Starting phenix.real_space_refine on Fri Sep 19 01:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iw0_60937/09_2025/9iw0_60937.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iw0_60937/09_2025/9iw0_60937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iw0_60937/09_2025/9iw0_60937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iw0_60937/09_2025/9iw0_60937.map" model { file = "/net/cci-nas-00/data/ceres_data/9iw0_60937/09_2025/9iw0_60937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iw0_60937/09_2025/9iw0_60937.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 14046 2.51 5 N 3735 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22122 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 7374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7374 Classifications: {'peptide': 927} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 866} Chain breaks: 1 Restraints were copied for chains: A, C Time building chain proxies: 8.18, per 1000 atoms: 0.37 Number of scatterers: 22122 At special positions: 0 Unit cell: (117.5, 120, 133.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4230 8.00 N 3735 7.00 C 14046 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: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5178 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 46 sheets defined 20.1% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.518A pdb=" N TYR B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 304 through 310 removed outlier: 3.568A pdb=" N GLY B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 310 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'B' and resid 334 through 338 removed outlier: 4.084A pdb=" N MET B 338 " --> pdb=" O THR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 470 through 473 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 518 through 523 removed outlier: 4.145A pdb=" N ASN B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 543 removed outlier: 3.803A pdb=" N LEU B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 615 through 627 Processing helix chain 'B' and resid 628 through 632 removed outlier: 4.032A pdb=" N ASP B 632 " --> pdb=" O ASP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 785 through 790 removed outlier: 4.121A pdb=" N ASN B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 814 Processing helix chain 'B' and resid 879 through 883 Processing helix chain 'B' and resid 884 through 889 Processing helix chain 'A' and resid 7 through 13 Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.518A pdb=" N TYR A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.568A pdb=" N GLY A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 310 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 327 Processing helix chain 'A' and resid 334 through 338 removed outlier: 4.084A pdb=" N MET A 338 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 473 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 518 through 523 removed outlier: 4.145A pdb=" N ASN A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 removed outlier: 3.803A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 615 through 627 Processing helix chain 'A' and resid 628 through 632 removed outlier: 4.032A pdb=" N ASP A 632 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 785 through 790 removed outlier: 4.121A pdb=" N ASN A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 879 through 883 Processing helix chain 'A' and resid 884 through 889 Processing helix chain 'C' and resid 7 through 13 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.518A pdb=" N TYR C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 24' Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 304 through 310 removed outlier: 3.568A pdb=" N GLY C 309 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 310 " --> pdb=" O ASN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 327 Processing helix chain 'C' and resid 334 through 338 removed outlier: 4.085A pdb=" N MET C 338 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 388 through 393 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 518 through 523 removed outlier: 4.145A pdb=" N ASN C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 543 removed outlier: 3.803A pdb=" N LEU C 542 " --> pdb=" O ARG C 538 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C 543 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 