Starting phenix.real_space_refine on Mon Jul 6 14:54:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lm3_63214/07_2026/9lm3_63214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lm3_63214/07_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_63214/07_2026/9lm3_63214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lm3_63214/07_2026/9lm3_63214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lm3_63214/07_2026/9lm3_63214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lm3_63214/07_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-dev-6108/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: 6.93, per 1000 atoms: 0.19 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: 3.63 Conformation dependent library (CDL) restraints added in 898.1 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: 6.20 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: 8.51 Time building geometry restraints manager: 4.83 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: 63736 1.49 - 2.99: 1854 2.99 - 4.48: 161 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=" 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=" C1' C D 9 " pdb=" N1 C D 9 " pdb=" C6 C D 9 " ideal model delta sigma weight residual 120.80 115.46 5.34 1.20e+00 6.94e-01 1.98e+01 angle pdb=" N9 G G 8 " pdb=" C4 G G 8 " pdb=" N3 G G 8 " ideal model delta sigma weight residual 126.00 128.65 -2.65 6.00e-01 2.78e+00 1.95e+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 - 0.040: 2429 0.040 - 0.079: 558 0.079 - 0.119: 156 0.119 - 0.158: 57 0.158 - 0.198: 26 Chirality restraints: 3226 Sorted by residual: 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 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 2.46 2.26 0.19 2.00e-01 2.50e+01 9.44e-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: 1.010 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: 0.250 Extract box with map and model: 0.550 Check model and map are aligned: 0.180 Set scattering table: 0.170 Process input model: 39.600 Find NCS groups from input model: 0.490 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: 0.020 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.490 ------------------------------------------------------------------------------- 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= 0.313 Angle : 0.590 7.474 27531 Z= 0.439 Chirality : 0.043 0.198 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 0.00424 / 0.31 (19666) covalent geometry : angle 0.58961 / 0.44 (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 : 0.855 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: 0.9330 time to fit residues: 179.8769 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 : 0.816 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.4126 r_free = 0.4126 target = 0.188164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139308 restraints weight = 48781.868| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.59 r_work: 0.3139 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0265 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= 0.194 Angle : 0.547 7.376 27531 Z= 0.319 Chirality : 0.042 0.261 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.785 175.946 5167 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.98 % Allowed : 16.78 % Favored : 81.24 % 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: -0.08 (0.21), residues: 1734 helix: 0.86 (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 0.00399 / 0.19 (19666) covalent geometry : angle 0.54664 / 0.32 (27531) hydrogen bonds : bond 0.05656 / 3.62 ( 857) hydrogen bonds : angle 5.02732 / 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 180 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7643 (mm110) REVERT: A 78 ASP cc_start: 0.8111 (m-30) cc_final: 0.7822 (m-30) REVERT: A 407 GLU cc_start: 0.6695 (pm20) cc_final: 0.6331 (pm20) REVERT: E 486 MET cc_start: 0.5042 (mtt) cc_final: 0.3802 (pmm) REVERT: E 491 TYR cc_start: 0.6644 (p90) cc_final: 0.6381 (p90) REVERT: I 24 ASP cc_start: 0.7946 (t0) cc_final: 0.7589 (t0) outliers start: 31 outliers final: 20 residues processed: 175 average time/residue: 0.9427 time to fit residues: 193.5391 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 : 0.604 ------------------------------------------------------------------------------- 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 120 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 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 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: 9.9990 chunk 64 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.189003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139577 restraints weight = 49453.599| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.57 r_work: 0.3161 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0353 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 : 0.521 7.461 27531 Z= 0.306 Chirality : 0.041 0.245 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.743 176.629 5145 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.85 % Allowed : 16.98 % Favored : 81.17 % 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: 0.03 (0.21), residues: 1734 helix: 0.98 (0.18), residues: 852 sheet: -0.15 (0.38), residues: 191 loop : -1.10 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 254 TYR 0.014 0.001 TYR E 446 PHE 0.012 0.001 PHE I 357 HIS 0.003 0.001 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (19666) covalent geometry : angle 0.52077 / 0.31 (27531) hydrogen bonds : bond 0.05189 / 3.32 ( 857) hydrogen bonds : angle 4.85027 / 3.37 ( 