Starting phenix.real_space_refine on Mon May 26 19:16:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xuq_38680/05_2025/8xuq_38680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xuq_38680/05_2025/8xuq_38680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xuq_38680/05_2025/8xuq_38680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xuq_38680/05_2025/8xuq_38680.map" model { file = "/net/cci-nas-00/data/ceres_data/8xuq_38680/05_2025/8xuq_38680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xuq_38680/05_2025/8xuq_38680.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.021 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 C 18240 2.51 5 N 4968 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28736 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7121 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 847} Chain: "E" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7121 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 847} Chain: "F" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7121 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 847} Chain: "G" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7121 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 847} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.88, per 1000 atoms: 0.59 Number of scatterers: 28736 At special positions: 0 Unit cell: (195.5, 198.9, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 P 32 15.00 O 5368 8.00 N 4968 7.00 C 18240 6.00 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: 6.64 Conformation dependent library (CDL) restraints added in 3.3 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6776 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 29 sheets defined 49.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 1 through 20 removed outlier: 4.364A pdb=" N ALA A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 51 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.530A pdb=" N ARG A 60 " --> pdb=" O ASN A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 91 Processing helix chain 'A' and resid 101 through 127 removed outlier: 3.818A pdb=" N ILE A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 4.227A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 199 through 206 removed outlier: 3.546A pdb=" N GLY A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 4.002A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.139A pdb=" N GLY A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 269 through 277 removed outlier: 3.543A pdb=" N TRP A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.888A pdb=" N ALA A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 335 through 346 Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 366 through 380 removed outlier: 3.705A pdb=" N GLU A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 400 removed outlier: 3.571A pdb=" N LEU A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 400 " --> pdb=" O MET A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.676A pdb=" N ALA A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 695 through 701 removed outlier: 4.513A pdb=" N LEU A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.725A pdb=" N LEU A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 766 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 removed outlier: 3.683A pdb=" N ILE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 869 Processing helix chain 'E' and resid 2 through 20 Processing helix chain 'E' and resid 22 through 26 removed outlier: 4.524A pdb=" N GLY E 26 " --> pdb=" O LEU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 51 removed outlier: 3.734A pdb=" N CYS E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 Processing helix chain 'E' and resid 56 through 64 removed outlier: 3.596A pdb=" N ARG E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 91 Processing helix chain 'E' and resid 97 through 127 removed outlier: 3.538A pdb=" N LYS E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG E 103 " --> pdb=" O PRO E 99 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG E 122 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 188 through 198 Processing helix chain 'E' and resid 199 through 206 Processing helix chain 'E' and resid 219 through 232 removed outlier: 3.539A pdb=" N LEU E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE E 231 " --> pdb=" O ILE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.548A pdb=" N MET E 241 " --> pdb=" O TYR E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 257 Processing helix chain 'E' and resid 269 through 277 removed outlier: 3.556A pdb=" N TRP E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.991A pdb=" N ALA E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 347 removed outlier: 3.511A pdb=" N LYS E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 364 Processing helix chain 'E' and resid 366 through 381 Processing helix chain 'E' and resid 387 through 400 removed outlier: 4.235A pdb=" N ARG E 400 " --> pdb=" O MET E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 413 Processing helix chain 'E' and resid 423 through 434 Processing helix chain 'E' and resid 443 through 458 Processing helix chain 'E' and resid 478 through 492 Processing helix chain 'E' and resid 509 through 514 Processing helix chain 'E' and resid 525 through 530 Processing helix chain 'E' and resid 557 through 563 Processing helix chain 'E' and resid 580 through 585 removed outlier: 3.682A pdb=" N TYR E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 609 Processing helix chain 'E' and resid 672 through 676 Processing helix chain 'E' and resid 677 through 683 Processing helix chain 'E' and resid 695 through 701 removed outlier: 4.254A pdb=" N LEU E 699 " --> pdb=" O LYS E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 711 Processing helix chain 'E' and resid 712 through 714 No H-bonds generated for 'chain 'E' and resid 712 through 714' Processing helix chain 'E' and resid 759 through 766 removed outlier: 3.743A pdb=" N LEU E 763 " --> pdb=" O ASP E 759 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 766 " --> pdb=" O ILE E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 836 Processing helix chain 'E' and resid 849 through 869 Processing helix chain 'F' and resid 2 through 20 Processing helix chain 'F' and resid 27 through 51 removed outlier: 3.595A pdb=" N CYS F 51 " --> pdb=" O GLN F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 64 removed outlier: 3.809A pdb=" N ARG F 60 " --> pdb=" O ASN F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 91 removed outlier: 3.524A pdb=" N VAL F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 125 Processing helix chain 'F' and resid 129 through 135 Processing helix chain 'F' and resid 158 through 169 Processing helix chain 'F' and resid 188 through 198 removed outlier: 3.655A pdb=" N LYS F 198 " --> pdb=" O ASN F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 206 Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.843A pdb=" N PHE F 231 " --> pdb=" O ILE F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 257 removed outlier: 3.619A pdb=" N GLY F 257 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 removed outlier: 3.983A pdb=" N TRP F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 296 through 303 Processing helix chain 'F' and resid 313 through 327 Processing helix chain 'F' and resid 332 through 334 No H-bonds generated for 'chain 'F' and resid 332 through 334' Processing helix chain 'F' and resid 335 through 346 Processing helix chain 'F' and resid 349 through 364 Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 400 removed outlier: 3.792A pdb=" N ASN F 391 " --> pdb=" O PRO F 387 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG F 400 " --> pdb=" O MET F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 410 Processing helix chain 'F' and resid 423 through 433 Processing helix chain 'F' and resid 443 through 459 Processing helix chain 'F' and resid 478 through 492 Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.962A pdb=" N THR F 515 " --> pdb=" O ARG F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 531 Processing helix