Processing helix chain 'C' and resid 615 through 627 Processing helix chain 'C' and resid 628 through 632 removed outlier: 4.033A pdb=" N ASP C 632 " --> pdb=" O ASP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 706 through 708 No H-bonds generated for 'chain 'C' and resid 706 through 708' Processing helix chain 'C' and resid 754 through 767 Processing helix chain 'C' and resid 785 through 790 removed outlier: 4.121A pdb=" N ASN C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 814 Processing helix chain 'C' and resid 879 through 883 Processing helix chain 'C' and resid 884 through 889 Processing sheet with id=AA1, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.603A pdb=" N ILE B 600 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP B 108 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE B 602 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 106 " --> pdb=" O PHE B 602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA4, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 159 removed outlier: 4.558A pdb=" N LYS B 209 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 443 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 153 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 157 through 159 removed outlier: 4.558A pdb=" N LYS B 209 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE B 210 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR B 281 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY B 212 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU B 283 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA B 214 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 278 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N MET B 261 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL A 424 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE B 263 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.907A pdb=" N ILE B 183 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 296 removed outlier: 6.285A pdb=" N GLN B 311 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AB1, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.541A pdb=" N TRP B 516 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 409 removed outlier: 4.120A pdb=" N ASN B 405 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN C 405 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 405 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 432 through 434 removed outlier: 6.846A pdb=" N GLU B 443 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA C 155 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR B 445 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS C 209 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 432 through 434 removed outlier: 4.076A pdb=" N PHE C 263 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL B 424 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N MET C 261 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 278 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE C 210 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR C 281 " --> pdb=" O PHE C 210 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY C 212 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU C 283 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 214 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS C 209 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 633 through 636 removed outlier: 3.732A pdb=" N GLN B 633 " --> pdb=" O VAL B 920 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 641 through 648 removed outlier: 4.416A pdb=" N GLY B 669 " --> pdb=" O GLU B 913 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER B 661 " --> pdb=" O HIS B 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS B 891 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 712 " --> pdb=" O GLU B 898 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER B 661 " --> pdb=" O HIS B 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS B 891 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 712 " --> pdb=" O GLU B 898 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 791 through 798 Processing sheet with id=AC1, first strand: chain 'A' and resid 65 through 68 removed outlier: 5.603A pdb=" N ILE A 600 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP A 108 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE A 602 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 