Starting phenix.real_space_refine on Sun Aug 9 16:20:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lm3_63214/08_2026/9lm3_63214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lm3_63214/08_2026/9lm3_63214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lm3_63214/08_2026/9lm3_63214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lm3_63214/08_2026/9lm3_63214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lm3_63214/08_2026/9lm3_63214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lm3_63214/08_2026/9lm3_63214.map" } resolution = 2.6 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= 0.002 sd= 0.149 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: 6 Type Number sf(0) Gaussians P 225 5.49 5 S 66 5.16 5 C 11162 2.51 5 N 3275 2.21 5 O 4125 1.98 5 H 16742 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 35595 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 9512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 9512 Classifications: {'peptide': 583} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 563} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 9479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9479 Classifications: {'peptide': 580} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 9512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 9512 Classifications: {'peptide': 583} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 563} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 399 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "C" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1805 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 25, 'rna3p_pyr': 16} Link IDs: {'rna2p': 16, 'rna3p': 40} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Classifications: {'RNA': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "F" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 399 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "G" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1805 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 37} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Classifications: {'RNA': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "J" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 399 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Classifications: {'RNA': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1} Chain: "M" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "N" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "O" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "K" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1805 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 27, 'rna3p_pyr': 14} Link IDs: {'rna2p': 16, 'rna3p': 40} Time building chain proxies: 6.21, per 1000 atoms: 0.17 Number of scatterers: 35595 At special positions: 0 Unit cell: (112.35, 142.31, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 225 15.00 O 4125 8.00 N 3275 7.00 C 11162 6.00 H 16742 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: 3.36 Conformation dependent library (CDL) restraints added in 983.7 milliseconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3302 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 25 sheets defined 52.6% alpha, 12.7% beta 63 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 7.07 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 63 through 88 removed outlier: 3.730A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.920A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 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: 4.700A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N MET A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 243 through 246 removed outlier: 3.830A pdb=" N THR A 246 " --> pdb=" O ASP A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 269 through 286 Processing helix chain 'A' and resid 302 through 326 removed outlier: 3.809A pdb=" N VAL A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.805A pdb=" N LYS A 344 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 346 " --> pdb=" O PHE A 343 " (cutoff:3.500A) 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 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 428 through 445 removed outlier: 4.472A pdb=" N LYS A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.742A pdb=" N MET A 489 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.506A pdb=" N LEU