chain 'F' and resid 552 through 556 removed outlier: 3.666A pdb=" N ILE F 556 " --> pdb=" O SER F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 603 through 609 Processing helix chain 'F' and resid 629 through 633 Processing helix chain 'F' and resid 672 through 676 Processing helix chain 'F' and resid 677 through 683 removed outlier: 3.593A pdb=" N PHE F 681 " --> pdb=" O THR F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 701 Processing helix chain 'F' and resid 706 through 711 Processing helix chain 'F' and resid 712 through 714 No H-bonds generated for 'chain 'F' and resid 712 through 714' Processing helix chain 'F' and resid 737 through 741 Processing helix chain 'F' and resid 756 through 758 No H-bonds generated for 'chain 'F' and resid 756 through 758' Processing helix chain 'F' and resid 759 through 766 removed outlier: 3.539A pdb=" N LEU F 763 " --> pdb=" O ASP F 759 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 766 " --> pdb=" O ILE F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 831 through 837 Processing helix chain 'F' and resid 849 through 869 Processing helix chain 'G' and resid 2 through 20 Processing helix chain 'G' and resid 27 through 51 removed outlier: 3.766A pdb=" N CYS G 51 " --> pdb=" O GLN G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 64 removed outlier: 3.684A pdb=" N ARG G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 91 removed outlier: 3.709A pdb=" N VAL G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 126 removed outlier: 3.661A pdb=" N LYS G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG G 103 " --> pdb=" O PRO G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 135 removed outlier: 3.716A pdb=" N ASP G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 169 Processing helix chain 'G' and resid 188 through 197 Processing helix chain 'G' and resid 199 through 206 Processing helix chain 'G' and resid 219 through 232 removed outlier: 4.021A pdb=" N LYS G 230 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE G 231 " --> pdb=" O ILE G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 257 removed outlier: 3.742A pdb=" N GLY G 257 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 278 removed outlier: 3.985A pdb=" N TRP G 273 " --> pdb=" O SER G 269 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 303 Processing helix chain 'G' and resid 313 through 327 Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 346 Processing helix chain 'G' and resid 349 through 364 Processing helix chain 'G' and resid 366 through 381 Processing helix chain 'G' and resid 387 through 400 removed outlier: 3.834A pdb=" N ASN G 391 " --> pdb=" O PRO G 387 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG G 400 " --> pdb=" O MET G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 410 removed outlier: 4.534A pdb=" N CYS G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 410 " --> pdb=" O LYS G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 415 Processing helix chain 'G' and resid 423 through 433 Processing helix chain 'G' and resid 443 through 458 removed outlier: 3.613A pdb=" N ARG G 458 " --> pdb=" O ASP G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 492 Processing helix chain 'G' and resid 509 through 515 removed outlier: 3.798A pdb=" N THR G 515 " --> pdb=" O ARG G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 531 Processing helix chain 'G' and resid 552 through 556 removed outlier: 3.860A pdb=" N ILE G 556 " --> pdb=" O SER G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 563 Processing helix chain 'G' and resid 580 through 586 Processing helix chain 'G' and resid 603 through 609 removed outlier: 3.525A pdb=" N LEU G 609 " --> pdb=" O MET G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 629 through 633 Processing helix chain 'G' and resid 672 through 676 Processing helix chain 'G' and resid 677 through 683 Processing helix chain 'G' and resid 696 through 701 Processing helix chain 'G' and resid 706 through 713 removed outlier: 3.905A pdb=" N ARG G 713 " --> pdb=" O LYS G 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 741 Processing helix chain 'G' and resid 756 through 758 No H-bonds generated for 'chain 'G' and resid 756 through 758' Processing helix chain 'G' and resid 759 through 766 removed outlier: 3.729A pdb=" N LEU G 763 " --> pdb=" O ASP G 759 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 766 " --> pdb=" O ILE G 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 833 through 837 Processing helix chain 'G' and resid 849 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 179 removed outlier: 6.416A pdb=" N GLU A 177 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU A 291 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 179 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR A 260 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU A 290 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 262 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 removed outlier: 3.713A pdb=" N VAL A 182 " --> pdb=" O HIS A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.566A pdb=" N GLU A 465 " --> pdb=" O LYS A 473 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 475 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 463 " --> pdb=" O CYS A 475 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 removed outlier: 7.002A pdb=" N GLN A 497 " --> pdb=" O CYS A 520 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 550 removed outlier: 6.566A pdb=" N ILE A 549 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 569 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N SER A 595 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N VAL A 571 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 601 through 602 removed outlier: 7.413A pdb=" N LEU A 624 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 668 through 671 removed outlier: 5.741A pdb=" N SER A 669 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 691 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU A 690 " --> pdb=" O LYS A 721 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE A 723 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 692 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 748 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS A 775 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 750 " --> pdb=" O LYS A 775 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU A 796 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 822 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A 798 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU A 819 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 756 removed outlier: 5.324A pdb=" N LEU A 755 " --> pdb=" O SER A 780 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AB1, first strand: chain 'E' and resid 177 through 179 removed outlier: 6.432A pdb=" N GLU E 177 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU E 291 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL E 179 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR E 293 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR E 260 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU E 290 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL E 262 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR E 292 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU E 264 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 181 through 182 removed outlier: 3.501A pdb=" N VAL E 182 " --> pdb=" O HIS E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.653A pdb=" N ILE E 472 " --> pdb=" O ARG E 466 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG E 466 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR E 474 " --> pdb=" O MET E 464 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 497 through 498 removed outlier: 6.439A pdb=" N LEU E 519 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 549 through 550 removed outlier: 6.637A pdb=" N ILE E 549 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 569 " --> pdb=" O ALA E 593 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N SER E 595 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N