106 " --> pdb=" O PHE A 602 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AC3, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AC4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AC5, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.558A pdb=" N LYS A 209 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU C 443 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 153 " --> pdb=" O GLU C 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.558A pdb=" N LYS A 209 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE A 210 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR A 281 " --> pdb=" O PHE A 210 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 212 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU A 283 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 214 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 278 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 12.828A pdb=" N MET A 261 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL C 424 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 263 " --> pdb=" O ILE C 422 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 168 through 171 removed outlier: 6.907A pdb=" N ILE A 183 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 292 through 296 removed outlier: 6.285A pdb=" N GLN A 311 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 320 through 322 Processing sheet with id=AD1, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.540A pdb=" N TRP A 516 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 633 through 636 removed outlier: 3.732A pdb=" N GLN A 633 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 641 through 648 removed outlier: 4.416A pdb=" N GLY A 669 " --> pdb=" O GLU A 913 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER A 661 " --> pdb=" O HIS A 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A 891 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 712 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER A 661 " --> pdb=" O HIS A 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A 891 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 712 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 791 through 798 Processing sheet with id=AD7, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.603A pdb=" N ILE C 600 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP C 108 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C 602 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 106 " --> pdb=" O PHE C 602 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AD9, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AE1, first strand: chain 'C' and resid 94 through 95 Processing sheet with id=AE2, first strand: chain 'C' and resid 168 through 171 removed outlier: 6.907A pdb=" N ILE C 183 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 292 through 296 removed outlier: 6.285A pdb=" N GLN C 311 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 320 through 322 Processing sheet with id=AE5, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.540A pdb=" N TRP C 516 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.732A pdb=" N GLN C 633 " --> pdb=" O VAL C 920 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 641 through 648 removed outlier: 4.416A pdb=" N GLY C 669 " --> pdb=" O GLU C 913 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER C 661 " --> pdb=" O HIS C 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS C 891 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 712 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 662 removed outlier: 4.394A pdb=" N SER C 661 " --> pdb=" O HIS C 891 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS C 891 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 712 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 791 through 798 701 hydrogen bonds defined for protein. 