Starting phenix.real_space_refine on Sun Aug 9 15:25:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s1f_54448/08_2026/9s1f_54448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s1f_54448/08_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_54448/08_2026/9s1f_54448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s1f_54448/08_2026/9s1f_54448.map" model { file = "/net/cci-nas-00/data/ceres_data/9s1f_54448/08_2026/9s1f_54448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s1f_54448/08_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 5.87, per 1000 atoms: 0.17 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: 3.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 6.85 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: 10.10 Time building geometry restraints manager: 4.51 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: 62756 1.72 - 3.44: 1646 3.44 - 5.16: 64 5.16 - 6.88: 9 6.88 - 8.61: 1 Bond angle restraints: 64476 Sorted by residual: angle pdb=" O5' G F 59 " pdb=" C5' G F 59 " pdb=" C4' G F 59 " ideal model delta sigma weight residual 109.40 113.39 -3.99 8.00e-01 1.56e+00 2.49e+01 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 ... (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: 2362 0.041 - 0.082: 426 0.082 - 0.124: 280 0.124 - 0.165: 58 0.165 - 0.206: 15 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: 1.070 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: 0.230 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 41.200 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.690 ------------------------------------------------------------------------------- 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= 0.243 Angle : 0.638 8.606 26823 Z= 0.484 Chirality : 0.046 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 0.00338 / 0.24 (19182) covalent geometry : angle 0.63809 / 0.48 (26823) hydrogen bonds : bond 0.15161 / 15.99 ( 830) hydrogen bonds : angle 6.85417 / 8.84 ( 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 : 0.848 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: 0.8872 (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: 0.8215 (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: 1.0468 time to fit residues: 229.0944 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 : 0.855 ------------------------------------------------------------------------------- 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: 9.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- 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 = 0.4805 r_free = 0.4805 target = 0.195828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.142317 restraints weight = 80165.196| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.80 r_work: 0.3923 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19182 Z= 0.166 Angle : 0.534 7.422 26823 Z= 0.306 Chirality : 0.038 0.198 3141 Planarity : 0.004 0.052 2611 Dihedral : 19.713 177.335 4915 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.26 % Favored : 96.56 % 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: -0.14 (0.21), residues: 1686 helix: 0.35 (0.17), residues: 801 sheet: -2.26 (0.38), residues: 159 loop : 0.15 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.012 0.001 TYR A 491 PHE 0.011 0.001 PHE C 435 HIS 0.004 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (19182) covalent geometry : angle 0.53436 / 0.31 (26823) hydrogen bonds : bond 0.05722 / 5.97 ( 830) hydrogen bonds : angle 5.24981 / 6.82 ( 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 : 0.853 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: 0.7701 (mm-30) cc_final: 0.7289 (mm-30) REVERT: B 431 ASP cc_start: 0.8132 (m-30) cc_final: 0.7792 (m-30) REVERT: B 446 TYR cc_start: 0.7861 (m-80) cc_final: 0.7288 (m-80) REVERT: B 486 MET cc_start: 0.8326 (mpp) cc_final: 0.7797 (mpm) REVERT: B 551 MET cc_start: 0.9187 (ttp) cc_final: 0.8484 (tpp) REVERT: B 571 ASP cc_start: 0.8436 (m-30) cc_final: 0.8224 (m-30) REVERT: A 27 