VAL E 571 " --> pdb=" O SER E 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 601 through 602 removed outlier: 7.235A pdb=" N LEU E 624 " --> pdb=" O LYS E 646 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 667 through 671 removed outlier: 6.899A pdb=" N LYS E 689 " --> pdb=" O THR E 667 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER E 669 " --> pdb=" O LYS E 689 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY E 691 " --> pdb=" O SER E 669 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU E 690 " --> pdb=" O LYS E 721 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE E 723 " --> pdb=" O LEU E 690 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE E 692 " --> pdb=" O ILE E 723 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU E 748 " --> pdb=" O LYS E 773 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS E 775 " --> pdb=" O LEU E 748 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU E 750 " --> pdb=" O LYS E 775 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU E 796 " --> pdb=" O VAL E 820 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE E 822 " --> pdb=" O LEU E 796 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE E 798 " --> pdb=" O ILE E 822 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU E 819 " --> pdb=" O MET E 844 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLN E 846 " --> pdb=" O LEU E 819 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU E 821 " --> pdb=" O GLN E 846 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 755 through 756 removed outlier: 5.521A pdb=" N LEU E 755 " --> pdb=" O SER E 780 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 783 through 785 Processing sheet with id=AC1, first strand: chain 'F' and resid 208 through 213 removed outlier: 4.929A pdb=" N TYR F 260 " --> pdb=" O PRO F 286 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG F 288 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N HIS F 175 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL F 289 " --> pdb=" O HIS F 175 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU F 177 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU F 291 " --> pdb=" O GLU F 177 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL F 179 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR F 293 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL F 181 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N HIS F 307 " --> pdb=" O VAL F 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.689A pdb=" N THR F 474 " --> pdb=" O MET F 464 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 497 through 498 removed outlier: 5.951A pdb=" N GLN F 497 " --> pdb=" O CYS F 520 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE F 541 " --> pdb=" O ASP F 570 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU F 572 " --> pdb=" O PHE F 541 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N SER F 543 " --> pdb=" O GLU F 572 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE F 574 " --> pdb=" O SER F 543 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER F 595 " --> pdb=" O VAL F 571 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N SER F 573 " --> pdb=" O SER F 595 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN F 618 " --> pdb=" O PHE F 594 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE F 615 " --> pdb=" O HIS F 640 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 639 " --> pdb=" O THR F 667 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER F 669 " --> pdb=" O LEU F 639 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 691 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG F 693 " --> pdb=" O THR F 670 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU F 796 " --> pdb=" O VAL F 820 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE F 822 " --> pdb=" O LEU F 796 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 798 " --> pdb=" O ILE F 822 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU F 819 " --> pdb=" O MET F 844 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN F 846 " --> pdb=" O LEU F 819 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU F 821 " --> pdb=" O GLN F 846 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 601 through 602 removed outlier: 4.175A pdb=" N LEU F 624 " --> pdb=" O SER F 644 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 783 through 785 Processing sheet with id=AC6, first strand: chain 'G' and resid 210 through 213 removed outlier: 5.890A pdb=" N HIS G 175 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL G 289 " --> pdb=" O HIS G 175 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU G 177 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU G 291 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G 179 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR G 293 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL G 181 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 421 through 422 removed outlier: 7.044A pdb=" N ILE G 472 " --> pdb=" O ARG G 466 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG G 466 " --> pdb=" O ILE G 472 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR G 474 " --> pdb=" O MET G 464 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 497 through 498 removed outlier: 6.140A pdb=" N GLN G 497 " --> pdb=" O CYS G 520 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU G 572 " --> pdb=" O SER G 543 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE G 549 " --> pdb=" O ASN G 575 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 497 through 498 removed outlier: 6.140A pdb=" N GLN G 497 " --> pdb=" O CYS G 520 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU G 572 " --> pdb=" O SER G 543 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER G 595 " --> pdb=" O VAL G 571 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N SER G 573 " --> pdb=" O SER G 595 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL G 592 " --> pdb=" O ILE G 616 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ASN G 618 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE G 594 " --> pdb=" O ASN G 618 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE G 615 " --> pdb=" O HIS G 640 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N LEU G 639 " --> pdb=" O SER G 669 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE G 671 " --> pdb=" O LEU G 639 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N THR G 641 " --> pdb=" O ILE G 671 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY G 691 " --> pdb=" O LEU G 668 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 670 " --> pdb=" O GLY G 691 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG G 693 " --> pdb=" O THR G 670 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU G 796 " --> pdb=" O VAL G 820 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE G 822 " --> pdb=" O LEU G 796 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE G 798 " --> pdb=" O ILE G 822 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU G 819 " --> pdb=" O MET G 844 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLN G 846 " --> pdb=" O LEU G 819 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU G 821 " --> pdb=" O GLN G 846 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 879 " --> pdb=" O MET G 843 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 601 through 602 Processing sheet with id=AD2, first strand: chain 'G' and resid 783 through 785 removed outlier: 6.626A pdb=" N TRP G 784 " --> pdb=" O LYS G 807 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 1235 hydrogen bonds defined for protein. 