A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 524' Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 556 through 560 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 removed outlier: 3.544A pdb=" N PHE A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.151A pdb=" N LEU E 7 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP E 8 " --> pdb=" O THR E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 38 through 41 Processing helix chain 'E' and resid 63 through 87 removed outlier: 3.629A pdb=" N ASP E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 129 through 140 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 169 through 193 removed outlier: 4.648A pdb=" N ILE E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N MET E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 236 Processing helix chain 'E' and resid 243 through 246 Processing helix chain 'E' and resid 269 through 286 Processing helix chain 'E' and resid 302 through 328 removed outlier: 3.627A pdb=" N LEU E 306 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL E 316 " --> pdb=" O PHE E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 346 removed outlier: 3.528A pdb=" N LYS E 344 " --> pdb=" O HIS E 341 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS E 346 " --> pdb=" O PHE E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 364 Processing helix chain 'E' and resid 375 through 389 removed outlier: 4.333A pdb=" N ARG E 379 " --> pdb=" O GLY E 375 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE E 380 " --> pdb=" O LYS E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 416 through 423 Processing helix chain 'E' and resid 428 through 445 removed outlier: 4.666A pdb=" N LYS E 440 " --> pdb=" O VAL E 436 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASN E 441 " --> pdb=" O GLU E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 Processing helix chain 'E' and resid 484 through 488 Processing helix chain 'E' and resid 513 through 518 removed outlier: 3.645A pdb=" N PHE E 518 " --> pdb=" O MET E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 524 Processing helix chain 'E' and resid 545 through 553 Processing helix chain 'E' and resid 556 through 560 removed outlier: 4.416A pdb=" N ARG E 559 " --> pdb=" O ASP E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 586 removed outlier: 3.642A pdb=" N PHE E 570 " --> pdb=" O PHE E 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 15 through 24 Processing helix chain 'I' and resid 26 through 35 Processing helix chain 'I' and resid 38 through 41 Processing helix chain 'I' and resid 62 through 87 removed outlier: 3.669A pdb=" N ILE I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 109 Processing helix chain 'I' and resid 124 through 128 removed outlier: 3.635A pdb=" N SER I 127 " --> pdb=" O PHE I 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE I 128 " --> pdb=" O PHE I 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 124 through 128' Processing helix chain 'I' and resid 129 through 140 Processing helix chain 'I' and resid 146 through 158 Processing helix chain 'I' and resid 169 through 192 removed outlier: 4.698A pdb=" N ILE I 180 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N MET I 181 " --> pdb=" O ILE I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 237 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.753A pdb=" N THR I 246 " --> pdb=" O ASP I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 269 through 287 Processing helix chain 'I' and resid 308 through 328 removed outlier: 3.810A pdb=" N VAL I 316 " --> pdb=" O PHE I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 364 Processing helix chain 'I' and resid 377 through 389 Processing helix chain 'I' and resid 416 through 424 Processing helix chain 'I' and resid 428 through 445 removed outlier: 4.676A pdb=" N LYS I 440 " --> pdb=" O VAL I 436 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASN I 441 " --> pdb=" O GLU I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 475 removed outlier: 3.616A pdb=" N ASN I 470 " --> pdb=" O SER I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 489 removed outlier: 3.788A pdb=" N MET I 489 " --> pdb=" O MET I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 518 Processing helix chain 'I' and resid 519 through 523 Processing helix chain 'I' and resid 545 through 556 Processing helix chain 'I' and resid 566 through 586 