Starting phenix.real_space_refine on Tue Jun 24 17:07:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xuq_38680/06_2025/8xuq_38680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xuq_38680/06_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_38680/06_2025/8xuq_38680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xuq_38680/06_2025/8xuq_38680.map" model { file = "/net/cci-nas-00/data/ceres_data/8xuq_38680/06_2025/8xuq_38680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xuq_38680/06_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-5710/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: 17.13, per 1000 atoms: 0.60 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: 8.25 Conformation dependent library (CDL) restraints added in 3.7 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: 4.95 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: 15.05 Time building geometry restraints manager: 9.59 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: 1.460 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: 0.040 Extract box with map and model: 1.180 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 72.450 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.410 ------------------------------------------------------------------------------- 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 : 3.362 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: 0.4145 time to fit residues: 226.6248 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 : 2.957 ------------------------------------------------------------------------------- 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 = 0.208158 restraints weight = 51100.501| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 3.90 r_work: 0.4021 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.6448 (ttt180) cc_final: 0.6143 (ttp80) REVERT: A 223 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7394 (tp) REVERT: A 241 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.5439 (ptp) REVERT: A 242 CYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5956 (t) REVERT: A 523 SER cc_start: 0.7152 (p) cc_final: 0.6939 (m) REVERT: A 776 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: E 159 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: E 776 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: E 807 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7168 (ptpp) REVERT: E 885 LEU cc_start: 0.4683 (OUTLIER) cc_final: 0.4382 (mm) REVERT: F 198 LYS cc_start: 0.6288 (pttp) cc_final: 0.5401 (tptp) REVERT: F 206 PHE cc_start: 0.1834 (m-80) cc_final: 0.1516 (m-80) REVERT: F 291 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4497 (tt) REVERT: F 318 TRP cc_start: 0.3898 (t60) cc_final: 0.3638 (t60) REVERT: F 588 HIS cc_start: 0.4787 (m90) cc_final: 0.4125 (m170) REVERT: F 747 LYS cc_start: 0.4924 (ttpp) cc_final: 0.4707 (mptt) REVERT: F 819 LEU cc_start: 0.7047 (tt) cc_final: 0.6571 (tt) REVERT: G 320 LEU cc_start: 0.4880 (tp) cc_final: 0.4290 (mt) REVERT: G 410 LEU cc_start: 0.3997 (OUTLIER) cc_final: 0.3607 (mt) REVERT: G 428 ARG cc_start: 0.3621 (mpt180) cc_final: 0.3383 (mpt-90) REVERT: G 469 ASP cc_start: 0.3617 (OUTLIER) cc_final: 0.2856 (t70) REVERT: G 481 LEU cc_start: 0.5485 (mt) cc_final: 0.5191 (mt) REVERT: G 501 LEU cc_start: 0.4536 (OUTLIER) cc_final: 0.4090 (mp) REVERT: G 532 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7479 (mmmt) REVERT: G 799 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7690 (mt-10) REVERT: G 873 ASN cc_start: 0.1250 (OUTLIER) cc_final: -0.1388 (p0) outliers start: 120 outliers final: 55 residues processed: 400 average time/residue: 0.4021 time to fit residues: 256.9246 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 : 2.937 ------------------------------------------------------------------------------- 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: 4.9990 chunk 318 optimal weight: 0.3980 chunk 205 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 325 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 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 ** 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 = 0.4883 r_free = 0.4883 target = 0.247383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.197959 restraints weight = 52117.281| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 4.84 r_work: 0.4032 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29300 Z= 0.132 Angle : 0.656 10.561 39640 Z= 0.321 Chirality : 0.045 0.602 4472 Planarity : 0.004 0.051 5012 Dihedral : 11.847 151.314 4031 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 21.30 % 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: -0.16 (0.14), residues: 3532 helix: 0.85 (0.13), residues: 1504 sheet: -0.77 (0.25), residues: 456 loop : -0.77 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 430 HIS 0.006 0.001 HIS G 638 PHE 0.017 0.001 PHE A 80 TYR 0.014 0.001 TYR F 101 ARG 0.006 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 1229) hydrogen bonds : angle 5.38059 ( 3492) covalent geometry : bond 0.00296 (29300) covalent geometry : angle 0.65557 (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: 93 poor density : 285 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7284 (mm) REVERT: A 104 VAL cc_start: 0.3944 (OUTLIER) cc_final: 0.3694 (t) REVERT: A 223 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7295 (tp) REVERT: A 523 SER cc_start: 0.7238 (p) cc_final: 0.7035 (m) REVERT: E 19 ASP cc_start: 0.7656 (t0) cc_final: 0.7443 (t0) REVERT: E 137 LEU cc_start: -0.0186 (OUTLIER) cc_final: -0.0513 (mp) REVERT: E 860 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7118 (tt0) REVERT: E 885 LEU cc_start: 0.4921 (OUTLIER) cc_final: 0.4597 (mm) REVERT: F 15 GLN cc_start: 0.2710 (OUTLIER) cc_final: 0.2205 (mm-40) REVERT: F 198 LYS cc_start: 0.6153 (pttp) cc_final: 0.5155 (tptp) REVERT: F 206 PHE cc_start: 0.1517 (m-80) cc_final: 0.1244 (m-80) REVERT: F 354 VAL cc_start: 0.7837 (t) cc_final: 0.7582 (m) REVERT: F 410 LEU cc_start: 0.5418 (mm) cc_final: 0.4796 (mt) REVERT: F 588 HIS cc_start: 0.4825 (m90) cc_final: 0.4122 (m170) REVERT: F 634 GLU cc_start: 0.2286 (pm20) cc_final: 0.1691 (mm-30) REVERT: F 747 LYS cc_start: 0.4982 (ttpp) cc_final: 0.4753 (mmtm) REVERT: F 772 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6602 (mp) REVERT: G 320 LEU cc_start: 0.5017 (tp) cc_final: 0.4306 (mt) REVERT: G 381 LEU cc_start: 0.0885 (OUTLIER) cc_final: 0.0585 (mm) REVERT: G 473 LYS cc_start: 0.4717 (tttt) cc_final: 0.4493 (mtpt) REVERT: G 501 LEU cc_start: 0.4995 (OUTLIER) cc_final: 0.4534 (mp) REVERT: G 532 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7292 (mmmt) REVERT: G 558 THR cc_start: 0.5889 (p) cc_final: 0.4287 (m) REVERT: G 799 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7628 (mt-10) REVERT: G 822 ILE cc_start: 0.5716 (mm) cc_final: 0.5493 (mm) REVERT: G 873 ASN cc_start: 0.0911 (OUTLIER) cc_final: -0.1475 (p0) outliers start: 93 outliers final: 45 residues processed: 357 average time/residue: 0.3836 time to fit residues: 222.3679 Evaluate side-chains 307 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 252 time to evaluate : 2.984 ------------------------------------------------------------------------------- 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 701 ASP 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 259 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 ** 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** G 873 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.244629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.192255 restraints weight = 50539.641| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.88 r_work: 0.4026 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29300 Z= 0.172 Angle : 0.670 9.414 39640 Z= 0.331 Chirality : 0.045 0.546 4472 Planarity : 0.005 0.055 5012 Dihedral : 11.304 152.206 4028 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 4.42 % Allowed : 20.58 % Favored : 75.00 % 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: -0.28 (0.14), residues: 3532 helix: 0.75 (0.13), residues: 1532 sheet: -0.96 (0.25), residues: 480 loop : -0.80 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 430 HIS 0.006 0.001 HIS E 307 PHE 0.013 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 0.04496 ( 1229) hydrogen bonds : angle 5.35399 ( 3492) covalent geometry : bond 0.00403 (29300) covalent geometry : angle 0.66958 (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 415 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 274 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6971 (mm) REVERT: A 223 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7328 (tp) REVERT: A 241 MET cc_start: 0.6173 (ttp) cc_final: 0.5681 (ttp) REVERT: A 523 SER cc_start: 0.7270 (p) cc_final: 0.7040 (m) REVERT: A 729 GLN cc_start: 0.4592 (OUTLIER) cc_final: 0.3059 (mp-120) REVERT: E 137 LEU cc_start: -0.0150 (OUTLIER) cc_final: -0.0453 (mp) REVERT: E 158 PHE cc_start: 0.7315 (m-80) cc_final: 0.7102 (m-80) REVERT: E 501 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7644 (tp) REVERT: E 776 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: E 846 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7526 (tm-30) REVERT: E 860 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7207 (tt0) REVERT: E 885 LEU cc_start: 0.4845 (OUTLIER) cc_final: 0.4511 (mm) REVERT: F 15 GLN cc_start: 0.2469 (OUTLIER) cc_final: 0.2033 (mm-40) REVERT: F 198 LYS cc_start: 0.6274 (pttp) cc_final: 0.5253 (tptp) REVERT: F 291 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.4952 (tt) REVERT: F 320 LEU cc_start: 0.4726 (OUTLIER) cc_final: 0.4474 (mt) REVERT: F 398 TYR cc_start: 0.6682 (t80) cc_final: 0.6365 (t80) REVERT: F 481 LEU cc_start: 0.5755 (mt) cc_final: 0.5412 (mt) REVERT: F 588 HIS cc_start: 0.4802 (m90) cc_final: 0.4185 (m170) REVERT: F 634 GLU cc_start: 0.2620 (pm20) cc_final: 0.1635 (mm-30) REVERT: F 747 LYS cc_start: 0.4806 (ttpp) cc_final: 0.4481 (mptt) REVERT: F 774 MET cc_start: 0.6707 (mpp) cc_final: 0.6463 (mpp) REVERT: G 1 MET cc_start: 0.4486 (mmp) cc_final: 0.4246 (mmm) REVERT: G 265 ASP