3492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.01 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4971 1.32 - 1.44: 7051 1.44 - 1.57: 17049 1.57 - 1.69: 37 1.69 - 1.81: 192 Bond restraints: 29300 Sorted by residual: bond pdb=" N LYS F 259 " pdb=" CA LYS F 259 " ideal model delta sigma weight residual 1.455 1.501 -0.046 1.27e-02 6.20e+03 1.32e+01 bond pdb=" N ARG A 384 " pdb=" CA ARG A 384 " ideal model delta sigma weight residual 1.461 1.496 -0.035 9.70e-03 1.06e+04 1.30e+01 bond pdb=" N VAL G 179 " pdb=" CA VAL G 179 " ideal model delta sigma weight residual 1.457 1.490 -0.032 9.00e-03 1.23e+04 1.30e+01 bond pdb=" N VAL F 182 " pdb=" CA VAL F 182 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.19e-02 7.06e+03 1.07e+01 ... (remaining 29295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 38100 2.08 - 4.17: 1307 4.17 - 6.25: 173 6.25 - 8.34: 46 8.34 - 10.42: 14 Bond angle restraints: 39640 Sorted by residual: angle pdb=" N SER F 468 " pdb=" CA SER F 468 " pdb=" C SER F 468 " ideal model delta sigma weight residual 111.28 102.36 8.92 1.09e+00 8.42e-01 6.70e+01 angle pdb=" N ILE E 66 " pdb=" CA ILE E 66 " pdb=" C ILE E 66 " ideal model delta sigma weight residual 110.72 103.16 7.56 1.01e+00 9.80e-01 5.60e+01 angle pdb=" N PRO G 147 " pdb=" CA PRO G 147 " pdb=" C PRO G 147 " ideal model delta sigma weight residual 110.70 101.83 8.87 1.22e+00 6.72e-01 5.28e+01 angle pdb=" N SER G 468 " pdb=" CA SER G 468 " pdb=" C SER G 468 " ideal model delta sigma weight residual 111.28 104.67 6.61 1.09e+00 8.42e-01 3.67e+01 angle pdb=" CA LYS F 64 " pdb=" C LYS F 64 " pdb=" O LYS F 64 " ideal model delta sigma weight residual 121.55 115.49 6.06 1.06e+00 8.90e-01 3.26e+01 ... (remaining 39635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 17122 31.79 - 63.59: 848 63.59 - 95.38: 70 95.38 - 127.17: 32 127.17 - 158.97: 16 Dihedral angle restraints: 18088 sinusoidal: 7704 harmonic: 10384 Sorted by residual: dihedral pdb=" O1B ADP G 902 " pdb=" O3A ADP G 902 " pdb=" PB ADP G 902 " pdb=" PA ADP G 902 " ideal model delta sinusoidal sigma weight residual -60.00 98.96 -158.97 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C2' ADP A 902 " pdb=" C1' ADP A 902 " pdb=" N9 ADP A 902 " pdb=" C4 ADP A 902 " ideal model delta sinusoidal sigma weight residual 91.55 -66.44 157.99 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C2' ADP G 902 " pdb=" C1' ADP G 902 " pdb=" N9 ADP G 902 " pdb=" C4 ADP G 902 " ideal model delta sinusoidal sigma weight residual 91.55 -56.70 148.25 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 18085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 4458 1.014 - 2.028: 0 2.028 - 3.041: 0 3.041 - 4.055: 0 4.055 - 5.069: 14 Chirality restraints: 4472 Sorted by residual: chirality pdb=" C2 IHP F 901 " pdb=" C1 IHP F 901 " pdb=" C3 IHP F 901 " pdb=" O12 IHP F 901 " both_signs ideal model delta sigma weight residual False -2.52 2.55 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C2 IHP G 901 " pdb=" C1 IHP G 901 " pdb=" C3 IHP G 901 " pdb=" O12 IHP G 901 " both_signs ideal model delta sigma weight residual False -2.52 2.54 -5.06 2.00e-01 2.50e+01 6.41e+02 chirality pdb=" C4 IHP F 901 " pdb=" C3 IHP F 901 " pdb=" C5 IHP F 901 " pdb=" O14 IHP F 901 " both_signs ideal model delta sigma weight residual False 2.48 -2.58 5.06 2.00e-01 2.50e+01 6.40e+02 ... (remaining 4469 not shown) Planarity restraints: 5012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 257 " -0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY F 257 " 0.073 2.00e-02 2.50e+03 pdb=" O GLY F 257 " -0.027 2.00e-02 2.50e+03 pdb=" N GLY F 258 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 195 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LYS F 195 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS F 195 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE F 196 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 805 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C SER G 805 " 0.054 2.00e-02 2.50e+03 pdb=" O SER G 805 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP G 806 " -0.019 2.00e-02 2.50e+03 ... (remaining 5009 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1496 2.72 - 3.26: 30972 3.26 - 3.81: 46281 3.81 - 4.35: 57817 4.35 - 4.90: 94641 Nonbonded interactions: 231207 Sorted by model distance: nonbonded pdb=" N GLU A 756 " pdb=" OE1 GLU A 756 " model vdw 2.174 3.120 nonbonded pdb=" N GLU G 572 " pdb=" OE1 GLU G 572 " model vdw 2.177 3.120 nonbonded pdb=" N GLU E 767 " pdb=" OE1 GLU E 767 " model vdw 2.194 3.120 nonbonded pdb=" OH TYR E 411 " pdb=" OE2 GLU E 433 " model vdw 2.195 3.040 nonbonded pdb=" N GLU E 782 " pdb=" OE1 GLU E 782 " model vdw 2.195 3.120 ... (remaining 231202 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.930 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: 0.020 Extract box with map and model: 1.330 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 60.790 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 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 0.060 29300 Z= 0.267 Angle : 0.889 10.424 39640 Z= 0.523 Chirality : 0.279 5.069 4472 Planarity : 0.006 0.076 5012 Dihedral : 19.140 158.968 11312 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.07 % Allowed : 21.46 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3532 helix: 0.37 (0.13), residues: 1476 sheet: -1.29 (0.25), residues: 440 loop : -1.13 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 318 HIS 0.008 0.001 HIS E 537 PHE 0.026 0.002 PHE A 41 TYR 0.046 0.002 TYR F 101 ARG 0.019 0.001 ARG G 486 Details of bonding type rmsd hydrogen bonds : bond 0.17490 ( 1229) hydrogen bonds : angle 6.92333 ( 3492) covalent geometry : bond 0.00446 (29300) covalent geometry : angle 0.88863 (39640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 320 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.4675 (p90) cc_final: 0.4466 (p90) REVERT: A 115 ARG cc_start: 0.6136 (ttt180) cc_final: 0.5926 (ttp80) REVERT: A 158 PHE cc_start: 0.7031 (m-80) cc_final: 0.6759 (m-80) REVERT: A 223 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6934 (tp) REVERT: A 303 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6423 (m-40) REVERT: A 523 SER cc_start: 0.7024 (p) cc_final: 0.6758 (m) REVERT: E 158 PHE cc_start: 0.6971 (m-80) cc_final: 0.6718 (m-10) REVERT: E 480 MET cc_start: 0.8307 (mmm) cc_final: 0.7915 (mmm) REVERT: E 885 LEU cc_start: 0.4546 (OUTLIER) cc_final: 0.4188 (mm) REVERT: F 747 LYS cc_start: 0.5233 (ttpp) cc_final: 0.5016 (mptt) REVERT: G 320 LEU cc_start: 0.4765 (tp) cc_final: 0.4104 (mt) REVERT: G 424 TRP cc_start: 0.6267 (p-90) cc_final: 0.5864 (p-90) REVERT: G 453 ASN cc_start: 0.6883 (t0) cc_final: 0.6540 (m-40) REVERT: G 490 MET cc_start: 0.5940 (ptt) cc_final: 0.5729 (ptm) REVERT: G 501 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.4477 (mp) REVERT: G 558 THR cc_start: 0.6008 (p) cc_final: 0.4677 (m) outliers start: 34 outliers final: 11 residues processed: 344 average time/residue: 0.4217 time to fit residues: 228.9335 Evaluate side-chains 274 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 643 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 469 ASP Chi-restraints excluded: chain G residue 501 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 179 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 319 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 234 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS A 818 HIS E 39 ASN E 52 HIS ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS E 478 HIS E 505 GLN E 777 ASN E 841 GLN F 116 ASN F 174 ASN ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 391 ASN G 710 ASN G 873 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.244793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.208160 restraints weight = 51100.496| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 3.90 r_work: 0.4010 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 29300 Z= 0.248 Angle : 0.845 16.073 39640 Z= 0.408 Chirality : 0.052 0.836 4472 Planarity : 0.006 0.051 5012 Dihedral : 12.764 153.816 4041 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.76 % Allowed : 19.79 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3532 helix: 0.40 (0.13), residues: 1508 sheet: -1.12 (0.25), residues: 456 loop : -1.07 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 754 HIS 0.009 0.002 HIS E 307 PHE 0.021 0.002 PHE E 779 TYR 0.021 0.003 TYR A 197 ARG 0.008 0.001 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05590 ( 1229) hydrogen bonds : angle 5.87043 ( 3492) covalent geometry : bond 0.00578 (29300) covalent geometry : angle 0.84511 (39640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 304 