 (0.21), residues: 1686 helix: 1.08 (0.19), residues: 801 sheet: -2.12 (0.38), residues: 159 loop : -0.05 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 379 TYR 0.013 0.001 TYR B 446 PHE 0.015 0.001 PHE A 97 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.23 (19182) covalent geometry : angle 0.52135 / 0.30 (26823) hydrogen bonds : bond 0.04935 / 4.73 ( 830) hydrogen bonds : angle 4.81218 / 6.00 ( 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 168 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.798 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: 0.7790 (mm-30) cc_final: 0.7310 (mm-30) REVERT: B 431 ASP cc_start: 0.8152 (m-30) cc_final: 0.7865 (m-30) REVERT: B 486 MET cc_start: 0.8416 (mpp) cc_final: 0.7835 (mpm) REVERT: B 531 LYS cc_start: 0.7408 (tptt) cc_final: 0.6765 (tppt) REVERT: B 551 MET cc_start: 0.9214 (ttp) cc_final: 0.8896 (ppp) REVERT: A 27 LEU cc_start: 0.7794 (tt) cc_final: 0.7495 (tt) REVERT: A 160 ASN cc_start: 0.8493 (m-40) cc_final: 0.8108 (t0) REVERT: A 307 GLU cc_start: 0.8216 (tp30) cc_final: 0.7979 (tp30) REVERT: A 333 TYR cc_start: 0.7424 (m-10) cc_final: 0.7008 (m-10) REVERT: A 452 LYS cc_start: 0.8604 (tptt) cc_final: 0.8193 (tptp) REVERT: C 269 ASP cc_start: 0.7598 (t0) cc_final: 0.7330 (t0) REVERT: C 271 CYS cc_start: 0.7985 (p) cc_final: 0.7202 (p) REVERT: C 376 LYS cc_start: 0.7964 (mptt) cc_final: 0.7125 (pttp) outliers start: 23 outliers final: 14 residues processed: 156 average time/residue: 0.9242 time to fit residues: 168.2528 Evaluate side-chains 153 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 455 VAL 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 218 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 36 optimal weight: 0.0030 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 441 ASN A 327 ASN A 329 GLN C 179 ASN C 320 ASN C 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.188867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.131900 restraints weight = 79144.819| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.82 r_work: 0.3723 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19182 Z= 0.206 Angle : 0.515 9.998 26823 Z= 0.297 Chirality : 0.038 0.155 3141 Planarity : 0.004 0.065 2611 Dihedral : 19.918 178.906 4913 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.62 % Allowed : 9.86 % Favored : 88.52 % 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: 0.32 (0.21), residues: 1686 helix: 1.09 (0.19), residues: 801 sheet: -2.12 (0.37), residues: 159 loop : -0.09 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 379 TYR 0.014 0.001 TYR B 446 PHE 0.015 0.001 PHE B 357 HIS 0.003 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (19182) covalent geometry : angle 0.51451 / 0.30 (26823) hydrogen bonds : bond 0.04862 / 4.67 ( 830) hydrogen bonds : angle 4.76735 / 5.95 ( 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 169 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 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 417 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7301 (mm-30) REVERT: B 431 ASP cc_start: 0.8146 (m-30) cc_final: 0.7865 (m-30) REVERT: B 486 MET cc_start: 0.8405 (mpp) cc_final: 0.7812 (mpm) REVERT: B 489 MET cc_start: 0.6470 (tpp) cc_final: 0.6210 (tpp) REVERT: B 531 LYS cc_start: 0.7457 (tptt) cc_final: 0.6818 (tppt) REVERT: B 551 MET cc_start: 0.9219 (ttp) cc_final: 0.8897 (ppp) REVERT: A 27 LEU cc_start: 0.7787 (tt) cc_final: 0.7478 (tt) REVERT: A 160 ASN cc_start: 0.8483 (m-40) cc_final: 0.8127 (t0) REVERT: A 307 GLU cc_start: 0.8209 (tp30) cc_final: 0.7979 (tp30) REVERT: A 333 TYR cc_start: 0.7426 (m-10) cc_final: 0.7013 (m-10) REVERT: A 452 LYS cc_start: 0.8581 (tptt) cc_final: 0.8182 (tptp) REVERT: C 269 ASP cc_start: 0.7578 (t0) cc_final: 0.7288 (t0) REVERT: C 271 CYS cc_start: 0.8004 (p) cc_final: 0.7198 (p) REVERT: C 376 LYS cc_start: 0.7949 (mptt) cc_final: 0.7106 (pttp) outliers start: 25 outliers final: 17 residues processed: 157 average time/residue: 1.0622 time to fit residues: 193.9586 Evaluate side-chains 154 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 418 LYS 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 463 THR 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 410 LEU Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN 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 = 0.4665 r_free = 0.4665 target = 0.189499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.132777 restraints weight = 79078.309| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.81 r_work: 0.3733 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19182 Z= 0.170 Angle : 0.507 10.797 26823 Z= 0.290 Chirality : 0.037 0.147 3141 Planarity : 0.004 0.060 2611 Dihedral : 19.916 177.470 4913 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 1.43 % Allowed : 9.99 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.41 (0.21), residues: 1686 helix: 1.19 (0.19), residues: 801 sheet: -2.08 (0.37), residues: 159 loop : -0.07 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 379 TYR 0.012 0.001 TYR A 446 PHE 0.013 0.001 PHE B 357 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (19182) covalent geometry : angle 0.50691 / 0.29 (26823) hydrogen bonds : bond 0.04625 / 4.44 ( 830) hydrogen bonds : angle 4.68957 / 5.86 ( 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: 22 poor density : 144 time to evaluate : 0.899 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 417 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 431 ASP cc_start: 0.8138 (m-30) cc_final: 0.7860 (m-30) REVERT: B 486 MET cc_start: 0.8373 (mpp) cc_final: 0.7790 (mpm) REVERT: B 489 MET cc_start: 0.6492 (tpp) cc_final: 0.6226 (tpp) REVERT: B 531 LYS cc_start: 0.7399 (tptt) cc_final: 0.6758 (tppt) REVERT: B 551 MET cc_start: 0.9206 (ttp) cc_final: 0.8887 (ppp) REVERT: A 27 LEU cc_start: 0.7773 (tt) cc_final: 0.7465 (tt) REVERT: A 160 ASN cc_start: 0.8487 (m-40) cc_final: 0.8147 (t0) REVERT: A 307 GLU cc_start: 0.8208 (tp30) cc_final: 0.7960 (tp30) REVERT: A 333 TYR cc_start: 0.7423 (m-80) cc_final: 0.7013 (m-10) REVERT: A 452 LYS cc_start: 0.8570 (tptt) cc_final: 0.8166 (tptp) REVERT: C 269 ASP cc_start: 0.7535 (t0) cc_final: 0.7250 (t0) REVERT: C 271 CYS cc_start: 0.8007 (p) cc_final: 0.7196 (p) REVERT: C 376 LYS cc_start: 0.7938 (mptt) cc_final: 0.7103 (pttp) outliers start: 22 outliers final: 18 residues processed: 155 average time/residue: 1.0107 time to fit residues: 183.6564 Evaluate side-chains 158 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 418 LYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain A residue 74 ASP 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 463 THR 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 410 LEU Chi-restraints excluded: chain C residue 456 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN 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 = 0.4645 r_free = 0.4645 target = 0.187657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.130462 restraints weight = 79073.920| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.83 r_work: 0.3706 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19182 Z= 0.246 Angle : 0.539 10.922 26823 Z= 0.308 Chirality : 0.038 0.153 3141 Planarity : 0.004 0.064 2611 Dihedral : 19.940 178.611 4913 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.56 % Allowed : 9.99 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1686 helix: 1.06 (0.19), residues: 804 sheet: -2.10 (0.37), residues: 159 loop : -0.19 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 70 TYR 0.019 0.002 TYR A 446 PHE 0.021 0.002 PHE B 495 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.25 (19182) covalent geometry : angle 0.53902 / 0.31 (26823) hydrogen bonds : bond 0.04952 / 4.73 ( 830) hydrogen bonds : angle 4.77618 / 5.96 ( 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 : 0.880 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: 0.7769 (mm-30) cc_final: 0.7275 (mm-30) REVERT: B 431 ASP cc_start: 0.8156 (m-30) cc_final: 0.7876 (m-30) REVERT: B 486 MET cc_start: 0.8393 (mpp) cc_final: 0.7809 (mpm) REVERT: B 489 MET cc_start: 0.6450 (tpp) cc_final: 0.6202 (tpp) REVERT: B 496 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.5964 (p90) REVERT: B 531 LYS cc_start: 0.7506 (tptt) cc_final: 0.6880 (tppt) REVERT: B 551 MET cc_start: 0.9224 (ttp) cc_final: 0.8560 (tpp) REVERT: A 27 LEU cc_start: 0.7803 (tt) cc_final: 0.7500 (tt) REVERT: A 160 ASN cc_start: 0.8529 (m-40) cc_final: 0.8243 (t0) REVERT: A 307 GLU cc_start: 0.8227 (tp30) cc_final: 0.8004 (tp30) REVERT: A 333 TYR cc_start: 0.7451 (m-80) cc_final: 0.7038 (m-10) REVERT: A 452 LYS cc_start: 0.8602 (tptt) cc_final: 0.8199 (tptp) REVERT: C 269 ASP cc_start: 0.7589 (t0) cc_final: 0.7287 (t0) REVERT: C 271 CYS cc_start: 0.8007 (p) cc_final: 0.7205 (p) REVERT: C 376 LYS cc_start: 0.7943 (mptt) cc_final: 0.7046 (pttp) outliers start: 24 outliers final: 18 residues processed: 157 average time/residue: 0.9541 time to fit residues: 176.0155 Evaluate side-chains 152 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 418 LYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain A residue 74 ASP 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 463 THR 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 410 LEU Chi-restraints excluded: chain C residue 456 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 5.9990 chunk 43 optimal weight: 0.0980 chunk 125 optimal weight: 0.4980 chunk 155 optimal weight: 0.0770 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 189 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN 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 = 0.4683 r_free = 0.4683 target = 0.191148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.135080 restraints weight = 79104.409| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.82 r_work: 0.3777 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19182 Z= 0.112 Angle : 0.501 11.556 26823 Z= 0.282 Chirality : 0.036 0.195 3141 Planarity : 0.004 0.062 2611 Dihedral : 19.952 177.039 4913 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 1.30 % Allowed : 10.64 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.57 (0.21), residues: 1686 helix: 1.41 (0.19), residues: 777 sheet: -1.98 (0.37), residues: 159 loop : -0.06 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 552 TYR 0.016 0.001 TYR B 159 PHE 0.039 0.001 PHE B 495 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (19182) covalent geometry : angle 0.50147 / 0.28 (26823) hydrogen bonds : bond 0.04258 / 4.08 ( 830) hydrogen bonds : angle 4.53765 / 5.68 ( 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 166 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.731 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: 0.7733 (mm-30) cc_final: 0.7237 (mm-30) REVERT: B 431 ASP cc_start: 0.8117 (m-30) cc_final: 0.7848 (m-30) REVERT: B 486 MET cc_start: 0.8378 (mpp) cc_final: 0.7785 (mpm) REVERT: B 551 MET cc_start: 0.9178 (ttp) cc_final: 0.8580 (tpp) REVERT: A 27 LEU cc_start: 0.7790 (tt) cc_final: 0.7497 (tt) REVERT: A 160 ASN cc_start: 0.8437 (m-40) cc_final: 0.8226 (t0) REVERT: A 307 GLU cc_start: 0.8141 (tp30) cc_final: 0.7892 (tp30) REVERT: A 333 TYR cc_start: 0.7419 (m-80) cc_final: 0.7010 (m-10) REVERT: A 417 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7629 (tt0) REVERT: A 452 LYS cc_start: 0.8565 (tptt) cc_final: 0.8153 (tptp) REVERT: C 269 ASP cc_start: 0.7455 (t0) cc_final: 0.7187 (t0) REVERT: C 271 CYS cc_start: 0.8017 (p) cc_final: 0.7197 (p) REVERT: C 376 LYS cc_start: 0.7926 (mptt) cc_final: 0.7042 (pttp) outliers start: 20 outliers final: 13 residues processed: 156 average time/residue: 0.9212 time to fit residues: 170.5301 Evaluate side-chains 150 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 486 MET 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 410 LEU Chi-restraints excluded: chain C residue 456 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 161 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN 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 = 0.189700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.133051 restraints weight = 79216.954| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.83 r_work: 0.3798 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19182 Z= 0.163 Angle : 0.505 11.667 26823 Z= 0.286 Chirality : 0.036 0.142 3141 Planarity : 0.004 0.067 2611 Dihedral : 19.886 177.617 4913 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.23 % Allowed : 11.02 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1686 helix: 1.31 (0.19), residues: 798 sheet: -2.02 (0.37), residues: 159 loop : -0.08 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 552 TYR 0.017 0.001 TYR B 159 PHE 0.021 0.001 PHE B 495 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (19182) covalent geometry : angle 0.50544 / 0.29 (26823) hydrogen bonds : bond 0.04347 / 4.14 ( 830) hydrogen bonds : angle 4.56587 / 5.70 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11061.68 seconds wall clock time: 188 minutes 18.27 seconds (11298.27 seconds total)