1788 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: 5.18 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5661 1.33 - 1.45: 4650 1.45 - 1.57: 12204 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 22725 Sorted by residual: bond pdb=" CA PRO C 481 " pdb=" C PRO C 481 " ideal model delta sigma weight residual 1.514 1.537 -0.022 5.50e-03 3.31e+04 1.63e+01 bond pdb=" CA PRO B 481 " pdb=" C PRO B 481 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.56e+01 bond pdb=" CA PRO A 481 " pdb=" C PRO A 481 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.55e+01 bond pdb=" N VAL A 721 " pdb=" CA VAL A 721 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" N VAL C 721 " pdb=" CA VAL C 721 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.17e-02 7.31e+03 1.18e+01 ... (remaining 22720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 30281 2.24 - 4.48: 608 4.48 - 6.72: 50 6.72 - 8.97: 9 8.97 - 11.21: 6 Bond angle restraints: 30954 Sorted by residual: angle pdb=" N ASN A 437 " pdb=" CA ASN A 437 " pdb=" C ASN A 437 " ideal model delta sigma weight residual 113.30 102.09 11.21 1.34e+00 5.57e-01 7.00e+01 angle pdb=" N ASN B 437 " pdb=" CA ASN B 437 " pdb=" C ASN B 437 " ideal model delta sigma weight residual 113.30 102.12 11.18 1.34e+00 5.57e-01 6.97e+01 angle pdb=" N ASN C 437 " pdb=" CA ASN C 437 " pdb=" C ASN C 437 " ideal model delta sigma weight residual 113.30 102.12 11.18 1.34e+00 5.57e-01 6.96e+01 angle pdb=" C ASN A 150 " pdb=" CA ASN A 150 " pdb=" CB ASN A 150 " ideal model delta sigma weight residual 110.22 119.51 -9.29 1.67e+00 3.59e-01 3.09e+01 angle pdb=" C ASN C 150 " pdb=" CA ASN C 150 " pdb=" CB ASN C 150 " ideal model delta sigma weight residual 110.22 119.50 -9.28 1.67e+00 3.59e-01 3.09e+01 ... (remaining 30949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 11403 16.77 - 33.54: 1517 33.54 - 50.32: 409 50.32 - 67.09: 105 67.09 - 83.86: 27 Dihedral angle restraints: 13461 sinusoidal: 5343 harmonic: 8118 Sorted by residual: dihedral pdb=" N THR B 148 " pdb=" C THR B 148 " pdb=" CA THR B 148 " pdb=" CB THR B 148 " ideal model delta harmonic sigma weight residual 123.40 133.84 -10.44 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" N THR A 148 " pdb=" C THR A 148 " pdb=" CA THR A 148 " pdb=" CB THR A 148 " ideal model delta harmonic sigma weight residual 123.40 133.84 -10.44 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" N THR C 148 " pdb=" C THR C 148 " pdb=" CA THR C 148 " pdb=" CB THR C 148 " ideal model delta harmonic sigma weight residual 123.40 133.83 -10.43 0 2.50e+00 1.60e-01 1.74e+01 ... (remaining 13458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2938 0.084 - 0.169: 336 0.169 - 0.253: 14 0.253 - 0.337: 3 0.337 - 0.422: 3 Chirality restraints: 3294 Sorted by residual: chirality pdb=" CA THR B 148 " pdb=" N THR B 148 " pdb=" C THR B 148 " pdb=" CB THR B 148 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA THR A 148 " pdb=" N THR A 148 " pdb=" C THR A 148 " pdb=" CB THR A 148 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA THR C 148 " pdb=" N THR C 148 " pdb=" C THR C 148 " pdb=" CB THR C 148 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 3291 not shown) Planarity restraints: 4089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 434 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C LYS C 434 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS C 434 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP C 435 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 434 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C LYS A 434 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS A 434 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 435 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 434 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C LYS B 434 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS B 434 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP B 435 " 0.013 2.00e-02 2.50e+03 ... (remaining 4086 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2210 2.74 - 3.28: 21242 3.28 - 3.82: 37548 3.82 - 4.36: 46868 4.36 - 4.90: 79170 Nonbonded interactions: 187038 Sorted by model distance: nonbonded pdb=" OG1 THR B 58 " pdb=" O MET B 614 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR A 58 " pdb=" O MET A 614 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 58 " pdb=" O MET C 614 " model vdw 2.204 3.040 nonbonded pdb=" N GLU A 208 " pdb=" OE1 GLU A 208 " model vdw 2.218 3.120 nonbonded pdb=" N GLU C 208 " pdb=" OE1 GLU C 208 " model vdw 2.218 3.120 ... (remaining 187033 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } 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: 2.330 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.430 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.005 0.040 22725 Z= 0.274 Angle : 0.722 11.208 30954 Z= 0.434 Chirality : 0.052 0.422 3294 Planarity : 0.005 0.053 4089 Dihedral : 