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 199 removed outlier: 4.629A pdb=" N GLU A 240 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 Processing sheet with id=AA5, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 292 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.118A pdb=" N VAL A 455 " --> pdb=" O TYR A 499 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 501 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET A 457 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 532 removed outlier: 6.718A pdb=" N LYS A 531 " --> pdb=" O TYR A 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 43 through 49 Processing sheet with id=AB2, first strand: chain 'E' and resid 195 through 199 removed outlier: 4.536A pdb=" N GLU E 240 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 195 through 199 Processing sheet with id=AB4, first strand: chain 'E' and resid 217 through 219 Processing sheet with id=AB5, first strand: chain 'E' and resid 256 through 257 Processing sheet with id=AB6, first strand: chain 'E' and resid 291 through 292 Processing sheet with id=AB7, first strand: chain 'E' and resid 411 through 412 removed outlier: 6.226A pdb=" N VAL E 455 " --> pdb=" O TYR E 499 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL E 501 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET E 457 " --> pdb=" O VAL E 501 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 397 through 399 Processing sheet with id=AB9, first strand: chain 'I' and resid 43 through 50 Processing sheet with id=AC1, first strand: chain 'I' and resid 195 through 199 removed outlier: 4.506A pdb=" N GLU I 240 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 195 through 199 Processing sheet with id=AC3, first strand: chain 'I' and resid 217 through 220 Processing sheet with id=AC4, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AC5, first strand: chain 'I' and resid 291 through 292 Processing sheet with id=AC6, first strand: chain 'I' and resid 411 through 412 removed outlier: 6.060A pdb=" N VAL I 455 " --> pdb=" O TYR I 499 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL I 501 " --> pdb=" O VAL I 455 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET I 457 " --> pdb=" O VAL I 501 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE I 500 " --> pdb=" O HIS I 493 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS I 493 " --> pdb=" O ILE I 500 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 397 through 398 734 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 159 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 9.94 Time building geometry restraints manager: 4.57 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: 16709 1.03 - 1.23: 199 1.23 - 1.42: 8609 1.42 - 1.62: 10792 1.62 - 1.81: 99 Bond restraints: 36408 Sorted by residual: bond pdb=" C1' DT B 57 " pdb=" N1 DT B 57 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C1' DT F 57 " pdb=" N1 DT F 57 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.78e+00 bond pdb=" C5' DT B 57 " pdb=" C4' DT B 57 " ideal model delta sigma weight residual 1.512 1.531 -0.019 7.00e-03 2.04e+04 7.49e+00 bond pdb=" C3' DC B 59 " pdb=" C2' DC B 59 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.77e+00 bond pdb=" C3' DC B 66 " pdb=" O3' DC B 66 " ideal model delta sigma weight residual 1.435 1.402 0.033 1.30e-02 5.92e+03 6.41e+00 ... (remaining 36403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 63297 1.49 - 2.99: 2279 2.99 - 4.48: 175 4.48 - 5.98: 16 5.98 - 7.47: 5 Bond angle restraints: 65772 Sorted by residual: angle pdb=" C1' C D 9 " pdb=" N1 C D 9 " pdb=" C2 C D 9 " ideal model delta sigma weight residual 118.80 124.26 -5.46 1.10e+00 8.26e-01 2.46e+01 angle pdb=" C1' G G 8 " pdb=" N9 G G 8 " pdb=" C4 G G 8 " ideal model delta sigma weight residual 126.50 132.87 -6.37 1.30e+00 5.92e-01 2.40e+01 angle pdb=" O4' G C 8 " pdb=" C1' G C 8 " pdb=" N9 G C 8 " ideal model delta sigma weight residual 108.50 111.77 -3.27 7.00e-01 2.04e+00 2.18e+01 angle pdb=" C1' G G 8 " pdb=" N9 G G 8 " pdb=" C8 G G 8 " ideal model delta sigma weight residual 127.00 121.05 5.95 1.30e+00 5.92e-01 2.10e+01 angle pdb=" O4' G G 8 " pdb=" C1' G G 8 " pdb=" N9 G G 8 " ideal model delta sigma weight residual 108.50 111.68 -3.18 7.00e-01 2.04e+00 2.06e+01 ... (remaining 65767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 16058 35.13 - 70.26: 920 70.26 - 105.39: 65 105.39 - 140.53: 17 140.53 - 175.66: 21 Dihedral angle restraints: 17081 sinusoidal: 11052 harmonic: 6029 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 200.00 25.47 174.53 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U K 9 " pdb=" C1' U K 9 " pdb=" N1 U K 9 " pdb=" C2 U K 9 " ideal model delta sinusoidal sigma weight residual 200.00 31.87 168.13 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual -160.00 -2.06 -157.94 1 1.50e+01 4.44e-03 8.22e+01 ... (remaining 17078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2342 0.042 - 0.083: 502 0.083 - 0.125: 311 0.125 - 0.166: 48 0.166 - 0.208: 23 Chirality restraints: 3226 Sorted by residual: chirality pdb=" C1' G G 8 " pdb=" O4' G G 8 " pdb=" C2' G G 8 " pdb=" N9 G G 8 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C3' DC J 66 " pdb=" C4' DC J 66 " pdb=" O3' DC J 66 " pdb=" C2' DC J 66 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C3' DT B 64 " pdb=" C4' DT B 64 " pdb=" O3' DT B 64 " pdb=" C2' DT B 64 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 3223 not shown) Planarity restraints: 4516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 8 " 0.022 2.00e-02 2.50e+03 1.07e-02 3.70e+00 pdb=" N9 G C 8 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G C 8 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G C 8 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 8 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G C 8 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G C 8 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G C 8 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 8 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G C 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G C 8 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G C 8 " -0.000 2.00e-02 2.50e+03 pdb=" H8 G C 8 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 9 " 0.019 2.00e-02 2.50e+03 1.08e-02 3.23e+00 pdb=" N1 U G 9 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U G 9 " 0.004 2.00e-02 2.50e+03 pdb=" O2 U G 9 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U G 9 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U G 9 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U G 9 " 0.004 2.00e-02 2.50e+03 pdb=" C5 U G 9 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U G 9 " 0.000 2.00e-02 2.50e+03 pdb=" H5 U G 9 " 0.002 2.00e-02 2.50e+03 pdb=" H6 U G 9 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 464 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO E 465 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 465 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 465 " 0.025 5.00e-02 4.00e+02 ... (remaining 4513 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 318 2.05 - 2.69: 52360 2.69 - 3.33: 101765 3.33 - 3.96: 136430 3.96 - 4.60: 210385 Nonbonded interactions: 501258 Sorted by model distance: nonbonded pdb=" O ASN I 160 " pdb="HD21 ASN I 160 " model vdw 1.417 2.450 nonbonded pdb=" H8 A G 16 " pdb=" H5 U G 17 " model vdw 1.788 2.100 nonbonded pdb=" H8 A C 16 " pdb=" H5 U C 17 " model vdw 1.789 2.100 nonbonded pdb=" OE1 GLU E 395 " pdb=" H GLU E 395 " model vdw 1.795 2.450 nonbonded pdb=" HD1 HIS E 110 " pdb=" HG SER E 206 " model vdw 1.807 2.100 ... (remaining 501253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 535 or resid 542 through 586)) selection = chain 'E' selection = (chain 'I' and (resid 1 through 535 or resid 542 through 586)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.180 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: 0.200 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 42.000 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19666 Z= 0.323 Angle : 0.648 7.474 27531 Z= 0.505 Chirality : 0.048 0.208 3226 Planarity : 0.004 0.044 2668 Dihedral : 21.787 175.657 8714 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.34 % Allowed : 16.91 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.17 (0.21), residues: 1734 helix: 0.72 (0.18), residues: 845 sheet: -0.11 (0.38), residues: 188 loop : -1.08 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 132 TYR 0.020 0.002 TYR I 273 PHE 0.013 0.001 PHE I 357 HIS 0.004 0.001 HIS E 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.32 (19666) covalent geometry : angle 0.64765 / 0.51 (27531) hydrogen bonds : bond 0.11510 / 7.23 ( 857) hydrogen bonds : angle 5.90490 / 4.06 ( 2316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8091 (m-30) cc_final: 