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.6416 (ttt180) cc_final: 0.6130 (ttp80) REVERT: A 223 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7393 (tp) REVERT: A 241 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5415 (ptp) REVERT: A 242 CYS cc_start: 0.6360 (OUTLIER) cc_final: 0.5902 (t) REVERT: A 523 SER cc_start: 0.7176 (p) cc_final: 0.6962 (m) REVERT: A 776 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: E 159 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6521 (m-30) REVERT: E 776 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.6831 (tm-30) REVERT: E 807 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7181 (ptpp) REVERT: E 885 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.4402 (mm) REVERT: F 198 LYS cc_start: 0.6298 (pttp) cc_final: 0.5409 (tptp) REVERT: F 206 PHE cc_start: 0.1831 (m-80) cc_final: 0.1508 (m-80) REVERT: F 291 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4543 (tt) REVERT: F 318 TRP cc_start: 0.3916 (t60) cc_final: 0.3651 (t60) REVERT: F 588 HIS cc_start: 0.4793 (m90) cc_final: 0.4134 (m170) REVERT: F 747 LYS cc_start: 0.4928 (ttpp) cc_final: 0.4692 (mptt) REVERT: F 819 LEU cc_start: 0.7065 (tt) cc_final: 0.6584 (tt) REVERT: G 320 LEU cc_start: 0.4883 (tp) cc_final: 0.4291 (mt) REVERT: G 410 LEU cc_start: 0.4025 (OUTLIER) cc_final: 0.3632 (mt) REVERT: G 428 ARG cc_start: 0.3572 (mpt180) cc_final: 0.3333 (mpt-90) REVERT: G 469 ASP cc_start: 0.3613 (OUTLIER) cc_final: 0.2897 (t70) REVERT: G 481 LEU cc_start: 0.5456 (mt) cc_final: 0.5168 (mt) REVERT: G 501 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.4127 (mp) REVERT: G 532 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7469 (mmmt) REVERT: G 799 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7690 (mt-10) REVERT: G 873 ASN cc_start: 0.1284 (OUTLIER) cc_final: -0.1372 (p0) outliers start: 120 outliers final: 55 residues processed: 400 average time/residue: 0.3960 time to fit residues: 252.6870 Evaluate side-chains 319 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 643 SER Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 725 ASP Chi-restraints excluded: chain E residue 743 THR Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 804 VAL Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 585 GLN Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 469 ASP Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain G residue 664 SER Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 873 ASN Chi-restraints excluded: chain G residue 878 LEU Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 174 optimal weight: 5.9990 chunk 318 optimal weight: 0.2980 chunk 205 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 325 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 380 HIS ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 HIS ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 ASN F 710 ASN F 873 ASN ** G 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 846 GLN G 873 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.247543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.195435 restraints weight = 52032.255| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 4.33 r_work: 0.4041 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29300 Z= 0.134 Angle : 0.651 10.741 39640 Z= 0.319 Chirality : 0.045 0.617 4472 Planarity : 0.004 0.050 5012 Dihedral : 11.778 150.699 4031 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 2.89 % Allowed : 21.33 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3532 helix: 0.86 (0.13), residues: 1504 sheet: -0.76 (0.25), residues: 456 loop : -0.77 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 430 HIS 0.006 0.001 HIS G 638 PHE 0.018 0.001 PHE A 80 TYR 0.014 0.002 TYR F 101 ARG 0.007 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 1229) hydrogen bonds : angle 5.35700 ( 3492) covalent geometry : bond 0.00294 (29300) covalent geometry : angle 0.65135 (39640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 286 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8394 (t0) cc_final: 0.7997 (t0) REVERT: A 45 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7285 (mm) REVERT: A 104 VAL cc_start: 0.3893 (OUTLIER) cc_final: 0.3660 (t) REVERT: A 223 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7264 (tp) REVERT: A 523 SER cc_start: 0.7148 (p) cc_final: 0.6944 (m) REVERT: E 137 LEU cc_start: -0.0179 (OUTLIER) cc_final: -0.0500 (mp) REVERT: E 860 GLN cc_start: 0.7456 (tm-30) cc_final: 0.7127 (tt0) REVERT: E 885 LEU cc_start: 0.4836 (OUTLIER) cc_final: 0.4530 (mm) REVERT: F 15 GLN cc_start: 0.2722 (OUTLIER) cc_final: 0.2208 (mm-40) REVERT: F 198 LYS cc_start: 0.6145 (pttp) cc_final: 0.5159 (tptp) REVERT: F 206 PHE cc_start: 0.1495 (m-80) cc_final: 0.1259 (m-80) REVERT: F 320 LEU cc_start: 0.4703 (OUTLIER) cc_final: 0.4426 (mt) REVERT: F 354 VAL cc_start: 0.7845 (t) cc_final: 0.7590 (m) REVERT: F 410 LEU cc_start: 0.5478 (mm) cc_final: 0.4873 (mt) REVERT: F 588 HIS cc_start: 0.4818 (m90) cc_final: 0.4116 (m170) REVERT: F 634 GLU cc_start: 0.2282 (pm20) cc_final: 0.1706 (mm-30) REVERT: F 747 LYS cc_start: 0.4965 (ttpp) cc_final: 0.4742 (mmtm) REVERT: F 772 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6699 (mp) REVERT: G 320 LEU cc_start: 0.5030 (tp) cc_final: 0.4327 (mt) REVERT: G 381 LEU cc_start: 0.0991 (OUTLIER) cc_final: 0.0694 (mm) REVERT: G 501 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4519 (mp) REVERT: G 532 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7360 (mmmt) REVERT: G 558 THR cc_start: 0.5836 (p) cc_final: 0.4133 (m) REVERT: G 799 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7652 (mt-10) REVERT: G 822 ILE cc_start: 0.5713 (mm) cc_final: 0.5494 (mm) outliers start: 92 outliers final: 42 residues processed: 359 average time/residue: 0.3973 time to fit residues: 229.5483 Evaluate side-chains 304 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 848 SER Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 583 PHE Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 583 PHE Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.0770 chunk 140 optimal weight: 3.9990 chunk 312 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 259 optimal weight: 0.5980 overall best weight: 2.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN A 777 ASN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 GLN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.244296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.190672 restraints weight = 50854.093| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 4.36 r_work: 0.4017 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29300 Z= 0.176 Angle : 0.673 9.446 39640 Z= 0.332 Chirality : 0.046 0.546 4472 Planarity : 0.005 0.055 5012 Dihedral : 11.313 152.378 4028 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 4.23 % Allowed : 20.80 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3532 helix: 0.74 (0.13), residues: 1532 sheet: -0.99 (0.25), residues: 480 loop : -0.82 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 754 HIS 0.008 0.001 HIS A 100 PHE 0.015 0.002 PHE G 409 TYR 0.020 0.002 TYR A 591 ARG 0.007 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1229) hydrogen bonds : angle 5.36945 ( 3492) covalent geometry : bond 0.00415 (29300) covalent geometry : angle 0.67264 (39640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 271 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6986 (mm) REVERT: A 223 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7323 (tp) REVERT: A 523 SER cc_start: 0.7298 (p) cc_final: 0.7065 (m) REVERT: E 137 LEU cc_start: -0.0208 (OUTLIER) cc_final: -0.0502 (mp) REVERT: E 501 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7636 (tp) REVERT: E 776 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: E 860 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7200 (tt0) REVERT: E 885 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4513 (mm) REVERT: F 15 GLN cc_start: 0.2492 (OUTLIER) cc_final: 0.2053 (mm-40) REVERT: F 291 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.4957 (tt) REVERT: F 320 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4546 (mt) REVERT: F 398 TYR