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 182 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8037 (m-30) cc_final: 0.7732 (m-30) REVERT: A 407 GLU cc_start: 0.6706 (pm20) cc_final: 0.6302 (pm20) REVERT: A 581 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7374 (ttpp) REVERT: E 187 LYS cc_start: 0.8496 (mttm) cc_final: 0.7914 (mtmt) REVERT: E 486 MET cc_start: 0.4981 (mtt) cc_final: 0.3694 (pmm) REVERT: E 491 TYR cc_start: 0.6592 (p90) cc_final: 0.6368 (p90) REVERT: I 24 ASP cc_start: 0.7897 (t0) cc_final: 0.7538 (t0) outliers start: 29 outliers final: 20 residues processed: 177 average time/residue: 0.9993 time to fit residues: 205.9305 Evaluate side-chains 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 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 303 LEU Chi-restraints excluded: chain I residue 334 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: 1.9990 chunk 105 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 94 optimal weight: 0.0770 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.190663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141941 restraints weight = 49499.193| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.49 r_work: 0.3206 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19666 Z= 0.118 Angle : 0.494 7.143 27531 Z= 0.289 Chirality : 0.039 0.230 3226 Planarity : 0.004 0.046 2668 Dihedral : 23.698 178.146 5144 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.98 % Allowed : 16.72 % Favored : 81.30 % 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: 0.15 (0.21), residues: 1734 helix: 1.12 (0.19), residues: 852 sheet: -0.21 (0.37), residues: 192 loop : -1.07 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.010 0.001 TYR I 273 PHE 0.019 0.001 PHE E 549 HIS 0.003 0.001 HIS I 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (19666) covalent geometry : angle 0.49364 / 0.29 (27531) hydrogen bonds : bond 0.04579 / 2.92 ( 857) hydrogen bonds : angle 4.62071 / 3.21 ( 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 187 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8044 (m-30) cc_final: 0.7732 (m-30) REVERT: A 256 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: A 407 GLU cc_start: 0.6710 (pm20) cc_final: 0.6248 (pm20) REVERT: A 581 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7473 (ttpp) REVERT: E 116 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8696 (mm) REVERT: E 187 LYS cc_start: 0.8492 (mttm) cc_final: 0.7909 (mtmt) REVERT: E 486 MET cc_start: 0.4947 (OUTLIER) cc_final: 0.3684 (pmm) REVERT: I 24 ASP cc_start: 0.7867 (t0) cc_final: 0.7510 (t0) outliers start: 31 outliers final: 15 residues processed: 179 average time/residue: 0.9579 time to fit residues: 201.2006 Evaluate side-chains 166 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS 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 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 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 148 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: 1.9990 chunk 56 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 119 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN I 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.187725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138241 restraints weight = 49059.610| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.63 r_work: 0.3138 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19666 Z= 0.240 Angle : 0.562 8.005 27531 Z= 0.324 Chirality : 0.043 0.244 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.700 176.809 5141 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.49 % Allowed : 16.59 % Favored : 80.92 % 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: 0.03 (0.21), residues: 1734 helix: 0.99 (0.18), residues: 852 sheet: -0.18 (0.38), residues: 192 loop : -1.13 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 132 TYR 0.019 0.002 TYR E 446 PHE 0.016 0.002 PHE A 97 HIS 0.005 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 (19666) covalent geometry : angle 0.56182 / 0.32 (27531) hydrogen bonds : bond 0.05366 / 3.43 ( 857) hydrogen bonds : angle 4.68819 / 3.26 ( 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 189 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7640 (mm110) REVERT: A 78 ASP cc_start: 0.8089 (m-30) cc_final: 0.7812 (m-30) REVERT: A 407 GLU cc_start: 0.6872 (pm20) cc_final: 0.6493 (pm20) REVERT: A 581 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7398 (ttpp) REVERT: E 116 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8733 (mm) REVERT: E 187 LYS cc_start: 0.8504 (mttm) cc_final: 0.7962 (mtmt) REVERT: E 486 MET cc_start: 0.4964 (OUTLIER) cc_final: 0.3708 (pmm) REVERT: E 491 TYR cc_start: 0.6899 (p90) cc_final: 0.6637 (p90) REVERT: I 24 ASP cc_start: 0.7909 (t0) cc_final: 0.7540 (t0) outliers start: 39 outliers final: 23 residues processed: 182 average time/residue: 0.9998 time to fit residues: 213.3195 Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 A residue 469 LEU 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 286 THR 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 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 303 LEU Chi-restraints excluded: chain I residue 366 ASN Chi-restraints excluded: chain I residue 463 THR 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: 10.0000 chunk 95 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138170 restraints weight = 49012.784| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.61 r_work: 0.3141 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0571 