0.7794 (m-30) REVERT: A 256 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: E 116 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8678 (mm) REVERT: E 486 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.3762 (pmm) REVERT: E 579 HIS cc_start: 0.6622 (t-170) cc_final: 0.6342 (t-170) REVERT: I 24 ASP cc_start: 0.7919 (t0) cc_final: 0.7565 (t0) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 0.9824 time to fit residues: 190.2601 Evaluate side-chains 162 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 463 THR Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 366 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 146 ASN E 179 ASN I 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.188242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143204 restraints weight = 48734.917| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.24 r_work: 0.3175 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19666 Z= 0.190 Angle : 0.560 7.869 27531 Z= 0.321 Chirality : 0.042 0.252 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.743 176.152 5167 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.91 % Allowed : 16.78 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.07 (0.21), residues: 1734 helix: 0.87 (0.18), residues: 854 sheet: -0.20 (0.38), residues: 192 loop : -1.12 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.016 0.002 TYR E 446 PHE 0.013 0.001 PHE A 97 HIS 0.003 0.001 HIS A 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (19666) covalent geometry : angle 0.56029 / 0.32 (27531) hydrogen bonds : bond 0.05622 / 3.60 ( 857) hydrogen bonds : angle 5.01818 / 3.49 ( 2316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7560 (mm110) REVERT: A 78 ASP cc_start: 0.8069 (m-30) cc_final: 0.7776 (m-30) REVERT: A 407 GLU cc_start: 0.6662 (pm20) cc_final: 0.6319 (pm20) REVERT: E 486 MET cc_start: 0.5043 (mtt) cc_final: 0.3817 (pmm) REVERT: E 491 TYR cc_start: 0.6630 (p90) cc_final: 0.6375 (p90) REVERT: I 24 ASP cc_start: 0.7894 (t0) cc_final: 0.7546 (t0) outliers start: 30 outliers final: 18 residues processed: 174 average time/residue: 0.9796 time to fit residues: 200.1995 Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 ASN A 179 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.189495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144524 restraints weight = 49529.300| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.34 r_work: 0.3195 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19666 Z= 0.140 Angle : 0.524 7.649 27531 Z= 0.300 Chirality : 0.041 0.252 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.688 177.181 5144 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.04 % Allowed : 16.53 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.07 (0.21), residues: 1734 helix: 1.03 (0.18), residues: 852 sheet: -0.20 (0.38), residues: 192 loop : -1.10 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 254 TYR 0.012 0.001 TYR E 446 PHE 0.013 0.001 PHE I 357 HIS 0.002 0.001 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (19666) covalent geometry : angle 0.52362 / 0.30 (27531) hydrogen bonds : bond 0.04996 / 3.19 ( 857) hydrogen bonds : angle 4.76704 / 3.31 ( 2316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8024 (m-30) cc_final: 0.7719 (m-30) REVERT: A 256 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: A 407 GLU cc_start: 0.6786 (pm20) cc_final: 0.6354 (pm20) REVERT: A 581 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7448 (ttpp) REVERT: E 187 LYS cc_start: 0.8491 (mttm) cc_final: 0.7916 (mtmt) REVERT: E 486 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.3705 (pmm) REVERT: E 491 TYR cc_start: 0.6600 (p90) cc_final: 0.6375 (p90) REVERT: I 24 ASP cc_start: 0.7876 (t0) cc_final: 0.7516 (t0) outliers start: 32 outliers final: 17 residues processed: 184 average time/residue: 0.9800 time to fit residues: 211.1149 Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.189184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144600 restraints weight = 49222.929| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.32 r_work: 0.3184 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19666 Z= 0.151 Angle : 0.525 7.833 27531 Z= 0.300 Chirality : 0.041 0.247 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.666 177.337 5142 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.04 % Allowed : 16.40 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1734 