cc_start: 0.6641 (t80) cc_final: 0.6350 (t80) REVERT: F 481 LEU cc_start: 0.5779 (mt) cc_final: 0.5436 (mt) REVERT: F 588 HIS cc_start: 0.4831 (m90) cc_final: 0.4217 (m170) REVERT: F 634 GLU cc_start: 0.2624 (pm20) cc_final: 0.1642 (mm-30) REVERT: F 747 LYS cc_start: 0.4827 (ttpp) cc_final: 0.4505 (mptt) REVERT: G 1 MET cc_start: 0.4460 (mmp) cc_final: 0.4201 (mmm) REVERT: G 265 ASP cc_start: 0.5335 (t0) cc_final: 0.5101 (t0) REVERT: G 271 GLU cc_start: 0.6873 (pm20) cc_final: 0.6587 (mt-10) REVERT: G 291 LEU cc_start: 0.5057 (OUTLIER) cc_final: 0.2709 (tt) REVERT: G 320 LEU cc_start: 0.5076 (tp) cc_final: 0.4410 (mt) REVERT: G 381 LEU cc_start: 0.1301 (OUTLIER) cc_final: 0.1011 (mm) REVERT: G 501 LEU cc_start: 0.4797 (OUTLIER) cc_final: 0.4463 (mp) REVERT: G 532 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7343 (mmmt) outliers start: 135 outliers final: 75 residues processed: 384 average time/residue: 0.3700 time to fit residues: 229.0233 Evaluate side-chains 330 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 243 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 725 ASP Chi-restraints excluded: chain E residue 743 THR Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 848 SER Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 583 PHE Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ILE Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 583 PHE Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 112 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 346 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 HIS E 846 GLN G 234 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.246194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.199537 restraints weight = 50552.988| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 4.97 r_work: 0.4033 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29300 Z= 0.122 Angle : 0.626 10.245 39640 Z= 0.303 Chirality : 0.044 0.510 4472 Planarity : 0.004 0.050 5012 Dihedral : 10.941 152.913 4028 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 3.42 % Allowed : 21.55 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3532 helix: 0.85 (0.13), residues: 1556 sheet: -0.79 (0.25), residues: 476 loop : -0.67 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 430 HIS 0.005 0.001 HIS F 638 PHE 0.012 0.001 PHE A 80 TYR 0.014 0.001 TYR A 218 ARG 0.005 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 1229) hydrogen bonds : angle 5.11248 ( 3492) covalent geometry : bond 0.00275 (29300) covalent geometry : angle 0.62554 (39640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 268 time to evaluate : 3.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7329 (tp) REVERT: A 523 SER cc_start: 0.7174 (p) cc_final: 0.6931 (m) REVERT: A 696 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8074 (mm) REVERT: E 137 LEU cc_start: -0.0184 (OUTLIER) cc_final: -0.0410 (mp) REVERT: E 318 TRP cc_start: 0.7453 (t-100) cc_final: 0.6885 (t-100) REVERT: E 347 LYS cc_start: 0.8601 (mptt) cc_final: 0.8293 (tptp) REVERT: E 501 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7645 (tp) REVERT: E 687 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8510 (tt) REVERT: E 776 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6415 (tm-30) REVERT: E 807 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7127 (ptpp) REVERT: F 15 GLN cc_start: 0.2731 (OUTLIER) cc_final: 0.2181 (mm-40) REVERT: F 291 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5128 (tt) REVERT: F 482 HIS cc_start: 0.5623 (t-90) cc_final: 0.5343 (t70) REVERT: F 588 HIS cc_start: 0.4923 (m90) cc_final: 0.4219 (m170) REVERT: F 634 GLU cc_start: 0.2739 (pm20) cc_final: 0.1822 (mm-30) REVERT: F 747 LYS cc_start: 0.4775 (ttpp) cc_final: 0.4461 (mptt) REVERT: F 775 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7222 (mmtm) REVERT: G 1 MET cc_start: 0.4394 (mmp) cc_final: 0.4100 (mmm) REVERT: G 271 GLU cc_start: 0.6888 (pm20) cc_final: 0.6610 (mt-10) REVERT: G 291 LEU cc_start: 0.5012 (OUTLIER) cc_final: 0.2646 (tt) REVERT: G 320 LEU cc_start: 0.4923 (tp) cc_final: 0.4270 (mt) REVERT: G 381 LEU cc_start: 0.1118 (OUTLIER) cc_final: 0.0855 (mm) REVERT: G 532 LYS cc_start: 0.7625 (mmtt) cc_final: 0.7353 (mmmt) outliers start: 109 outliers final: 60 residues processed: 357 average time/residue: 0.3806 time to fit residues: 220.2870 Evaluate side-chains 316 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 244 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 695 LYS Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 725 ASP Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 848 SER Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 745 LEU Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 775 LYS Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 633 MET Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 745 LEU Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 878 LEU Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 207 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 338 optimal weight: 9.9990 chunk 315 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN E 52 HIS E 777 ASN E 846 GLN F 386 HIS ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.244061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.196031 restraints weight = 50359.533| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.89 r_work: 0.4027 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29300 Z= 0.148 Angle : 0.644 9.815 39640 Z= 0.315 Chirality : 0.045 0.488 4472 Planarity : 0.004 0.052 5012 Dihedral : 10.686 154.920 4022 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 3.80 % Allowed : 22.05 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3532 helix: 0.80 (0.13), residues: 1572 sheet: -0.83 (0.24), residues: 512 loop : -0.62 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 754 HIS 0.007 0.001 HIS F 818 PHE 0.028 0.001 PHE F 311 TYR 0.018 0.002 TYR E 591 ARG 0.007 0.000 ARG E 275 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1229) hydrogen bonds : angle 5.12694 ( 3492) covalent geometry : bond 0.00347 (29300) covalent geometry : angle 0.64432 (39640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 264 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7289 (tp) REVERT: E 137 LEU cc_start: 0.0127 (OUTLIER) cc_final: -0.0130 (mp) REVERT: E 347 LYS cc_start: 0.8618 (mptt) cc_final: 0.8327 (tptp) REVERT: E 501 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7686 (tp) REVERT: E 687 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8566 (tt) REVERT: E 776 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: E 807 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.6917 (ptpp) REVERT: F 15 GLN cc_start: 0.2659 (OUTLIER) cc_final: 0.2130 (mm-40) REVERT: F 291 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5425 (tt) REVERT: F 320 LEU cc_start: 0.4703 (OUTLIER) cc_final: 0.4435 (mt) REVERT: F 383 ASN cc_start: 0.4346 (m-40) cc_final: 0.4040 (m-40) REVERT: F 403 TYR cc_start: 0.3473 (p90) cc_final: 0.3266 (p90) REVERT: F 482 HIS cc_start: 0.5802 (t-90) cc_final: 0.5532 (t70) REVERT: F 588 HIS cc_start: 0.4965 (m90) cc_final: 0.4318 (m170) REVERT: F 747 LYS cc_start: 0.4743 (ttpp) cc_final: 0.4386 (mptt) REVERT: G 1 MET cc_start: 0.4365 (mmp) cc_final: 0.4157 (mmt) REVERT: G 252 GLU cc_start: 0.6558 (mm-30) cc_final: 0.5655 (tt0) REVERT: G 291 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.3106 (tt) REVERT: G 320 LEU cc_start: 0.4945 (tp) cc_final: 0.4341 (mt) REVERT: G 481 LEU cc_start: 0.5829 (mt) cc_final: 0.5489 (mt) REVERT: G 532 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7413 (mmmt) REVERT: G 822 ILE cc_start: 0.5654 (mm) cc_final: 0.5210 (mp) outliers start: 121 outliers final: 76 residues processed: 368 average time/residue: 0.3818 time to fit residues: 228.5443 Evaluate side-chains 319 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 233 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 695 LYS Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 725 ASP Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 799 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 848 SER Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 745 