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7598 (tt) REVERT: A 160 ASN cc_start: 0.8254 (m-40) cc_final: 0.8026 (t0) REVERT: A 307 GLU cc_start: 0.8125 (tp30) cc_final: 0.7781 (tm-30) REVERT: A 333 TYR cc_start: 0.7421 (m-10) cc_final: 0.6945 (m-10) REVERT: A 452 LYS cc_start: 0.8502 (tptt) cc_final: 0.8165 (tptp) REVERT: A 496 TYR cc_start: 0.6918 (p90) cc_final: 0.6549 (p90) REVERT: C 269 ASP cc_start: 0.7242 (t0) cc_final: 0.7035 (t0) REVERT: C 271 CYS cc_start: 0.7845 (p) cc_final: 0.7295 (p) REVERT: C 376 LYS cc_start: 0.7973 (mptt) cc_final: 0.7213 (pttp) outliers start: 14 outliers final: 6 residues processed: 161 average time/residue: 1.0481 time to fit residues: 196.1883 Evaluate side-chains 143 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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: 6.9990 chunk 184 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 GLN B 255 GLN B 441 ASN A 327 ASN C 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.197273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.139899 restraints weight = 82162.518| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.89 r_work: 0.3857 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19182 Z= 0.223 Angle : 0.542 10.888 26823 Z= 0.310 Chirality : 0.038 0.199 3141 Planarity : 0.004 0.065 2611 Dihedral : 19.725 176.978 4915 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.91 % Favored : 96.92 % Rotamer: Outliers : 0.91 % Allowed : 6.94 % Favored : 92.15 % 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: 0.21 (0.21), residues: 1686 helix: 0.85 (0.18), residues: 801 sheet: -2.28 (0.37), residues: 159 loop : 0.10 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 379 TYR 0.012 0.001 TYR A 496 PHE 0.014 0.001 PHE A 97 HIS 0.003 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (19182) covalent geometry : angle 0.54248 / 0.31 (26823) hydrogen bonds : bond 0.05439 / 5.71 ( 830) hydrogen bonds : angle 5.03581 / 6.56 ( 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 160 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.906 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: 0.7762 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 431 ASP cc_start: 0.8152 (m-30) cc_final: 0.7830 (m-30) REVERT: B 446 TYR cc_start: 0.7837 (m-80) cc_final: 0.7364 (m-80) REVERT: B 486 MET cc_start: 0.8320 (mpp) cc_final: 0.7709 (mpm) REVERT: B 551 MET cc_start: 0.9215 (ttp) cc_final: 0.8881 (ppp) REVERT: B 571 ASP cc_start: 0.8462 (m-30) cc_final: 0.8237 (m-30) REVERT: A 27 LEU cc_start: 0.7836 (tt) cc_final: 0.7553 (tt) REVERT: A 160 ASN cc_start: 0.8349 (m-40) cc_final: 0.8118 (t0) REVERT: A 307 GLU cc_start: 0.8166 (tp30) cc_final: 0.7957 (tp30) REVERT: A 333 TYR cc_start: 0.7433 (m-10) cc_final: 0.6962 (m-10) REVERT: A 452 LYS cc_start: 0.8545 (tptt) cc_final: 0.8203 (tptp) REVERT: C 376 LYS cc_start: 0.7975 (mptt) cc_final: 0.7172 (pttp) outliers start: 14 outliers final: 10 residues processed: 151 average time/residue: 1.0453 time to fit residues: 183.5824 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 : 1.042 ------------------------------------------------------------------------------- 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 495 PHE Chi-restraints excluded: chain A residue 496 TYR 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: 0.9980 chunk 175 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 174 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 ASN B 441 ASN A 327 ASN C 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.198745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.142226 restraints weight = 81594.924| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.88 r_work: 0.3885 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1326 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= 0.136 Angle : 0.499 8.169 26823 Z= 0.284 Chirality : 0.037 0.179 3141 Planarity : 0.004 0.057 2611 Dihedral : 19.734 176.967 4913 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.74 % Rotamer: Outliers : 0.78 % Allowed : 7.98 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1686 helix: 1.12 (0.18), residues: 801 sheet: -2.20 (0.38), residues: 159 loop : 0.13 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 379 TYR 0.022 0.001 TYR B 159 PHE 0.012 0.001 PHE B 357 HIS 0.003 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (19182) covalent geometry : angle 0.49852 / 0.28 (26823) hydrogen bonds : bond 0.04785 / 5.04 ( 830) hydrogen bonds : angle 4.80070 / 6.28 ( 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 162 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.892 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: 0.7741 (mm-30) cc_final: 0.7257 (mm-30) REVERT: B 431 ASP cc_start: 0.8130 (m-30) cc_final: 0.7812 (m-30) REVERT: B 486 MET cc_start: 0.8341 (mpp) cc_final: 0.7733 (mpm) REVERT: B 495 PHE cc_start: 0.7975 (p90) cc_final: 0.7415 (p90) REVERT: A 27 LEU cc_start: 0.7733 (tt) cc_final: 0.7435 (tt) REVERT: A 160 ASN cc_start: 0.8343 (m-40) cc_final: 0.8125 (t0) REVERT: A 307 GLU cc_start: 0.8122 (tp30) cc_final: 0.7898 (tp30) REVERT: A 333 TYR cc_start: 0.7412 (m-10) cc_final: 0.6940 (m-10) REVERT: A 452 LYS cc_start: 0.8521 (tptt) cc_final: 0.8180 (tptp) REVERT: C 201 ASP cc_start: 0.8368 (p0) cc_final: 0.8111 (p0) REVERT: C 376 LYS cc_start: 0.7961 (mptt) cc_final: 0.7163 (pttp) outliers start: 12 outliers final: 8 residues processed: 152 average time/residue: 0.9989 time to fit residues: 177.8538 Evaluate side-chains 145 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 463 THR 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 410 LEU Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN C 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.191177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.135150 restraints weight = 79022.211| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.80 r_work: 0.3824 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19182 Z= 0.193 Angle : 0.514 8.203 26823 Z= 0.293 Chirality : 0.037 0.196 3141 Planarity : 0.004 0.066 2611 Dihedral : 19.713 176.699 4913 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.17 % Allowed : 8.17 % 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: 0.54 (0.21), residues: 1686 helix: 1.27 (0.19), residues: 780 sheet: -2.14 (0.38), residues: 159 loop : 0.09 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 379 TYR 0.012 0.001 TYR A 446 PHE 0.014 0.001 PHE A 97 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (19182) covalent geometry : angle 0.51441 / 0.29 (26823) hydrogen bonds : bond 0.04857 / 5.12 ( 830) hydrogen bonds : angle 4.76891 / 6.24 ( 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 163 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.888 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: 0.7759 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 431 ASP cc_start: 0.8138 (m-30) cc_final: 0.7832 (m-30) REVERT: B 486 MET cc_start: 0.8388 (mpp) cc_final: 0.7789 (mpm) REVERT: A 27 LEU cc_start: 0.7699 (tt) cc_final: 0.7392 (tt) REVERT: A 160 ASN cc_start: 0.8421 (m-40) cc_final: 0.8196 (t0) REVERT: A 307 GLU cc_start: 0.8210 (tp30) cc_final: 0.7916 (tp30) REVERT: A 333 TYR cc_start: 0.7410 (m-10) cc_final: 0.6931 (m-10) REVERT: A 452 LYS cc_start: 0.8558 (tptt) cc_final: 0.8181 (tptp) REVERT: C 376 LYS cc_start: 0.7948 (mptt) cc_final: 0.7132 (pttp) outliers start: 18 outliers final: 9 residues processed: 150 average time/residue: 1.0096 time to fit residues: 176.1643 Evaluate side-chains 147 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 185 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN C 92 ASN C 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.191243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.135134 restraints weight = 79140.308| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.81 r_work: 0.3824 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1662 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= 0.167 Angle : 0.504 8.695 26823 Z= 0.286 Chirality : 0.037 0.189 3141 