16.703 83.860 8283 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.33 % Favored : 95.45 % Rotamer: Outliers : 1.54 % Allowed : 23.87 % Favored : 74.60 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.15), residues: 2769 helix: 0.22 (0.30), residues: 327 sheet: 0.14 (0.20), residues: 585 loop : -0.98 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 668 TYR 0.025 0.002 TYR A 23 PHE 0.011 0.001 PHE C 667 TRP 0.015 0.002 TRP C 723 HIS 0.007 0.001 HIS C 708 Details of bonding type rmsd covalent geometry : bond 0.00486 (22725) covalent geometry : angle 0.72221 (30954) hydrogen bonds : bond 0.23756 ( 623) hydrogen bonds : angle 9.07879 ( 1788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 587 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8006 (tppp) cc_final: 0.7749 (tppp) REVERT: B 190 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7737 (mm-40) REVERT: B 490 THR cc_start: 0.7768 (p) cc_final: 0.7563 (m) REVERT: B 823 TYR cc_start: 0.8670 (t80) cc_final: 0.8377 (t80) REVERT: A 14 HIS cc_start: 0.8079 (m-70) cc_final: 0.7694 (m-70) REVERT: A 22 GLU cc_start: 0.6825 (mp0) cc_final: 0.6490 (mp0) REVERT: A 23 TYR cc_start: 0.8176 (p90) cc_final: 0.7968 (p90) REVERT: A 33 ARG cc_start: 0.6736 (mtm180) cc_final: 0.6427 (mtm180) REVERT: A 84 TYR cc_start: 0.7765 (m-80) cc_final: 0.7432 (m-80) REVERT: A 88 VAL cc_start: 0.8465 (t) cc_final: 0.8125 (m) REVERT: A 181 LYS cc_start: 0.8045 (tptp) cc_final: 0.7720 (mptp) REVERT: A 190 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7491 (mm-40) REVERT: A 221 MET cc_start: 0.8056 (mtt) cc_final: 0.7664 (mtp) REVERT: A 288 GLU cc_start: 0.7352 (pt0) cc_final: 0.7150 (pt0) REVERT: A 372 ASP cc_start: 0.8031 (t0) cc_final: 0.7787 (t0) REVERT: A 612 PHE cc_start: 0.8579 (t80) cc_final: 0.8144 (t80) REVERT: A 614 MET cc_start: 0.7134 (ttm) cc_final: 0.6901 (ttm) REVERT: A 663 ASN cc_start: 0.8325 (t0) cc_final: 0.7995 (t0) REVERT: A 678 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7805 (tttm) REVERT: A 692 VAL cc_start: 0.8432 (m) cc_final: 0.8085 (t) REVERT: A 723 TRP cc_start: 0.8354 (t60) cc_final: 0.8130 (t60) REVERT: A 727 ASP cc_start: 0.8020 (t0) cc_final: 0.7475 (t0) REVERT: A 774 TYR cc_start: 0.8206 (p90) cc_final: 0.7900 (p90) REVERT: A 864 ARG cc_start: 0.7557 (mtp85) cc_final: 0.7339 (mtp-110) REVERT: C 22 GLU cc_start: 0.7161 (mp0) cc_final: 0.6848 (mp0) REVERT: C 49 THR cc_start: 0.8102 (m) cc_final: 0.7861 (p) REVERT: C 81 LYS cc_start: 0.8257 (tppp) cc_final: 0.7886 (tptt) REVERT: C 92 ARG cc_start: 0.7488 (mmt90) cc_final: 0.7140 (mtt-85) REVERT: C 137 VAL cc_start: 0.8147 (t) cc_final: 0.7832 (p) REVERT: C 161 ASN cc_start: 0.8343 (t0) cc_final: 0.8087 (t0) REVERT: C 190 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7164 (mm-40) REVERT: C 294 VAL cc_start: 0.8586 (t) cc_final: 0.8283 (p) REVERT: C 330 MET cc_start: 0.8104 (mtp) cc_final: 0.7835 (mtt) REVERT: C 443 GLU cc_start: 0.7592 (pt0) cc_final: 0.7075 (pm20) REVERT: C 540 MET cc_start: 0.8498 (mtt) cc_final: 0.8246 (mtt) REVERT: C 570 SER cc_start: 0.8060 (m) cc_final: 0.7415 (p) REVERT: C 604 SER cc_start: 0.8339 (m) cc_final: 0.8037 (p) REVERT: C 622 LEU cc_start: 0.7854 (tp) cc_final: 0.7563 (tp) REVERT: C 623 GLU cc_start: 0.7082 (pm20) cc_final: 0.6679 (mp0) REVERT: C 629 ASP cc_start: 0.7455 (t0) cc_final: 0.6882 (m-30) REVERT: C 630 THR cc_start: 0.8425 (p) cc_final: 0.8089 (p) REVERT: C 716 MET cc_start: 0.7529 (tpp) cc_final: 0.7180 (mpp) REVERT: C 727 ASP cc_start: 0.7929 (t0) cc_final: 0.7263 (t0) REVERT: C 747 ASN cc_start: 0.8281 (m-40) cc_final: 0.7968 (m-40) REVERT: C 752 ASN cc_start: 0.7869 (p0) cc_final: 0.7632 (p0) REVERT: C 762 MET cc_start: 0.8448 (mmp) cc_final: 0.8098 (mmt) REVERT: C 811 LEU cc_start: 0.8451 (tp) cc_final: 0.8229 (tp) REVERT: C 864 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7205 (mtm-85) outliers start: 37 outliers final: 15 residues processed: 610 average time/residue: 0.1867 time to fit residues: 168.5064 Evaluate side-chains 576 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 557 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 678 LYS Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 935 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN B 143 ASN B 220 ASN B 284 ASN A 122 ASN A 143 ASN A 726 ASN A 747 ASN C 122 ASN C 143 ASN C 382 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090035 restraints weight = 