LEU Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 633 MET Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 745 LEU Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 846 GLN Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 HIS G 588 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.242845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.194458 restraints weight = 50054.598| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 4.43 r_work: 0.4004 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29300 Z= 0.151 Angle : 0.641 14.419 39640 Z= 0.313 Chirality : 0.045 0.488 4472 Planarity : 0.004 0.052 5012 Dihedral : 10.517 156.180 4022 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 3.61 % Allowed : 22.65 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3532 helix: 0.83 (0.13), residues: 1572 sheet: -0.86 (0.24), residues: 512 loop : -0.66 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 273 HIS 0.005 0.001 HIS F 818 PHE 0.024 0.001 PHE F 311 TYR 0.017 0.002 TYR E 591 ARG 0.004 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1229) hydrogen bonds : angle 5.08830 ( 3492) covalent geometry : bond 0.00353 (29300) covalent geometry : angle 0.64093 (39640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 252 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7309 (tp) REVERT: A 303 ASN cc_start: 0.6609 (OUTLIER) cc_final: 0.6306 (m-40) REVERT: A 696 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8139 (mm) REVERT: E 137 LEU cc_start: 0.0114 (OUTLIER) cc_final: -0.0137 (mp) REVERT: E 347 LYS cc_start: 0.8657 (mptt) cc_final: 0.8327 (tptp) REVERT: E 501 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7653 (tp) REVERT: E 776 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6447 (tm-30) REVERT: E 807 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7193 (ptpp) REVERT: E 829 GLU cc_start: 0.5371 (OUTLIER) cc_final: 0.4410 (pm20) REVERT: E 860 GLN cc_start: 0.7662 (tm-30) cc_final: 0.6530 (pt0) REVERT: F 15 GLN cc_start: 0.2612 (OUTLIER) cc_final: 0.2084 (mm-40) REVERT: F 291 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5761 (tt) REVERT: F 320 LEU cc_start: 0.4814 (OUTLIER) cc_final: 0.4561 (mt) REVERT: F 383 ASN cc_start: 0.4223 (m-40) cc_final: 0.3918 (m-40) REVERT: F 403 TYR cc_start: 0.3269 (p90) cc_final: 0.3044 (p90) REVERT: F 588 HIS cc_start: 0.4824 (m90) cc_final: 0.4149 (m170) REVERT: F 617 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7145 (tp) REVERT: F 747 LYS cc_start: 0.4786 (ttpp) cc_final: 0.4386 (mptt) REVERT: G 1 MET cc_start: 0.4374 (mmp) cc_final: 0.4114 (mmt) REVERT: G 252 GLU cc_start: 0.6613 (mm-30) cc_final: 0.5788 (tt0) REVERT: G 320 LEU cc_start: 0.4938 (tp) cc_final: 0.4320 (mt) REVERT: G 354 VAL cc_start: 0.7952 (p) cc_final: 0.7638 (m) REVERT: G 381 LEU cc_start: 0.1040 (OUTLIER) cc_final: 0.0835 (mm) REVERT: G 481 LEU cc_start: 0.5674 (mt) cc_final: 0.5368 (mt) REVERT: G 532 LYS cc_start: 0.7601 (mmtt) cc_final: 0.7380 (mmmt) outliers start: 115 outliers final: 78 residues processed: 351 average time/residue: 0.3834 time to fit residues: 216.0046 Evaluate side-chains 327 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 236 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 725 ASP Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 829 GLU Chi-restraints excluded: chain E residue 848 SER Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 220 ARG Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 617 ILE Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 745 LEU Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 633 MET Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 745 LEU Chi-restraints excluded: chain G residue 768 HIS Chi-restraints excluded: chain G residue 846 GLN Chi-restraints excluded: chain G residue 878 LEU Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 53 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 294 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 241 optimal weight: 0.3980 chunk 218 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 182 optimal weight: 0.0020 chunk 91 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 818 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.244802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.197258 restraints weight = 50615.036| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 4.00 r_work: 0.4045 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29300 Z= 0.108 Angle : 0.606 10.517 39640 Z= 0.292 Chirality : 0.043 0.482 4472 Planarity : 0.004 0.049 5012 Dihedral : 10.185 155.975 4022 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 2.54 % Allowed : 23.90 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3532 helix: 0.99 (0.13), residues: 1568 sheet: -0.64 (0.26), residues: 472 loop : -0.50 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 273 HIS 0.007 0.001 HIS F 482 PHE 0.023 0.001 PHE F 311 TYR 0.013 0.001 TYR A 438 ARG 0.006 0.000 ARG E 233 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 1229) hydrogen bonds : angle 4.83634 ( 3492) covalent geometry : bond 0.00238 (29300) covalent geometry : angle 0.60633 (39640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7170 (tp) REVERT: A 696 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8111 (mm) REVERT: E 137 LEU cc_start: 0.0257 (OUTLIER) cc_final: -0.0039 (mp) REVERT: E 347 LYS cc_start: 0.8612 (mptt) cc_final: 0.8331 (tptm) REVERT: E 501 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7653 (tp) REVERT: E 776 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6452 (tm-30) REVERT: E 807 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6820 (ptpp) REVERT: E 860 GLN cc_start: 0.7723 (tm-30) cc_final: 0.6659 (pt0) REVERT: F 15 GLN cc_start: 0.2816 (OUTLIER) cc_final: 0.2206 (mm-40) REVERT: F 19 ASP cc_start: 0.3354 (OUTLIER) cc_final: 0.2400 (t70) REVERT: F 291 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5722 (tt) REVERT: F 320 LEU cc_start: 0.4631 (OUTLIER) cc_final: 0.4369 (mt) REVERT: F 383 ASN cc_start: 0.4221 (m-40) cc_final: 0.3900 (m-40) REVERT: F 403 TYR cc_start: 0.3231 (p90) cc_final: 0.3001 (p90) REVERT: F 410 LEU cc_start: 0.4632 (OUTLIER) cc_final: 0.3431 (pp) REVERT: F 460 LEU cc_start: 0.5222 (mt) cc_final: 0.4936 (mp) REVERT: F 551 MET cc_start: 0.7298 (mmp) cc_final: 0.7078 (mmp) REVERT: F 588 HIS cc_start: 0.4729 (m90) cc_final: 0.4081 (m170) REVERT: F 617 ILE cc_start: 0.7490 (mt) cc_final: 0.7111 (tp) REVERT: G 1 MET cc_start: 0.4209 (mmp) cc_final: 0.3919 (mmt) REVERT: G 233 ARG cc_start: 0.7806 (mmt180) cc_final: 0.7294 (mmp-170) REVERT: G 252 GLU cc_start: 0.6571 (mm-30) cc_final: 0.5729 (tt0) REVERT: G 265 ASP cc_start: 0.6084 (t0) cc_final: 0.5854 (t0) REVERT: G 320 LEU cc_start: 0.4867 (tp) cc_final: 0.4304 (mt) REVERT: G 354 VAL cc_start: 0.7922 (p) cc_final: 0.7613 (m) REVERT: G 481 LEU cc_start: 0.5606 (mt) cc_final: 0.5333 (mt) outliers start: 81 outliers final: 51 residues processed: 335 average time/residue: 0.3877 time to fit residues: 208.5187 Evaluate side-chains 302 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 695 LYS Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 848 SER Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 846 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 167 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 282 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 263 optimal weight: 0.0060 chunk 270 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 254 optimal weight: 40.0000 chunk 135 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 HIS ** 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 = 0.4883 r_free = 0.4883 target = 0.245281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.196358 restraints weight = 50354.850| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 4.29 r_work: 0.4050 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29300 Z= 0.107 Angle : 0.605 9.886 39640 Z= 0.291 Chirality : 0.043 0.471 4472 Planarity : 0.004 0.050 5012 Dihedral : 9.966 156.101 4022 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 2.26 % Allowed : 24.22 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3532 helix: 1.03 (0.13), residues: 1576 