Planarity : 0.004 0.058 2611 Dihedral : 19.733 176.478 4913 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 1.17 % Allowed : 8.95 % Favored : 89.88 % 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: 1.35 (0.19), residues: 780 sheet: -2.10 (0.38), residues: 159 loop : 0.05 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 552 TYR 0.015 0.001 TYR B 159 PHE 0.016 0.001 PHE B 495 HIS 0.002 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (19182) covalent geometry : angle 0.50396 / 0.29 (26823) hydrogen bonds : bond 0.04653 / 4.92 ( 830) hydrogen bonds : angle 4.67663 / 6.13 ( 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 163 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7205 (mm-30) REVERT: B 431 ASP cc_start: 0.8137 (m-30) cc_final: 0.7854 (m-30) REVERT: B 486 MET cc_start: 0.8395 (mpp) cc_final: 0.7811 (mpm) REVERT: B 531 LYS cc_start: 0.7545 (tptt) cc_final: 0.6884 (tppt) REVERT: B 551 MET cc_start: 0.9164 (ttp) cc_final: 0.8499 (tpp) REVERT: A 27 LEU cc_start: 0.7718 (tt) cc_final: 0.7398 (tt) REVERT: A 307 GLU cc_start: 0.8201 (tp30) cc_final: 0.7915 (tp30) REVERT: A 333 TYR cc_start: 0.7404 (m-10) cc_final: 0.6931 (m-10) REVERT: A 452 LYS cc_start: 0.8576 (tptt) cc_final: 0.8208 (tptp) REVERT: C 376 LYS cc_start: 0.7966 (mptt) cc_final: 0.7127 (pttp) outliers start: 18 outliers final: 12 residues processed: 151 average time/residue: 1.0165 time to fit residues: 179.2259 Evaluate side-chains 149 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 218 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 554 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN C 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.188326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.131422 restraints weight = 79068.840| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.79 r_work: 0.3714 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19182 Z= 0.263 Angle : 0.562 10.687 26823 Z= 0.318 Chirality : 0.039 0.212 3141 Planarity : 0.005 0.093 2611 Dihedral : 19.756 178.212 4913 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.03 % Rotamer: Outliers : 1.62 % Allowed : 9.14 % Favored : 89.23 % 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: 0.35 (0.21), residues: 1686 helix: 1.17 (0.19), residues: 780 sheet: -2.17 (0.37), residues: 159 loop : -0.08 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 552 TYR 0.017 0.002 TYR B 446 PHE 0.025 0.002 PHE B 495 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 (19182) covalent geometry : angle 0.56193 / 0.32 (26823) hydrogen bonds : bond 0.05118 / 5.42 ( 830) hydrogen bonds : angle 4.80840 / 6.29 ( 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 164 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 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: B 417 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 431 ASP cc_start: 0.8139 (m-30) cc_final: 0.7862 (m-30) REVERT: B 486 MET cc_start: 0.8410 (mpp) cc_final: 0.7820 (mpm) REVERT: B 531 LYS cc_start: 0.7589 (tptt) cc_final: 0.6933 (tppt) REVERT: B 551 MET cc_start: 0.9159 (ttp) cc_final: 0.8477 (tpp) REVERT: A 27 LEU cc_start: 0.7818 (tt) cc_final: 0.7514 (tt) REVERT: A 307 GLU cc_start: 0.8177 (tp30) cc_final: 0.7929 (tp30) REVERT: A 333 TYR cc_start: 0.7439 (m-10) cc_final: 0.7013 (m-10) REVERT: A 452 LYS cc_start: 0.8607 (tptt) cc_final: 0.8267 (tptp) REVERT: C 376 LYS cc_start: 0.7953 (mptt) cc_final: 0.7103 (pttp) outliers start: 25 outliers final: 15 residues processed: 152 average time/residue: 0.9177 time to fit residues: 165.0716 Evaluate side-chains 148 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 218 THR 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 435 PHE 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: 5.9990 chunk 14 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 159 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN C 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.190510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.134257 restraints weight = 79108.662| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.83 r_work: 0.3810 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19182 Z= 0.142 Angle : 0.507 10.812 26823 Z= 0.285 Chirality : 0.037 0.174 3141 Planarity : 0.004 0.057 2611 Dihedral : 19.744 176.197 4913 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 1.23 % Allowed : 10.05 % Favored : 88.72 % 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: 0.54 (0.21), residues: 1686 helix: 1.35 (0.19), residues: 780 sheet: -2.05 (0.37), residues: 159 loop : -0.02 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 552 TYR 0.013 0.001 TYR B 159 PHE 0.023 0.001 PHE B 495 HIS 0.003 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (19182) covalent geometry : angle 0.50685 / 0.29 (26823) hydrogen bonds : bond 0.04519 / 4.80 ( 830) hydrogen bonds : angle 4.63102 / 6.08 ( 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 163 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.623 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 214 LEU cc_start: 0.8661 (pp) cc_final: 0.8401 (pp) REVERT: B 417 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 431 ASP cc_start: 0.8137 (m-30) cc_final: 0.7861 (m-30) REVERT: B 486 MET cc_start: 0.8373 (mpp) cc_final: 0.7797 (mpm) REVERT: B 531 LYS cc_start: 0.7503 (tptt) cc_final: 0.6853 (tppt) REVERT: B 551 MET cc_start: 0.9167 (ttp) cc_final: 0.8507 (tpp) REVERT: A 27 LEU cc_start: 0.7759 (tt) cc_final: 0.7457 (tt) REVERT: A 160 ASN cc_start: 0.8463 (m-40) cc_final: 0.8105 (t0) REVERT: A 307 GLU cc_start: 0.8176 (tp30) cc_final: 0.7903 (tp30) REVERT: A 333 TYR cc_start: 0.7422 (m-10) cc_final: 0.6958 (m-10) REVERT: A 417 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7618 (tt0) REVERT: A 452 LYS cc_start: 0.8576 (tptt) cc_final: 0.8233 (tptp) REVERT: C 376 LYS cc_start: 0.7945 (mptt) cc_final: 0.7089 (pttp) outliers start: 19 outliers final: 10 residues processed: 150 average time/residue: 0.9753 time to fit residues: 171.4213 Evaluate side-chains 146 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 410 LEU 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: 10.0000 chunk 4 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 0.0050 chunk 73 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN C 179 ASN C 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.187689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.130622 restraints weight = 79057.789| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.78 r_work: 0.3765 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19182 Z= 0.244 Angle : 0.552 11.137 26823 Z= 0.311 Chirality : 0.038 0.200 3141 Planarity : 0.004 0.065 2611 Dihedral : 19.732 177.527 4913 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 1.23 % Allowed : 10.44 % Favored : 88.33 % 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: 1.23 (0.19), residues: 780 sheet: -2.10 (0.37), residues: 159 loop : -0.13 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 552 TYR 0.016 0.002 TYR B 446 PHE 0.018 0.002 PHE C 124 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.24 (19182) covalent geometry : angle 0.55197 / 0.31 (26823) hydrogen bonds : bond 0.04948 / 5.23 ( 830) hydrogen bonds : angle 4.73902 / 6.19 ( 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 154 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.968 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: B 417 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 431 ASP cc_start: 0.8152 (m-30) cc_final: 0.7878 (m-30) REVERT: B 486 MET cc_start: 0.8386 (mpp) cc_final: 0.7802 (mpm) REVERT: B 531 LYS cc_start: 0.7507 (tptt) cc_final: 0.6836 (tppt) REVERT: B 551 MET cc_start: 0.9160 (ttp) cc_final: 0.8481 (tpp) REVERT: A 27 LEU cc_start: 0.7792 (tt) cc_final: 0.7489 (tt) REVERT: A 160 ASN cc_start: 0.8527 (m-40) cc_final: 0.8194 (t0) REVERT: A 307 GLU cc_start: 0.8182 (tp30) cc_final: 0.7953 (tp30) REVERT: A 333 TYR cc_start: 0.7448 (m-80) cc_final: 0.7026 (m-10) REVERT: A 452 LYS cc_start: 0.8612 (tptt) cc_final: 0.8188 (tptp) REVERT: C 376 LYS cc_start: 0.7946 (mptt) cc_final: 0.7045 (pttp) outliers start: 19 outliers final: 12 residues processed: 143 average time/residue: 0.8731 time to fit residues: 147.2014 Evaluate side-chains 142 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 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 435 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN C 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.189998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.133697 restraints weight = 78959.818| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.80 r_work: 0.3754 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19182 Z= 0.145 Angle : 0.512 11.562 26823 Z= 0.288 Chirality : 0.037 0.166 3141 Planarity : 0.004 0.061 2611 Dihedral : 19.740 176.732 4913 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.50 % Favored : 96.38 % Rotamer: Outliers : 1.10 % Allowed : 10.96 % Favored : 87.94 % 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: 0.52 (0.21), residues: 1686 helix: 1.38 (0.19), residues: 777 sheet: -2.01 (0.37), residues: 159 loop : -0.09 (0.25), residues: 750 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 0.016 0.001 PHE B 495 HIS 0.003 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (19182) covalent geometry : angle 0.51202 / 0.29 (26823) hydrogen bonds : bond 0.04494 / 4.76 ( 830) hydrogen bonds : angle 4.61048 / 6.04 ( 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 153 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.854 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: 0.7749 (mm-30) cc_final: 0.7230 (mm-30) REVERT: B 431 ASP cc_start: 0.8128 (m-30) cc_final: 0.7859 (m-30) REVERT: B 486 MET cc_start: 0.8380 (mpp) cc_final: 0.7792 (mpm) REVERT: B 496 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.5346 (p90) REVERT: B 531 LYS cc_start: 0.7530 (tptt) cc_final: 0.6868 (tppt) REVERT: B 551 MET cc_start: 0.9158 (ttp) cc_final: 0.8477 (tpp) REVERT: A 27 LEU cc_start: 0.7822 (tt) cc_final: 0.7526 (tt) REVERT: A 160 ASN cc_start: 0.8523 (m-40) cc_final: 0.8204 (t0) REVERT: A 307 GLU cc_start: 0.8147 (tp30) cc_final: 0.7909 (tp30) REVERT: A 333 TYR cc_start: 0.7438 (m-80) cc_final: 0.7014 (m-10) REVERT: A 417 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7650 (tt0) REVERT: A 452 LYS cc_start: 0.8600 (tptt) cc_final: 0.8175 (tptp) REVERT: C 376 LYS cc_start: 0.7918 (mptt) cc_final: 0.7025 (pttp) outliers start: 17 outliers final: 9 residues processed: 142 average time/residue: 0.9709 time to fit residues: 161.7092 Evaluate side-chains 144 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 268 ILE 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 410 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 161 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 190 optimal weight: 30.0000 chunk 188 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 329 GLN C 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.188257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.131232 restraints weight = 79085.416| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.81 r_work: 0.3716 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19182 Z= 0.223 Angle : 0.540 10.029 26823 Z= 0.304 Chirality : 0.038 0.180 3141 Planarity : 0.004 0.065 2611 Dihedral : 19.731 177.481 4913 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 0.97 % Allowed : 11.15 % Favored : 87.87 % 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: 0.37 (0.21), residues: 1686 helix: 1.28 (0.19), residues: 777 sheet: -2.09 (0.37), residues: 159 loop : -0.20 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 552 TYR 0.017 0.001 TYR B 159 PHE 0.017 0.002 PHE C 124 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (19182) covalent geometry : angle 0.53965 / 0.30 (26823) hydrogen bonds : bond 0.04793 / 5.06 ( 830) hydrogen bonds : angle 4.69595 / 6.14 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10546.87 seconds wall clock time: 179 minutes 29.48 seconds (10769.48 seconds total)