cc_start: 0.5292 (t0) cc_final: 0.5068 (t0) REVERT: G 271 GLU cc_start: 0.6866 (pm20) cc_final: 0.6584 (mt-10) REVERT: G 291 LEU cc_start: 0.5039 (OUTLIER) cc_final: 0.2725 (tt) REVERT: G 320 LEU cc_start: 0.5201 (tp) cc_final: 0.4511 (mt) REVERT: G 381 LEU cc_start: 0.1325 (OUTLIER) cc_final: 0.1017 (mm) REVERT: G 501 LEU cc_start: 0.4791 (OUTLIER) cc_final: 0.4474 (mp) REVERT: G 532 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7320 (mmmt) outliers start: 141 outliers final: 73 residues processed: 394 average time/residue: 0.3801 time to fit residues: 242.2494 Evaluate side-chains 332 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 246 time to evaluate : 3.069 ------------------------------------------------------------------------------- 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 729 GLN 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 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 521 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 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 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 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: 0.8980 chunk 314 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 346 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 241 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 F 873 ASN 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 = 0.4882 r_free = 0.4882 target = 0.246589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.207838 restraints weight = 50505.715| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 4.01 r_work: 0.4048 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3182 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= 0.115 Angle : 0.618 9.425 39640 Z= 0.299 Chirality : 0.043 0.511 4472 Planarity : 0.004 0.051 5012 Dihedral : 10.983 152.245 4028 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 3.29 % Allowed : 21.77 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.00 (0.15), residues: 3532 helix: 0.88 (0.13), residues: 1556 sheet: -0.77 (0.24), residues: 516 loop : -0.55 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 754 HIS 0.006 0.001 HIS G 638 PHE 0.015 0.001 PHE F 206 TYR 0.014 0.001 TYR A 438 ARG 0.005 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 1229) hydrogen bonds : angle 5.10739 ( 3492) covalent geometry : bond 0.00258 (29300) covalent geometry : angle 0.61833 (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 378 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 273 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7243 (tp) REVERT: A 523 SER cc_start: 0.7119 (p) cc_final: 0.6869 (m) REVERT: A 696 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8013 (mm) REVERT: A 729 GLN cc_start: 0.4666 (OUTLIER) cc_final: 0.3827 (mp-120) REVERT: A 754 TRP cc_start: 0.6390 (m100) cc_final: 0.6003 (m100) REVERT: A 807 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7524 (mmtm) REVERT: E 137 LEU cc_start: -0.0074 (OUTLIER) cc_final: -0.0340 (mp) REVERT: E 318 TRP cc_start: 0.7507 (t-100) cc_final: 0.7022 (t-100) REVERT: E 347 LYS cc_start: 0.8667 (mptt) cc_final: 0.8360 (tptp) REVERT: E 501 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7720 (tp) REVERT: E 687 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8551 (tt) REVERT: E 776 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: E 807 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7127 (ptpp) REVERT: F 15 GLN cc_start: 0.2760 (OUTLIER) cc_final: 0.2190 (mm-40) REVERT: F 291 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5134 (tt) REVERT: F 320 LEU cc_start: 0.4621 (OUTLIER) cc_final: 0.4369 (mt) REVERT: F 410 LEU cc_start: 0.4499 (mm) cc_final: 0.3657 (mt) REVERT: F 481 LEU cc_start: 0.5914 (mt) cc_final: 0.5611 (mt) REVERT: F 588 HIS cc_start: 0.4967 (m90) cc_final: 0.4356 (m170) REVERT: F 634 GLU cc_start: 0.2699 (pm20) cc_final: 0.1845 (mm-30) REVERT: F 747 LYS cc_start: 0.4748 (ttpp) cc_final: 0.4462 (mptt) REVERT: G 1 MET cc_start: 0.4506 (mmp) cc_final: 0.4228 (mmm) REVERT: G 265 ASP cc_start: 0.5837 (t0) cc_final: 0.5594 (t0) REVERT: G 291 LEU cc_start: 0.5184 (OUTLIER) cc_final: 0.2566 (tt) REVERT: G 320 LEU cc_start: 0.5095 (tp) cc_final: 0.4449 (mt) REVERT: G 381 LEU cc_start: 0.1136 (OUTLIER) cc_final: 0.0892 (mm) REVERT: G 532 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7405 (mmmt) REVERT: G 633 MET cc_start: 0.5371 (tmm) cc_final: 0.3336 (mmp) outliers start: 105 outliers final: 57 residues processed: 359 average time/residue: 0.3887 time to fit residues: 226.7527 Evaluate side-chains 317 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 246 time to evaluate : 3.023 ------------------------------------------------------------------------------- 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 729 GLN Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 807 LYS 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 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 278 ILE Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE 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 