sheet: -0.54 (0.26), residues: 476 loop : -0.43 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 273 HIS 0.006 0.001 HIS F 818 PHE 0.023 0.001 PHE F 311 TYR 0.009 0.001 TYR G 398 ARG 0.009 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 1229) hydrogen bonds : angle 4.74991 ( 3492) covalent geometry : bond 0.00240 (29300) covalent geometry : angle 0.60519 (39640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 256 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7165 (tp) REVERT: A 696 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8114 (mm) REVERT: E 137 LEU cc_start: 0.0221 (OUTLIER) cc_final: -0.0030 (mp) REVERT: E 347 LYS cc_start: 0.8588 (mptt) cc_final: 0.8369 (tptm) REVERT: E 501 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7627 (tp) REVERT: E 776 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: E 807 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6904 (ptpp) REVERT: E 860 GLN cc_start: 0.7650 (tm-30) cc_final: 0.6633 (pt0) REVERT: F 15 GLN cc_start: 0.2825 (OUTLIER) cc_final: 0.2217 (mm-40) REVERT: F 19 ASP cc_start: 0.3431 (OUTLIER) cc_final: 0.2495 (t70) REVERT: F 265 ASP cc_start: 0.5311 (t70) cc_final: 0.4869 (p0) REVERT: F 291 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5657 (tt) REVERT: F 320 LEU cc_start: 0.4500 (OUTLIER) cc_final: 0.4244 (mt) REVERT: F 383 ASN cc_start: 0.4090 (m-40) cc_final: 0.3784 (m-40) REVERT: F 403 TYR cc_start: 0.3387 (p90) cc_final: 0.3144 (p90) REVERT: F 410 LEU cc_start: 0.4606 (OUTLIER) cc_final: 0.3402 (pp) REVERT: F 460 LEU cc_start: 0.5140 (mt) cc_final: 0.4870 (mp) REVERT: F 551 MET cc_start: 0.7385 (mmp) cc_final: 0.7142 (mmp) REVERT: F 588 HIS cc_start: 0.4703 (m90) cc_final: 0.4099 (m170) REVERT: F 617 ILE cc_start: 0.7414 (mt) cc_final: 0.6986 (tp) REVERT: F 838 ARG cc_start: 0.3546 (mtm110) cc_final: 0.2640 (ttt180) REVERT: G 1 MET cc_start: 0.4245 (mmp) cc_final: 0.3924 (mmt) REVERT: G 233 ARG cc_start: 0.7741 (mmt180) cc_final: 0.7212 (mmp-170) REVERT: G 252 GLU cc_start: 0.6561 (mm-30) cc_final: 0.5721 (tt0) REVERT: G 354 VAL cc_start: 0.7942 (p) cc_final: 0.7623 (m) REVERT: G 428 ARG cc_start: 0.2605 (mpt-90) cc_final: 0.2211 (mpt-90) REVERT: G 476 ARG cc_start: 0.2745 (OUTLIER) cc_final: 0.2432 (ptm160) REVERT: G 481 LEU cc_start: 0.5610 (mt) cc_final: 0.5340 (mt) REVERT: G 482 HIS cc_start: 0.6265 (t-90) cc_final: 0.5836 (t70) REVERT: G 612 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4410 (tp) outliers start: 72 outliers final: 49 residues processed: 316 average time/residue: 0.4002 time to fit residues: 203.9401 Evaluate side-chains 311 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 249 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 848 SER Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 476 ARG Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 612 ILE Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 846 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 298 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 288 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 303 ASN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.245200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.196827 restraints weight = 50025.382| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 3.80 r_work: 0.4047 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29300 Z= 0.108 Angle : 0.599 9.981 39640 Z= 0.288 Chirality : 0.043 0.464 4472 Planarity : 0.004 0.050 5012 Dihedral : 9.774 157.031 4022 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 2.16 % Allowed : 24.37 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3532 helix: 1.24 (0.14), residues: 1544 sheet: -0.43 (0.28), residues: 440 loop : -0.35 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 273 HIS 0.005 0.001 HIS E 87 PHE 0.022 0.001 PHE F 311 TYR 0.014 0.001 TYR A 438 ARG 0.007 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 1229) hydrogen bonds : angle 4.70577 ( 3492) covalent geometry : bond 0.00245 (29300) covalent geometry : angle 0.59932 (39640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 270 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7181 (tp) REVERT: A 696 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 860 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6390 (tp40) REVERT: E 137 LEU cc_start: 0.0187 (OUTLIER) cc_final: -0.0061 (mp) REVERT: E 241 MET cc_start: 0.5869 (ttm) cc_final: 0.5615 (ttm) REVERT: E 501 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7642 (tp) REVERT: E 776 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6461 (tm-30) REVERT: E 807 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6749 (ptpp) REVERT: E 829 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.4442 (pm20) REVERT: E 844 MET cc_start: 0.7920 (tmm) cc_final: 0.7716 (tmm) REVERT: E 860 GLN cc_start: 0.7599 (tm-30) cc_final: 0.6569 (pt0) REVERT: F 15 GLN cc_start: 0.2773 (OUTLIER) cc_final: 0.2273 (mm-40) REVERT: F 19 ASP cc_start: 0.3375 (OUTLIER) cc_final: 0.2475 (t70) REVERT: F 265 ASP cc_start: 0.5383 (t70) cc_final: 0.4868 (p0) REVERT: F 291 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5843 (tt) REVERT: F 320 LEU cc_start: 0.4481 (OUTLIER) cc_final: 0.4223 (mt) REVERT: F 383 ASN cc_start: 0.4023 (m-40) cc_final: 0.3716 (m-40) REVERT: F 403 TYR cc_start: 0.3468 (p90) cc_final: 0.3213 (p90) REVERT: F 410 LEU cc_start: 0.4554 (OUTLIER) cc_final: 0.3392 (pp) REVERT: F 551 MET cc_start: 0.7333 (mmp) cc_final: 0.6989 (mmp) REVERT: F 588 HIS cc_start: 0.4738 (m90) cc_final: 0.4098 (m170) REVERT: F 617 ILE cc_start: 0.7436 (mt) cc_final: 0.6995 (tp) REVERT: F 760 MET cc_start: 0.3503 (tmm) cc_final: 0.2370 (ptt) REVERT: F 800 ARG cc_start: 0.6576 (ptm160) cc_final: 0.5664 (mmm-85) REVERT: F 838 ARG cc_start: 0.3726 (mtm110) cc_final: 0.2515 (mmp80) REVERT: G 233 ARG cc_start: 0.7733 (mmt180) cc_final: 0.7185 (mmp-170) REVERT: G 252 GLU cc_start: 0.6623 (mm-30) cc_final: 0.5818 (tt0) REVERT: G 320 LEU cc_start: 0.4818 (tp) cc_final: 0.4218 (mt) REVERT: G 354 VAL cc_start: 0.7929 (p) cc_final: 0.7616 (m) REVERT: G 428 ARG cc_start: 0.2543 (mpt-90) cc_final: 0.2284 (mpt180) REVERT: G 481 LEU cc_start: 0.5823 (mt) cc_final: 0.5560 (mt) REVERT: G 482 HIS cc_start: 0.6322 (t-90) cc_final: 0.5972 (t70) REVERT: G 612 ILE cc_start: 0.4993 (OUTLIER) cc_final: 0.4423 (tp) outliers start: 69 outliers final: 45 residues processed: 327 average time/residue: 0.3874 time to fit residues: 203.4382 Evaluate side-chains 310 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 829 GLU Chi-restraints excluded: chain E residue 848 SER Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ILE Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 612 ILE Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 745 LEU Chi-restraints excluded: chain G residue 846 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 218 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 319 optimal weight: 0.9980 chunk 161 optimal weight: 0.0980 chunk 145 optimal weight: 0.0870 chunk 219 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 191 optimal weight: 8.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.245743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.195972 restraints weight = 50331.058| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 4.05 r_work: 0.4057 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29300 Z= 0.104 Angle : 0.599 9.842 39640 Z= 0.287 Chirality : 0.042 0.460 4472 Planarity : 0.004 0.050 5012 Dihedral : 9.587 157.040 4022 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 1.91 % Allowed : 24.78 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3532 helix: 1.27 (0.13), residues: 1544 sheet: -0.26 (0.28), residues: 432 loop : -0.30 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 273 HIS 0.009 0.001 HIS E 52 PHE 0.021 0.001 PHE F 311 TYR 0.011 0.001 TYR E 197 ARG 0.010 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 1229) hydrogen bonds : angle 4.64655 ( 3492) covalent geometry : bond 0.00232 (29300) covalent geometry : angle 0.59918 (39640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19810.41 seconds wall clock time: 341 minutes 47.99 seconds (20507.99 seconds total)