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= 0.213 Angle : 0.551 7.559 27531 Z= 0.318 Chirality : 0.043 0.241 3226 Planarity : 0.004 0.044 2668 Dihedral : 23.730 176.507 5141 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.36 % Allowed : 16.66 % Favored : 80.98 % 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: -0.02 (0.21), residues: 1734 helix: 0.97 (0.18), residues: 850 sheet: -0.23 (0.38), residues: 192 loop : -1.16 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.020 0.002 TYR I 273 PHE 0.018 0.002 PHE E 549 HIS 0.004 0.001 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (19666) covalent geometry : angle 0.55118 / 0.32 (27531) hydrogen bonds : bond 0.05246 / 3.35 ( 857) hydrogen bonds : angle 4.66972 / 3.25 ( 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 188 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7633 (mm110) REVERT: A 78 ASP cc_start: 0.8100 (m-30) cc_final: 0.7803 (m-30) REVERT: A 407 GLU cc_start: 0.6855 (pm20) cc_final: 0.6409 (pm20) REVERT: E 116 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8760 (mm) REVERT: E 187 LYS cc_start: 0.8500 (mttm) cc_final: 0.7951 (mtmt) REVERT: E 486 MET cc_start: 0.4971 (OUTLIER) cc_final: 0.3698 (pmm) REVERT: E 491 TYR cc_start: 0.6812 (p90) cc_final: 0.6573 (p90) REVERT: I 24 ASP cc_start: 0.7895 (t0) cc_final: 0.7529 (t0) outliers start: 37 outliers final: 24 residues processed: 179 average time/residue: 0.9796 time to fit residues: 206.1770 Evaluate side-chains 175 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 A residue 469 LEU Chi-restraints excluded: chain A residue 571 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 286 THR 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 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 Chi-restraints excluded: chain I residue 489 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 0.0010 chunk 128 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4118 r_free = 0.4118 target = 0.187804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139041 restraints weight = 49111.324| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.55 r_work: 0.3144 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19666 Z= 0.210 Angle : 0.552 7.607 27531 Z= 0.319 Chirality : 0.042 0.240 3226 Planarity : 0.004 0.045 2668 Dihedral : 23.738 176.339 5141 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.30 % Allowed : 16.72 % Favored : 80.98 % 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: -0.03 (0.21), residues: 1734 helix: 0.96 (0.18), residues: 850 sheet: -0.23 (0.38), residues: 192 loop : -1.17 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.023 0.002 TYR I 273 PHE 0.016 0.001 PHE A 29 HIS 0.004 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (19666) covalent geometry : angle 0.55221 / 0.32 (27531) hydrogen bonds : bond 0.05237 / 3.35 ( 857) hydrogen bonds : angle 4.65340 / 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 186 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7608 (mm110) REVERT: A 78 ASP cc_start: 0.8101 (m-30) cc_final: 0.7801 (m-30) REVERT: A 407 GLU cc_start: 0.6902 (pm20) cc_final: 0.6443 (pm20) REVERT: E 116 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8764 (mm) REVERT: E 187 LYS cc_start: 0.8496 (mttm) cc_final: 0.7945 (mtmt) REVERT: E 486 MET cc_start: 0.4967 (OUTLIER) cc_final: 0.3693 (pmm) REVERT: I 24 ASP cc_start: 0.7883 (t0) cc_final: 0.7517 (t0) outliers start: 36 outliers final: 27 residues processed: 179 average time/residue: 0.9626 time to fit residues: 203.1949 Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 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 286 THR 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 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 372 ILE 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: 8.9990 chunk 166 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN I 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.188268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138909 restraints weight = 49286.495| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.68 r_work: 0.3140 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19666 Z= 0.170 Angle : 0.535 7.449 27531 Z= 0.310 Chirality : 0.041 0.235 3226 Planarity : 0.004 0.045 2668 Dihedral : 23.737 176.682 5141 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.04 % Allowed : 17.29 % Favored : 80.66 % 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: 0.12 (0.21), residues: 1734 helix: 1.06 (0.18), residues: 842 sheet: -0.24 (0.38), residues: 192 loop : -1.00 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.018 0.002 TYR I 273 PHE 0.016 0.001 PHE A 29 HIS 0.004 0.001 HIS E 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (19666) covalent geometry : angle 0.53526 / 0.31 (27531) hydrogen bonds : bond 0.04990 / 3.19 ( 857) hydrogen bonds : angle 4.61573 / 3.21 ( 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 177 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7642 (mm110) REVERT: A 78 ASP cc_start: 0.8118 (m-30) cc_final: 0.7843 (m-30) REVERT: A 407 GLU cc_start: 0.6871 (pm20) cc_final: 0.6396 (pm20) REVERT: E 116 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8761 (mm) REVERT: E 187 LYS cc_start: 0.8527 (mttm) cc_final: 0.7974 (mtmt) REVERT: E 486 MET cc_start: 0.4954 (OUTLIER) cc_final: 0.3671 (pmm) REVERT: I 24 ASP cc_start: 0.7887 (t0) cc_final: 0.7515 (t0) outliers start: 32 outliers final: 23 residues processed: 170 average time/residue: 0.9482 time to fit residues: 189.3650 Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 59 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 94 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 48 optimal weight: 0.0870 chunk 118 optimal weight: 4.