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 776 GLU Chi-restraints excluded: chain E residue 804 VAL 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 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 745 LEU Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 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 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 671 ILE Chi-restraints excluded: chain G residue 687 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: 0.8980 chunk 106 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 171 optimal weight: 0.0470 chunk 338 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 212 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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** E 52 HIS E 777 ASN ** E 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 HIS ** 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 = 0.4881 r_free = 0.4881 target = 0.246684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.195006 restraints weight = 51495.128| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 4.30 r_work: 0.4066 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29300 Z= 0.112 Angle : 0.596 9.380 39640 Z= 0.290 Chirality : 0.043 0.492 4472 Planarity : 0.004 0.048 5012 Dihedral : 10.592 152.598 4022 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.89 % Allowed : 22.18 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.15), residues: 3532 helix: 1.05 (0.13), residues: 1540 sheet: -0.50 (0.27), residues: 436 loop : -0.45 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 754 HIS 0.005 0.001 HIS F 638 PHE 0.027 0.001 PHE F 311 TYR 0.011 0.001 TYR F 101 ARG 0.004 0.000 ARG F 486 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 1229) hydrogen bonds : angle 4.91238 ( 3492) covalent geometry : bond 0.00246 (29300) covalent geometry : angle 0.59613 (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 363 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 271 time to evaluate : 3.198 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: 0.8283 (t0) cc_final: 0.7846 (t0) REVERT: A 45 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7002 (mm) REVERT: A 223 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7194 (tp) REVERT: A 523 SER cc_start: 0.7095 (p) cc_final: 0.6871 (m) REVERT: A 696 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8059 (mm) REVERT: A 729 GLN cc_start: 0.5453 (OUTLIER) cc_final: 0.3973 (mp-120) REVERT: E 137 LEU cc_start: 0.0040 (OUTLIER) cc_final: -0.0217 (mp) REVERT: E 347 LYS cc_start: 0.8541 (mptt) cc_final: 0.8258 (tptp) REVERT: E 501 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7659 (tp) REVERT: E 776 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: E 807 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6797 (ptpp) REVERT: E 860 GLN cc_start: 0.7583 (tm-30) cc_final: 0.6529 (pt0) REVERT: F 15 GLN cc_start: 0.2818 (OUTLIER) cc_final: 0.2291 (mm-40) REVERT: F 291 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.5077 (tt) REVERT: F 320 LEU cc_start: 0.4487 (OUTLIER) cc_final: 0.4220 (mt) REVERT: F 386 HIS cc_start: 0.4620 (t-90) cc_final: 0.4399 (t-90) REVERT: F 570 ASP cc_start: 0.6097 (t0) cc_final: 0.5896 (p0) REVERT: F 588 HIS cc_start: 0.4961 (m90) cc_final: 0.4313 (m170) REVERT: F 634 GLU cc_start: 0.2617 (pm20) cc_final: 0.1638 (mm-30) REVERT: F 747 LYS cc_start: 0.4807 (ttpp) cc_final: 0.4499 (mptt) REVERT: G 265 ASP cc_start: 0.5515 (t0) cc_final: 0.5273 (t0) REVERT: G 291 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.2828 (tt) REVERT: G 320 LEU cc_start: 0.5035 (tp) cc_final: 0.4350 (mt) REVERT: G 481 LEU cc_start: 0.5549 (mt) cc_final: 0.5169 (mt) REVERT: G 532 LYS cc_start: 0.7540 (mmtt) cc_final: 0.7298 (mmmt) REVERT: G 633 MET cc_start: 0.5350 (tmm) cc_final: 0.3420 (mmp) REVERT: G 799 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7357 (mt-10) REVERT: G 822 ILE cc_start: 0.5570 (mm) cc_final: 0.5103 (mp) outliers start: 92 outliers final: 56 residues processed: 346 average time/residue: 0.3963 time to fit residues: 221.9378 Evaluate side-chains 312 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET 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 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 649 VAL Chi-restraints excluded: chain E residue 725 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 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 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 542 LEU Chi-restraints excluded: chain F residue 549 ILE 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 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 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 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 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: 8.