helix: 1.06 (0.18), residues: 852 sheet: -0.19 (0.38), residues: 192 loop : -1.10 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.013 0.002 TYR E 446 PHE 0.013 0.001 PHE E 549 HIS 0.003 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (19666) covalent geometry : angle 0.52549 / 0.30 (27531) hydrogen bonds : bond 0.04913 / 3.13 ( 857) hydrogen bonds : angle 4.67423 / 3.25 ( 2316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7573 (mm110) REVERT: A 78 ASP cc_start: 0.8053 (m-30) cc_final: 0.7749 (m-30) REVERT: A 407 GLU cc_start: 0.6746 (pm20) cc_final: 0.6281 (pm20) REVERT: A 581 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7498 (ttpp) REVERT: E 116 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8729 (mm) REVERT: E 187 LYS cc_start: 0.8496 (mttm) cc_final: 0.7912 (mtmt) REVERT: E 486 MET cc_start: 0.4963 (mtt) cc_final: 0.3697 (pmm) REVERT: I 24 ASP cc_start: 0.7859 (t0) cc_final: 0.7501 (t0) outliers start: 32 outliers final: 19 residues processed: 178 average time/residue: 0.9534 time to fit residues: 200.0507 Evaluate side-chains 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 132 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 327 ASN A 411 ASN I 92 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.186974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139526 restraints weight = 48940.297| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.42 r_work: 0.3134 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 19666 Z= 0.273 Angle : 0.606 8.789 27531 Z= 0.341 Chirality : 0.045 0.266 3226 Planarity : 0.005 0.044 2668 Dihedral : 23.724 178.233 5141 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.81 % Allowed : 15.89 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1734 helix: 0.86 (0.18), residues: 852 sheet: -0.22 (0.38), residues: 192 loop : -1.21 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 132 TYR 0.020 0.002 TYR I 273 PHE 0.019 0.002 PHE A 97 HIS 0.006 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.27 (19666) covalent geometry : angle 0.60640 / 0.34 (27531) hydrogen bonds : bond 0.05687 / 3.65 ( 857) hydrogen bonds : angle 4.77114 / 3.32 ( 2316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7648 (mm110) REVERT: A 78 ASP cc_start: 0.8105 (m-30) cc_final: 0.7835 (m-30) REVERT: A 407 GLU cc_start: 0.6854 (pm20) cc_final: 0.6483 (pm20) REVERT: A 581 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7434 (ttpp) REVERT: E 116 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8743 (mm) REVERT: E 187 LYS cc_start: 0.8504 (mttm) cc_final: 0.7974 (mtmt) REVERT: E 486 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.3779 (pmm) REVERT: I 24 ASP cc_start: 0.7904 (t0) cc_final: 0.7549 (t0) outliers start: 44 outliers final: 26 residues processed: 192 average time/residue: 0.9140 time to fit residues: 207.3957 Evaluate side-chains 181 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 179 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141264 restraints weight = 49348.116| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.49 r_work: 0.3196 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19666 Z= 0.125 Angle : 0.526 7.495 27531 Z= 0.299 Chirality : 0.041 0.242 3226 Planarity : 0.004 0.045 2668 Dihedral : 23.695 177.257 5141 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.98 % Allowed : 17.04 % Favored : 80.98 % 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: 1734 helix: 1.13 (0.19), residues: 840 sheet: -0.23 (0.38), residues: 192 loop : -0.97 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.014 0.001 TYR E 491 PHE 0.017 0.001 PHE E 549 HIS 0.005 0.001 HIS E 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (19666) covalent geometry : angle 0.52601 / 0.30 (27531) hydrogen bonds : bond 0.04739 / 3.03 ( 857) hydrogen bonds : angle 4.59980 / 3.20 ( 2316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8035 (m-30) cc_final: 0.7707 (m-30) REVERT: A 407 GLU cc_start: 0.6896 (pm20) cc_final: 0.6452 (pm20) REVERT: E 116 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8739 (mm) REVERT: E 187 LYS cc_start: 0.8479 (mttm) cc_final: 0.7889 (mtmt) REVERT: E 216 MET cc_start: 0.9056 (mmp) cc_final: 0.8615 (mmt) REVERT: E 486 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.3691 (pmm) REVERT: E 491 TYR cc_start: 0.6853 (p90) cc_final: 0.6577 (p90) REVERT: I 24 ASP cc_start: 0.7818 (t0) cc_final: 0.7454 (t0) outliers start: 31 outliers final: 