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 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 = 0.4127 r_free = 0.4127 target = 0.188855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139054 restraints weight = 49198.184| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.73 r_work: 0.3156 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19666 Z= 0.154 Angle : 0.522 8.011 27531 Z= 0.302 Chirality : 0.040 0.229 3226 Planarity : 0.004 0.052 2668 Dihedral : 23.719 177.332 5141 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.11 % Allowed : 17.23 % Favored : 80.66 % 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: 1.14 (0.19), residues: 842 sheet: -0.21 (0.38), residues: 192 loop : -0.95 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 11 TYR 0.017 0.002 TYR I 273 PHE 0.030 0.001 PHE E 549 HIS 0.005 0.001 HIS E 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (19666) covalent geometry : angle 0.52244 / 0.30 (27531) hydrogen bonds : bond 0.04803 / 3.07 ( 857) hydrogen bonds : angle 4.54647 / 3.16 ( 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 185 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8047 (m-30) cc_final: 0.7764 (m-30) REVERT: A 407 GLU cc_start: 0.6848 (pm20) cc_final: 0.6437 (pm20) REVERT: E 116 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8765 (mm) REVERT: E 187 LYS cc_start: 0.8477 (mttm) cc_final: 0.7922 (mtmt) REVERT: E 216 MET cc_start: 0.9085 (mmp) cc_final: 0.8647 (mmt) REVERT: E 486 MET cc_start: 0.4946 (OUTLIER) cc_final: 0.3653 (pmm) REVERT: I 24 ASP cc_start: 0.7853 (t0) cc_final: 0.7479 (t0) outliers start: 33 outliers final: 24 residues processed: 177 average time/residue: 0.9901 time to fit residues: 206.2835 Evaluate side-chains 171 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 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 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 463 THR 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 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: 0.8980 chunk 50 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4128 r_free = 0.4128 target = 0.188836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140781 restraints weight = 49312.442| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.52 r_work: 0.3174 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.250 19666 Z= 0.211 Angle : 0.686 59.195 27531 Z= 0.415 Chirality : 0.042 0.506 3226 Planarity : 0.004 0.051 2668 Dihedral : 23.719 177.329 5141 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.02 % Favored : 91.93 % Rotamer: Outliers : 1.66 % Allowed : 17.80 % Favored : 80.54 % Cbeta Deviations : 0.06 % 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: 1.14 (0.19), residues: 842 sheet: -0.21 (0.38), residues: 192 loop : -0.95 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 11 TYR 0.015 0.002 TYR I 273 PHE 0.020 0.001 PHE E 549 HIS 0.004 0.001 HIS E 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (19666) covalent geometry : angle 0.68612 / 0.41 (27531) hydrogen bonds : bond 0.04810 / 3.08 ( 857) hydrogen bonds : angle 4.54703 / 3.16 ( 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 170 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8053 (m-30) cc_final: 0.7769 (m-30) REVERT: A 407 GLU cc_start: 0.6888 (pm20) cc_final: 0.6435 (pm20) REVERT: E 116 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8757 (mm) REVERT: E 187 LYS cc_start: 0.8482 (mttm) cc_final: 0.7939 (mtmt) REVERT: E 216 MET cc_start: 0.9062 (mmp) cc_final: 0.8619 (mmt) REVERT: E 486 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.3675 (pmm) REVERT: I 24 ASP cc_start: 0.7844 (t0) cc_final: 0.7475 (t0) outliers start: 26 outliers final: 24 residues processed: 164 average time/residue: 1.0021 time to fit residues: 193.2688 Evaluate side-chains 170 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS 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 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 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 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 463 THR 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 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: 7.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4127 r_free = 0.4127 target = 0.188826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142349 restraints weight = 49150.451| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.41 r_work: 0.3179 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.250 19666 Z= 0.211 Angle : 0.686 59.195 27531 Z= 0.415 Chirality : 0.042 0.506 3226 Planarity : 0.004 0.051 2668 Dihedral : 23.719 177.329 5141 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.02 % Favored : 91.93 % Rotamer: Outliers : 1.66 % Allowed : 17.80 % Favored : 80.54 % Cbeta Deviations : 0.06 % 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: 1.14 (0.19), residues: 842 sheet: -0.21 (0.38), residues: 192 loop : -0.95 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 11 TYR 0.015 0.002 TYR I 273 PHE 0.020 0.001 PHE E 549 HIS 0.004 0.001 HIS E 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (19666) covalent geometry : angle 0.68612 / 0.41 (27531) hydrogen bonds : bond 0.04810 / 3.08 ( 857) hydrogen bonds : angle 4.54703 / 3.16 ( 2316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12438.03 seconds wall clock time: 211 minutes 11.28 seconds (12671.28 seconds total)