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 150 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 234 optimal weight: 0.0970 chunk 242 optimal weight: 20.0000 chunk 23 optimal weight: 0.0570 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 E 234 ASN E 777 ASN ** E 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 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 = 0.4889 r_free = 0.4889 target = 0.246693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.199236 restraints weight = 51573.626| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 4.03 r_work: 0.4061 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3733 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= 0.104 Angle : 0.581 9.210 39640 Z= 0.281 Chirality : 0.043 0.485 4472 Planarity : 0.004 0.063 5012 Dihedral : 10.308 152.897 4022 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 2.63 % Allowed : 22.90 % Favored : 74.47 % 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: 0.41 (0.15), residues: 3532 helix: 1.15 (0.13), residues: 1544 sheet: -0.38 (0.27), residues: 440 loop : -0.32 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 424 HIS 0.004 0.001 HIS F 818 PHE 0.023 0.001 PHE F 311 TYR 0.014 0.001 TYR A 438 ARG 0.012 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 1229) hydrogen bonds : angle 4.74585 ( 3492) covalent geometry : bond 0.00227 (29300) covalent geometry : angle 0.58106 (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 350 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 266 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7180 (tp) REVERT: A 523 SER cc_start: 0.6966 (p) cc_final: 0.6752 (m) REVERT: A 696 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8094 (mm) REVERT: A 729 GLN cc_start: 0.5746 (OUTLIER) cc_final: 0.4284 (mp-120) REVERT: A 844 MET cc_start: 0.7641 (tmm) cc_final: 0.7103 (tmm) REVERT: E 137 LEU cc_start: 0.0073 (OUTLIER) cc_final: -0.0175 (mp) REVERT: E 347 LYS cc_start: 0.8578 (mptt) cc_final: 0.8280 (tptp) REVERT: E 501 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7688 (tp) REVERT: E 776 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6522 (tm-30) REVERT: E 785 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: E 807 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6533 (ptpp) REVERT: E 860 GLN cc_start: 0.7570 (tm-30) cc_final: 0.6549 (pt0) REVERT: F 15 GLN cc_start: 0.2798 (OUTLIER) cc_final: 0.2189 (mm-40) REVERT: F 19 ASP cc_start: 0.3370 (OUTLIER) cc_final: 0.2442 (t70) REVERT: F 265 ASP cc_start: 0.4800 (t70) cc_final: 0.4322 (p0) REVERT: F 291 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5071 (tt) REVERT: F 320 LEU cc_start: 0.4445 (OUTLIER) cc_final: 0.4183 (mt) REVERT: F 428 ARG cc_start: 0.2736 (mpt-90) cc_final: 0.2445 (mpt-90) REVERT: F 588 HIS cc_start: 0.4923 (m90) cc_final: 0.4257 (m170) REVERT: F 634 GLU cc_start: 0.2806 (pm20) cc_final: 0.1816 (mm-30) REVERT: F 747 LYS cc_start: 0.4825 (ttpp) cc_final: 0.4527 (mptt) REVERT: G 265 ASP cc_start: 0.5606 (t0) cc_final: 0.5343 (t0) REVERT: G 291 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.2871 (tt) REVERT: G 320 LEU cc_start: 0.4941 (tp) cc_final: 0.4295 (mt) REVERT: G 460 LEU cc_start: 0.4635 (OUTLIER) cc_final: 0.4432 (mm) REVERT: G 481 LEU cc_start: 0.5547 (mt) cc_final: 0.5193 (mt) REVERT: G 633 MET cc_start: 0.5383 (tmm) cc_final: 0.3573 (mmp) outliers start: 84 outliers final: 53 residues processed: 336 average time/residue: 0.4015 time to fit residues: 222.4569 Evaluate side-chains 311 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 244 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 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 246 LEU 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 729 GLN Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 842 VAL 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 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 284 ASN Chi-restraints excluded: chain E residue 328 LYS 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 612 ILE Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 785 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 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 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 469 ASP Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 549 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 617 ILE 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 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 291 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 460 LEU 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 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 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: 6.9990 chunk 227 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 121 optimal weight: 0.0000 chunk 139 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 241 optimal weight: 0.4980 chunk 218 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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** E 846 GLN G 237 GLN G 588 HIS G 818 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.247859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.199337 restraints weight = 51125.169| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 4.21 r_work: 0.4058 