23 residues processed: 179 average time/residue: 0.8588 time to fit residues: 181.7112 Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 187 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.187557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139246 restraints weight = 49218.345| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.53 r_work: 0.3144 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19666 Z= 0.222 Angle : 0.571 8.451 27531 Z= 0.322 Chirality : 0.043 0.256 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.695 176.624 5141 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.17 % Allowed : 17.10 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.00 (0.21), residues: 1734 helix: 0.98 (0.18), residues: 852 sheet: -0.22 (0.38), residues: 192 loop : -1.14 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 132 TYR 0.021 0.002 TYR I 273 PHE 0.015 0.002 PHE E 95 HIS 0.004 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (19666) covalent geometry : angle 0.57076 / 0.32 (27531) hydrogen bonds : bond 0.05254 / 3.37 ( 857) hydrogen bonds : angle 4.65724 / 3.24 ( 2316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7619 (mm110) REVERT: A 78 ASP cc_start: 0.8093 (m-30) cc_final: 0.7796 (m-30) REVERT: A 407 GLU cc_start: 0.6896 (pm20) cc_final: 0.6438 (pm20) REVERT: E 116 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8770 (mm) REVERT: E 187 LYS cc_start: 0.8501 (mttm) cc_final: 0.7955 (mtmt) REVERT: E 486 MET cc_start: 0.4963 (mtt) cc_final: 0.3680 (pmm) REVERT: E 491 TYR cc_start: 0.6865 (p90) cc_final: 0.6568 (p90) REVERT: I 24 ASP cc_start: 0.7890 (t0) cc_final: 0.7524 (t0) outliers start: 34 outliers final: 24 residues processed: 180 average time/residue: 0.8745 time to fit residues: 187.2428 Evaluate side-chains 174 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 137 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 327 ASN I 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.189290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140342 restraints weight = 49432.184| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.44 r_work: 0.3188 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19666 Z= 0.136 Angle : 0.525 7.629 27531 Z= 0.299 Chirality : 0.041 0.244 3226 Planarity : 0.004 0.046 2668 Dihedral : 23.680 177.449 5141 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.98 % Allowed : 17.17 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1734 helix: 1.15 (0.19), residues: 842 sheet: -0.23 (0.38), residues: 192 loop : -0.96 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 134 TYR 0.016 0.001 TYR I 273 PHE 0.017 0.001 PHE A 29 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (19666) covalent geometry : angle 0.52501 / 0.30 (27531) hydrogen bonds : bond 0.04733 / 3.02 ( 857) hydrogen bonds : angle 4.55541 / 3.17 ( 2316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8054 (m-30) cc_final: 0.7752 (m-30) REVERT: A 407 GLU cc_start: 0.6872 (pm20) cc_final: 0.6429 (pm20) REVERT: E 32 ASN cc_start: 0.5834 (OUTLIER) cc_final: 0.5534 (t0) REVERT: E 116 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8737 (mm) REVERT: E 187 LYS cc_start: 0.8501 (mttm) cc_final: 0.7962 (mtmt) REVERT: E 216 MET cc_start: 0.9064 (mmp) cc_final: 0.8632 (mmt) REVERT: E 486 MET cc_start: 0.4932 (OUTLIER) cc_final: 0.3658 (pmm) REVERT: E 491 TYR cc_start: 0.6875 (p90) cc_final: 0.6556 (p90) REVERT: I 24 ASP cc_start: 0.7845 (t0) cc_final: 0.7475 (t0) outliers start: 31 outliers final: 19 residues processed: 176 average time/residue: 0.9095 time to fit residues: 188.4866 Evaluate side-chains 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 59 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 94 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 327 ASN I 160 ASN I 411 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142630 restraints weight = 49295.109| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.57 r_work: 0.3186 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19666 Z= 0.131 Angle : 0.520 9.113 27531 Z= 0.295 Chirality : 0.040 0.246 3226 Planarity : 0.004 0.045 2668 Dihedral : 23.644 178.118 5141 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.72 % Allowed : 17.49 % Favored : 80.79 % 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: 0.29 (0.21), residues: 1734 helix: 1.21 (0.19), residues: 844 sheet: -0.20 (0.38), residues: 192 loop : -0.92 (0.26), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 134 TYR 0.016 0.001 TYR I 273 PHE 0.032 0.001 PHE E 549 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (19666) covalent geometry : angle 0.52011 / 0.30 (27531) hydrogen bonds : bond 0.04581 / 2.92 ( 857) hydrogen bonds : angle 4.48388 / 3.12 ( 2316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8073 (m-30) cc_final: 0.7765 (m-30) REVERT: A 407 GLU cc_start: 0.6899 (pm20) cc_final: 0.6436 (pm20) REVERT: A 581 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7532 (ttpp) REVERT: E 32 ASN cc_start: 0.5801 (OUTLIER) cc_final: 0.5505 (t0) REVERT: E 116 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8743 (mm) REVERT: E 187 LYS cc_start: 0.8491 (mttm) cc_final: 0.7940 (mtmt) REVERT: E 216 MET cc_start: 0.9063 (mmp) cc_final: 0.8629 (mmt) REVERT: E 486 MET cc_start: 0.4932 (mtt) cc_final: 0.3673 (pmm) REVERT: E 491 TYR cc_start: 0.6781 (p90) cc_final: 0.6544 (p90) REVERT: I 24 ASP cc_start: 0.7880 (t0) cc_final: 0.7510 (t0) outliers start: 27 outliers final: 19 residues processed: 172 average time/residue: 0.9105 time to fit residues: 183.6633 Evaluate side-chains 167 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 463 THR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 160 ASN Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141980 restraints weight = 49440.500| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.60 r_work: 0.3179 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.267 19666 Z= 0.211 Angle : 0.684 59.200 27531 Z= 0.408 Chirality : 0.041 0.449 3226 Planarity : 0.004 0.045 2668 Dihedral : 23.643 178.106 5141 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.04 % Rotamer: Outliers : 1.28 % Allowed : 18.25 % Favored : 80.47 % Cbeta Deviations : 0.06 % 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: 0.28 (0.21), residues: 1734 helix: 1.21 (0.19), residues: 844 sheet: -0.19 (0.38), residues: 192 loop : -0.92 (0.26), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 11 TYR 0.014 0.001 TYR I 273 PHE 0.023 0.001 PHE E 549 HIS 0.003 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.21 (19666) covalent geometry : angle 0.68357 / 0.41 (27531) hydrogen bonds : bond 0.04606 / 2.94 ( 857) hydrogen bonds : angle 4.48427 / 3.12 ( 2316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Residue TYR 333 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8087 (m-30) cc_final: 0.7778 (m-30) REVERT: A 407 GLU cc_start: 0.6885 (pm20) cc_final: 0.6422 (pm20) REVERT: A 581 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7558 (ttpp) REVERT: E 32 ASN cc_start: 0.5839 (OUTLIER) cc_final: 0.5542 (t0) REVERT: E 116 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8743 (mm) REVERT: E 187 LYS cc_start: 0.8507 (mttm) cc_final: 0.7966 (mtmt) REVERT: E 216 MET cc_start: 0.9053 (mmp) cc_final: 0.8625 (mmt) REVERT: E 486 MET cc_start: 0.4962 (mtt) cc_final: 0.3684 (pmm) REVERT: E 491 TYR cc_start: 0.6770 (p90) cc_final: 0.6538 (p90) REVERT: I 24 ASP cc_start: 0.7891 (t0) cc_final: 0.7521 (t0) outliers start: 20 outliers final: 18 residues processed: 163 average time/residue: 0.9565 time to fit residues: 183.3633 Evaluate side-chains 166 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 368 CYS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 463 THR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141616 restraints weight = 49247.239| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.46 r_work: 0.3195 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.267 19666 Z= 0.211 Angle : 0.684 59.200 27531 Z= 0.408 Chirality : 0.041 0.449 3226 Planarity : 0.004 0.045 2668 Dihedral : 23.643 178.106 5141 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.04 % Rotamer: Outliers : 1.28 % Allowed : 18.25 % Favored : 80.47 % Cbeta Deviations : 0.06 % 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: 0.28 (0.21), residues: 1734 helix: 1.21 (0.19), residues: 844 sheet: -0.19 (0.38), residues: 192 loop : -0.92 (0.26), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 11 TYR 0.014 0.001 TYR I 273 PHE 0.023 0.001 PHE E 549 HIS 0.003 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.21 (19666) covalent geometry : angle 0.68357 / 0.41 (27531) hydrogen bonds : bond 0.04606 / 2.94 ( 857) hydrogen bonds : angle 4.48427 / 3.12 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11910.09 seconds wall clock time: 202 minutes 16.74 seconds (12136.74 seconds total)