34570.306| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.01 r_work: 0.2935 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22725 Z= 0.175 Angle : 0.587 7.427 30954 Z= 0.313 Chirality : 0.047 0.165 3294 Planarity : 0.005 0.048 4089 Dihedral : 5.708 58.499 3108 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.78 % Allowed : 22.62 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.15), residues: 2769 helix: 0.69 (0.30), residues: 309 sheet: 0.19 (0.20), residues: 606 loop : -0.98 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 925 TYR 0.016 0.002 TYR A 779 PHE 0.016 0.002 PHE A 667 TRP 0.014 0.002 TRP B 723 HIS 0.005 0.001 HIS C 815 Details of bonding type rmsd covalent geometry : bond 0.00394 (22725) covalent geometry : angle 0.58665 (30954) hydrogen bonds : bond 0.04572 ( 623) hydrogen bonds : angle 6.11862 ( 1788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 558 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8366 (tppp) cc_final: 0.8044 (ttpt) REVERT: B 190 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: B 192 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7289 (mm-30) REVERT: B 438 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8699 (m) REVERT: B 583 MET cc_start: 0.8566 (mmm) cc_final: 0.7996 (mmm) REVERT: B 623 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: B 630 THR cc_start: 0.8342 (p) cc_final: 0.8058 (p) REVERT: B 658 SER cc_start: 0.8232 (t) cc_final: 0.7772 (p) REVERT: B 716 MET cc_start: 0.7587 (tpp) cc_final: 0.7179 (mmm) REVERT: B 823 TYR cc_start: 0.8731 (t80) cc_final: 0.8419 (t80) REVERT: A 14 HIS cc_start: 0.8180 (m-70) cc_final: 0.7846 (m-70) REVERT: A 30 GLN cc_start: 0.6623 (mp-120) cc_final: 0.6148 (mp-120) REVERT: A 33 ARG cc_start: 0.7242 (mtm180) cc_final: 0.6804 (mtm180) REVERT: A 74 GLU cc_start: 0.7321 (tp30) cc_final: 0.7060 (tp30) REVERT: A 81 LYS cc_start: 0.8483 (tppp) cc_final: 0.8209 (tttp) REVERT: A 82 VAL cc_start: 0.8089 (m) cc_final: 0.7843 (m) REVERT: A 181 LYS cc_start: 0.7966 (tptp) cc_final: 0.7664 (mptp) REVERT: A 190 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7530 (mt0) REVERT: A 221 MET cc_start: 0.8214 (mtt) cc_final: 0.7803 (mtp) REVERT: A 353 ASP cc_start: 0.7567 (t0) cc_final: 0.7324 (t0) REVERT: A 372 ASP cc_start: 0.8155 (t0) cc_final: 0.7895 (t0) REVERT: A 494 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7364 (tt0) REVERT: A 496 MET cc_start: 0.7930 (mtt) cc_final: 0.7534 (mtp) REVERT: A 574 GLU cc_start: 0.7783 (tt0) cc_final: 0.7346 (tm-30) REVERT: A 612 PHE cc_start: 0.8589 (t80) cc_final: 0.8083 (t80) REVERT: A 622 LEU cc_start: 0.8031 (tp) cc_final: 0.7775 (tt) REVERT: A 623 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: A 630 THR cc_start: 0.8364 (p) cc_final: 0.8118 (p) REVERT: A 632 ASP cc_start: 0.7726 (m-30) cc_final: 0.7440 (m-30) REVERT: A 644 MET cc_start: 0.7824 (tpp) cc_final: 0.7594 (mmp) REVERT: A 663 ASN cc_start: 0.8344 (t0) cc_final: 0.8023 (t0) REVERT: A 668 ARG cc_start: 0.6249 (mtm-85) cc_final: 0.5860 (mtm-85) REVERT: A 692 VAL cc_start: 0.8436 (m) cc_final: 0.8032 (t) REVERT: A 716 MET cc_start: 0.7515 (tpp) cc_final: 0.7178 (mmm) REVERT: A 727 ASP cc_start: 0.7957 (t0) cc_final: 0.7503 (t0) REVERT: A 774 TYR cc_start: 0.8179 (p90) cc_final: 0.7561 (p90) REVERT: A 864 ARG cc_start: 0.7475 (mtp85) cc_final: 0.7257 (ttm-80) REVERT: A 925 ARG cc_start: 0.7503 (mtp-110) cc_final: 0.7275 (mtp-110) REVERT: C 29 VAL cc_start: 0.7298 (p) cc_final: 0.7003 (m) REVERT: C 33 ARG cc_start: 0.7132 (mtm180) cc_final: 0.6702 (mtm110) REVERT: C 49 THR cc_start: 0.8111 (m) cc_final: 0.7830 (p) REVERT: C 81 LYS cc_start: 0.8481 (tppp) cc_final: 0.8258 (tttt) REVERT: C 92 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7415 (mtt-85) REVERT: C 137 VAL cc_start: 0.8264 (t) cc_final: 0.7988 (p) REVERT: C 161 ASN cc_start: 0.8402 (t0) cc_final: 0.8139 (t0) REVERT: C 190 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: C 294 VAL cc_start: 0.8548 (t) cc_final: 0.8261 (p) REVERT: C 330 MET cc_start: 0.8126 (mtp) cc_final: 0.7885 (mtt) REVERT: C 443 GLU cc_start: 0.7823 (pt0) cc_final: 0.7468 (pm20) REVERT: C 510 ILE cc_start: 0.7573 (tp) cc_final: 0.7367 (tt) REVERT: C 540 MET cc_start: 0.8460 (mtt) cc_final: 0.8168 (mtt) REVERT: C 570 SER cc_start: 0.8091 (m) cc_final: 0.7619 (p) REVERT: C 571 TYR cc_start: 0.8054 (m-10) cc_final: 0.7808 (m-80) REVERT: C 622 LEU cc_start: 0.7896 (tp) cc_final: 0.7613 (tt) REVERT: C 630 THR cc_start: 0.8350 (p) cc_final: 0.8083 (p) REVERT: C 664 TRP cc_start: 0.8037 (m100) cc_final: 0.7735 (m100) REVERT: C 716 MET cc_start: 0.7664 (tpp) cc_final: 0.7160 (mpp) REVERT: C 727 ASP cc_start: 0.7869 (t0) cc_final: 0.7234 (t0) REVERT: C 747 ASN cc_start: 0.8261 (m-40) cc_final: 0.7974 (m110) REVERT: C 784 TYR cc_start: 0.7299 (m-80) cc_final: 0.6656 (m-80) REVERT: C 864 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7349 (mtm-85) REVERT: C 916 ASP cc_start: 0.7747 (t0) cc_final: 0.7417 (t0) outliers start: 91 outliers final: 49 residues processed: 606 average time/residue: 0.1804 time to fit residues: 162.4916 Evaluate side-chains 594 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 539 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 935 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 284 ASN B 606 ASN C 643 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.089381 restraints weight = 34416.504| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.02 r_work: 0.2910 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22725 Z= 0.194 Angle : 0.573 7.690 30954 Z= 0.305 Chirality : 0.046 0.164 3294 Planarity : 0.005 0.052 4089 Dihedral : 5.489 58.154 3093 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.69 % Allowed : 22.67 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.15), residues: 2769 helix: 0.39 (0.30), residues: 327 sheet: -0.04 (0.19), residues: 630 loop : -0.94 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 829 TYR 0.016 0.002 TYR B 116 PHE 0.018 0.002 PHE B 672 TRP 0.016 0.002 TRP B 723 HIS 0.007 0.001 HIS C 815 Details of bonding type rmsd covalent geometry : bond 0.00445 (22725) covalent geometry : angle 0.57276 (30954) hydrogen bonds : bond 0.04443 ( 623) hydrogen bonds : angle 5.81945 ( 1788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 564 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7369 (mp0) cc_final: 0.6943 (mp0) REVERT: B 81 LYS cc_start: 0.8381 (tppp) cc_final: 0.8081 (ttpt) REVERT: B 190 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: B 192 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 583 MET cc_start: 0.8554 (mmm) cc_final: 0.7943 (mmm) REVERT: B 623 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: B 630 THR cc_start: 0.8337 (p) cc_final: 0.8052 (p) REVERT: B 658 SER cc_start: 0.8190 (t) cc_final: 0.7785 (p) REVERT: B 716 MET cc_start: 0.7595 (tpp) cc_final: 0.7157 (mmm) REVERT: B 734 GLU cc_start: 0.7911 (pm20) cc_final: 0.7659 (pm20) REVERT: B 823 TYR cc_start: 0.8734 (t80) cc_final: 0.8475 (t80) REVERT: B 828 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7608 (ttm) REVERT: A 14 HIS cc_start: 0.8223 (m-70) cc_final: 0.7981 (m-70) REVERT: A 30 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6148 (mp-120) REVERT: A 33 ARG cc_start: 0.7210 (mtm180) cc_final: 0.6761 (mtm180) REVERT: A 58 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7798 (m) REVERT: A 81 LYS cc_start: 0.8427 (tppp) cc_final: 0.8056 (tttm) REVERT: A 164 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8249 (ttpp) REVERT: A 181 LYS cc_start: 0.7990 (tptp) cc_final: 0.7686 (mptp) REVERT: A 190 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: A 198 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: A 221 MET cc_start: 0.8216 (mtt) cc_final: 0.7787 (mtp) REVERT: A 288 GLU cc_start: 0.7535 (pt0) cc_final: 0.7274 (pt0) REVERT: A 295 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 353 ASP cc_start: 0.7606 (t0) cc_final: 0.7381 (t0) REVERT: A 438 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8520 (m) REVERT: A 574 GLU cc_start: 0.7787 (tt0) cc_final: 0.7215 (tm-30) REVERT: A 622 LEU cc_start: 0.8093 (tp) cc_final: 0.7856 (tt) REVERT: A 623 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: A 630 THR cc_start: 0.8387 (p) cc_final: 0.8129 (p) REVERT: A 632 ASP cc_start: 0.7723 (m-30) cc_final: 0.7392 (m-30) REVERT: A 637 ASP cc_start: 0.7727 (t0) cc_final: 0.7432 (t70) REVERT: A 644 MET cc_start: 0.7823 (tpp) cc_final: 0.7586 (mmp) REVERT: A 663 ASN cc_start: 0.8305 (t0) cc_final: 0.7992 (t0) REVERT: A 668 ARG cc_start: 0.6497 (mtm-85) cc_final: 0.6039 (mtm-85) REVERT: A 692 VAL cc_start: 0.8440 (m) cc_final: 0.8009 (t) REVERT: A 716 MET cc_start: 0.7573 (tpp) cc_final: 0.7192 (mmm) REVERT: A 727 ASP cc_start: 0.7916 (t0) cc_final: 0.7479 (t0) REVERT: A 774 TYR cc_start: 0.8165 (p90) cc_final: 0.7652 (p90) REVERT: C 29 