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29300 Z= 0.106 Angle : 0.586 9.349 39640 Z= 0.283 Chirality : 0.043 0.481 4472 Planarity : 0.004 0.049 5012 Dihedral : 10.148 153.357 4022 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 2.70 % Allowed : 22.99 % Favored : 74.31 % 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: 0.48 (0.15), residues: 3532 helix: 1.20 (0.13), residues: 1544 sheet: -0.32 (0.28), residues: 440 loop : -0.29 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 430 HIS 0.006 0.001 HIS F 818 PHE 0.030 0.001 PHE G 507 TYR 0.010 0.001 TYR E 197 ARG 0.007 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 1229) hydrogen bonds : angle 4.71057 ( 3492) covalent geometry : bond 0.00237 (29300) covalent geometry : angle 0.58588 (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 351 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 265 time to evaluate : 3.013 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: 0.7604 (OUTLIER) cc_final: 0.7187 (tp) REVERT: A 523 SER cc_start: 0.6946 (p) cc_final: 0.6729 (m) REVERT: A 696 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8015 (mm) REVERT: A 729 GLN cc_start: 0.5577 (OUTLIER) cc_final: 0.4123 (mp10) REVERT: A 860 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6411 (tt0) REVERT: E 137 LEU cc_start: 0.0103 (OUTLIER) cc_final: -0.0119 (mp) REVERT: E 347 LYS cc_start: 0.8607 (mptt) cc_final: 0.8351 (tptp) REVERT: E 501 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7712 (tp) REVERT: E 776 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: E 785 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: E 807 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6523 (ptpp) REVERT: E 860 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7202 (tt0) REVERT: F 15 GLN cc_start: 0.2794 (OUTLIER) cc_final: 0.2197 (mm-40) REVERT: F 19 ASP cc_start: 0.3580 (OUTLIER) cc_final: 0.2685 (t70) REVERT: F 265 ASP cc_start: 0.4684 (t70) cc_final: 0.4110 (p0) REVERT: F 291 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5072 (tt) REVERT: F 320 LEU cc_start: 0.4428 (OUTLIER) cc_final: 0.4166 (mt) REVERT: F 428 ARG cc_start: 0.2783 (mpt-90) cc_final: 0.2548 (mpt-90) REVERT: F 588 HIS cc_start: 0.4841 (m90) cc_final: 0.4159 (m170) REVERT: F 634 GLU cc_start: 0.2735 (pm20) cc_final: 0.1727 (mm-30) REVERT: F 747 LYS cc_start: 0.4872 (ttpp) cc_final: 0.4494 (mptt) REVERT: G 265 ASP cc_start: 0.5696 (t0) cc_final: 0.5405 (t0) REVERT: G 291 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.2950 (tt) REVERT: G 320 LEU cc_start: 0.4992 (tp) cc_final: 0.4317 (mt) REVERT: G 354 VAL cc_start: 0.7980 (p) cc_final: 0.7679 (m) REVERT: G 481 LEU cc_start: 0.5523 (mt) cc_final: 0.5166 (mt) REVERT: G 505 GLN cc_start: 0.5497 (mm110) cc_final: 0.5095 (mt0) REVERT: G 558 THR cc_start: 0.5805 (p) cc_final: 0.5568 (p) REVERT: G 633 MET cc_start: 0.5457 (tmm) cc_final: 0.3629 (mmp) outliers start: 86 outliers final: 55 residues processed: 336 average time/residue: 0.3878 time to fit residues: 210.9327 Evaluate side-chains 321 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 3.367 ------------------------------------------------------------------------------- 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 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 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 729 GLN Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET 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 58 VAL Chi-restraints excluded: chain E residue 87 HIS 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 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 649 VAL Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 785 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 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 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 469 ASP Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 549 ILE Chi-restraints excluded: chain F residue 565 LEU 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 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 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 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 745 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 167 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 270 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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** ** G 588 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 = 0.4890 r_free = 0.4890 target = 0.247528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.199745 restraints weight = 51080.460| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 4.28 r_work: 0.4051 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29300 Z= 0.108 Angle : 0.589 9.656 39640 Z= 0.284 Chirality : 0.043 0.476 4472 Planarity : 0.004 0.051 5012 Dihedral : 9.930 154.082 4022 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 2.38 % Allowed : 23.18 % Favored : 74.44 % 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: 0.55 (0.15), residues: 3532 helix: 1.29 (0.14), residues: 1544 sheet: -0.28 (0.28), residues: 440 loop : -0.29 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 430 HIS 0.005 0.001 HIS F 818 PHE 0.020 0.001 PHE F 311 TYR 0.015 0.001 TYR A 438 ARG 0.007 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 1229) hydrogen bonds : angle 4.64644 ( 3492) covalent geometry : bond 0.00244 (29300) covalent geometry : angle 0.58901 (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 351 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 275 time to evaluate : 2.982 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 12 ASN cc_start: 0.8324 (t0) cc_final: 0.7874 (t0) REVERT: A 223 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7162 (tp) REVERT: A 347 LYS cc_start: 0.8307 (tttt) cc_final: 0.7902 (tptm) REVERT: A 523 SER cc_start: 0.6925 (p) cc_final: 0.6712 (m) REVERT: A 696 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8016 (mm) REVERT: A 729 GLN cc_start: 0.5485 (OUTLIER) cc_final: 0.4160 (mp10) REVERT: A 860 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6419 (tt0) REVERT: E 137 LEU cc_start: 0.0265 (OUTLIER) cc_final: 0.0020 (mp) REVERT: E 347 LYS cc_start: 0.8622 (mptt) cc_final: 0.8341 (tptp) REVERT: E 390 CYS cc_start: 0.5903 (OUTLIER) cc_final: 0.5693 (t) REVERT: E 501 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7692 (tp) REVERT: E 776 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: E 860 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7258 (tt0) REVERT: F 15 GLN cc_start: 0.2779 (OUTLIER) cc_final: 0.2192 (mm-40) REVERT: F 19 ASP cc_start: 0.3553 (OUTLIER) cc_final: 0.2644 (t70) REVERT: F 265 ASP cc_start: 0.5025 (t70) cc_final: 0.4444 (p0) REVERT: F 291 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5364 (tt) REVERT: F 320 LEU cc_start: 0.4463 (OUTLIER) cc_final: 0.4202 (mt) REVERT: F 410 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.3491 (pp) REVERT: F 460 LEU cc_start: 0.5036 (mt) cc_final: 0.4798 (mp) REVERT: F 588 HIS cc_start: 0.4808 (m90) cc_final: 0.4127 (m170) REVERT: F 634 GLU cc_start: 0.2770 (pm20) cc_final: 0.1713 (mm-30) REVERT: F 800 ARG cc_start: 0.5933 (ptm160) cc_final: 0.5009 (mmm-85) REVERT: G 265 ASP cc_start: 0.5790 (t0) cc_final: 0.5498 (t0) REVERT: G 291 LEU cc_start: 0.5118 (OUTLIER) cc_final: 0.3041 (tt) REVERT: G 354 VAL cc_start: 0.7842 (p) cc_final: 0.7521 (m) REVERT: G 481 LEU cc_start: 0.5597 (mt) cc_final: 0.5272 (mt) REVERT: G 482 HIS cc_start: 0.6052 (t-90) cc_final: 0.5608 (t70) REVERT: G 633 MET cc_start: 0.5445 (tmm) cc_final: 0.3612 (mmp) REVERT: G 776 GLU cc_start: 0.6852 (tt0) cc_final: 0.6633 (tm-30) outliers start: 76 outliers final: 56 residues processed: 337 average time/residue: 0.3872 time to fit residues: 208.5716 Evaluate side-chains 330 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 3.011 ------------------------------------------------------------------------------- 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 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 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 729 GLN Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET 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 58 VAL Chi-restraints excluded: chain E residue 87 HIS 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 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 649 VAL Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 707 SER 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 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 542 LEU Chi-restraints excluded: chain F residue 549 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER 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 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 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 745 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 298 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 588 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.246865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.211189 restraints weight = 51524.143| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 4.08 r_work: 0.4053 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29300 Z= 0.109 Angle : 0.598 11.590 39640 Z= 0.288 Chirality : 0.043 0.472 4472 Planarity : 0.004 0.052 5012 Dihedral : 9.824 155.100 4022 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.42 % Allowed : 23.34 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.15), residues: 3532 helix: 1.29 (0.13), residues: 1544 sheet: -0.27 (0.28), residues: 440 loop : -0.27 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 430 HIS 0.007 0.001 HIS E 52 PHE 0.020 0.001 PHE F 311 TYR 0.010 0.001 TYR A 591 ARG 0.007 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 1229) hydrogen bonds : angle 4.63373 ( 3492) covalent geometry : bond 0.00247 (29300) covalent geometry : angle 0.59805 (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 349 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 272 time to evaluate : 3.004 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: 0.7549 (OUTLIER) cc_final: 0.7148 (tp) REVERT: A 347 LYS cc_start: 0.8326 (tttt) cc_final: 0.7959 (tptm) REVERT: A 523 SER cc_start: 0.6986 (p) cc_final: 0.6779 (m) REVERT: A 696 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8032 (mm) REVERT: A 729 GLN cc_start: 0.5556 (OUTLIER) cc_final: 0.4225 (mp10) REVERT: A 860 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6554 (tt0) REVERT: E 137 LEU cc_start: 0.0330 (OUTLIER) cc_final: 0.0047 (mp) REVERT: E 347 LYS cc_start: 0.8743 (mptt) cc_final: 0.8420 (tptp) REVERT: E 390 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5831 (t) REVERT: E 501 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7714 (tp) REVERT: E 776 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: E 807 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6917 (ptpp) REVERT: E 860 GLN cc_start: 0.7603 (tm-30) cc_final: 0.6616 (pt0) REVERT: F 15 GLN cc_start: 0.2814 (OUTLIER) cc_final: 0.2184 (mm-40) REVERT: F 19 ASP cc_start: 0.3204 (OUTLIER) cc_final: 0.2187 (t70) REVERT: F 265 ASP cc_start: 0.5532 (t70) cc_final: 0.5013 (p0) REVERT: F 291 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5491 (tt) REVERT: F 320 LEU cc_start: 0.4440 (OUTLIER) cc_final: 0.4183 (mt) REVERT: F 410 LEU cc_start: 0.4400 (OUTLIER) cc_final: 0.3409 (pp) REVERT: F 460 LEU cc_start: 0.5264 (mt) cc_final: 0.5001 (mp) REVERT: F 588 HIS cc_start: 0.4912 (m90) cc_final: 0.4285 (m170) REVERT: F 633 MET cc_start: 0.4328 (ttm) cc_final: 0.4042 (ttm) REVERT: F 634 GLU cc_start: 0.2802 (pm20) cc_final: 0.1777 (mm-30) REVERT: F 800 ARG cc_start: 0.5810 (ptm160) cc_final: 0.4911 (mmm-85) REVERT: G 233 ARG cc_start: 0.7762 (mmt180) cc_final: 0.7270 (mmp-170) REVERT: G 249 GLU cc_start: 0.6356 (tp30) cc_final: 0.6140 (tp30) REVERT: G 252 GLU cc_start: 0.6693 (mm-30) cc_final: 0.5790 (tt0) REVERT: G 265 ASP cc_start: 0.6247 (t0) cc_final: 0.5951 (t0) REVERT: G 291 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.3261 (tt) REVERT: G 320 LEU cc_start: 0.5042 (tp) cc_final: 0.4444 (mt) REVERT: G 354 VAL cc_start: 0.7796 (p) cc_final: 0.7449 (m) REVERT: G 481 LEU cc_start: 0.5885 (mt) cc_final: 0.5531 (mt) REVERT: G 482 HIS cc_start: 0.6353 (t-90) cc_final: 0.5884 (t70) REVERT: G 633 MET cc_start: 0.5307 (tmm) cc_final: 0.3518 (mmp) REVERT: G 776 GLU cc_start: 0.6569 (tt0) cc_final: 0.6349 (tm-30) outliers start: 77 outliers final: 57 residues processed: 334 average time/residue: 0.3883 time to fit residues: 209.1372 Evaluate side-chains 333 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 261 time to evaluate : 3.043 ------------------------------------------------------------------------------- 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 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 612 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET 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 58 VAL Chi-restraints excluded: chain E residue 87 HIS 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 284 ASN Chi-restraints excluded: chain E residue 328 LYS 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 649 VAL Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 707 SER 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 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 542 LEU Chi-restraints excluded: chain F residue 549 ILE Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER 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 291 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 431 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 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 745 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 218 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 319 optimal weight: 0.0980 chunk 161 optimal weight: 0.0020 chunk 145 optimal weight: 0.5980 chunk 219 optimal weight: 0.6980 chunk 313 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 HIS F 389 ASN G 611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.247565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.212995 restraints weight = 51987.884| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 4.09 r_work: 0.4070 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29300 Z= 0.102 Angle : 0.590 10.411 39640 Z= 0.283 Chirality : 0.042 0.470 4472 Planarity : 0.004 0.051 5012 Dihedral : 9.602 154.692 4022 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 2.07 % Allowed : 23.81 % Favored : 74.12 % 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: 0.69 (0.15), residues: 3532 helix: 1.35 (0.13), residues: 1544 sheet: -0.02 (0.28), residues: 432 loop : -0.22 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 430 HIS 0.005 0.000 HIS F 818 PHE 0.019 0.001 PHE F 311 TYR 0.009 0.001 TYR A 438 ARG 0.007 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 1229) hydrogen bonds : angle 4.53867 ( 3492) covalent geometry : bond 0.00225 (29300) covalent geometry : angle 0.58973 (39640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20492.70 seconds wall clock time: 351 minutes 35.58 seconds (21095.58 seconds total)