VAL cc_start: 0.7299 (p) cc_final: 0.6957 (m) REVERT: C 33 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6715 (mtm110) REVERT: C 49 THR cc_start: 0.8142 (m) cc_final: 0.7805 (p) REVERT: C 58 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7843 (m) REVERT: C 137 VAL cc_start: 0.8267 (t) cc_final: 0.8001 (p) REVERT: C 161 ASN cc_start: 0.8372 (t0) cc_final: 0.8079 (t0) REVERT: C 190 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7389 (mt0) REVERT: C 277 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6931 (mp0) REVERT: C 294 VAL cc_start: 0.8564 (t) cc_final: 0.8293 (p) REVERT: C 330 MET cc_start: 0.8149 (mtp) cc_final: 0.7893 (mtt) REVERT: C 438 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8517 (m) REVERT: C 453 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.7020 (mm-30) REVERT: C 510 ILE cc_start: 0.7616 (tp) cc_final: 0.7400 (tt) REVERT: C 540 MET cc_start: 0.8431 (mtt) cc_final: 0.8144 (mtt) REVERT: C 570 SER cc_start: 0.8086 (m) cc_final: 0.7600 (p) REVERT: C 571 TYR cc_start: 0.8088 (m-10) cc_final: 0.7811 (m-80) REVERT: C 622 LEU cc_start: 0.7894 (tp) cc_final: 0.7631 (tt) REVERT: C 630 THR cc_start: 0.8397 (p) cc_final: 0.8185 (p) REVERT: C 664 TRP cc_start: 0.8025 (m100) cc_final: 0.7788 (m100) REVERT: C 716 MET cc_start: 0.7666 (tpp) cc_final: 0.7161 (mpp) REVERT: C 727 ASP cc_start: 0.7881 (t0) cc_final: 0.7305 (t0) REVERT: C 747 ASN cc_start: 0.8278 (m-40) cc_final: 0.7953 (m110) REVERT: C 779 TYR cc_start: 0.7765 (p90) cc_final: 0.7506 (p90) REVERT: C 864 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7438 (mtm-85) REVERT: C 916 ASP cc_start: 0.7759 (t0) cc_final: 0.7406 (t0) outliers start: 113 outliers final: 67 residues processed: 619 average time/residue: 0.1866 time to fit residues: 170.0683 Evaluate side-chains 637 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 556 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 711 LYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 935 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 156 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN A 726 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.088463 restraints weight = 34586.597| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.04 r_work: 0.2899 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22725 Z= 0.200 Angle : 0.571 7.246 30954 Z= 0.304 Chirality : 0.046 0.166 3294 Planarity : 0.005 0.055 4089 Dihedral : 5.436 56.634 3093 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.77 % Allowed : 23.04 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.15), residues: 2769 helix: 0.07 (0.29), residues: 348 sheet: -0.11 (0.19), residues: 630 loop : -0.94 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 242 TYR 0.017 0.002 TYR A 84 PHE 0.019 0.002 PHE B 672 TRP 0.014 0.002 TRP B 723 HIS 0.007 0.001 HIS C 815 Details of bonding type rmsd covalent geometry : bond 0.00461 (22725) covalent geometry : angle 0.57117 (30954) hydrogen bonds : bond 0.04170 ( 623) hydrogen bonds : angle 5.68853 ( 1788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 571 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7459 (mp0) cc_final: 0.6945 (mp0) REVERT: B 81 LYS cc_start: 0.8404 (tppp) cc_final: 0.8100 (ttpt) REVERT: B 190 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: B 192 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 475 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: B 583 MET cc_start: 0.8547 (mmm) cc_final: 0.7968 (mmm) REVERT: B 623 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: B 630 THR cc_start: 0.8311 (p) cc_final: 0.8059 (p) REVERT: B 658 SER cc_start: 0.8205 (t) cc_final: 0.7798 (p) REVERT: B 716 MET cc_start: 0.7598 (tpp) cc_final: 0.7126 (mmm) REVERT: B 734 GLU cc_start: 0.7855 (pm20) cc_final: 0.7558 (pm20) REVERT: B 823 TYR cc_start: 0.8734 (t80) cc_final: 0.8444 (t80) REVERT: B 828 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7604 (ttm) REVERT: A 30 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.6405 (mp-120) REVERT: A 58 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7815 (m) REVERT: A 74 GLU cc_start: 0.7365 (tp30) cc_final: 0.7067 (tp30) REVERT: A 81 LYS cc_start: 0.8403 (tppp) cc_final: 0.8096 (tttm) REVERT: A 181 LYS cc_start: 0.8034 (tptp) cc_final: 0.7713 (mptp) REVERT: A 190 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: A 198 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 221 MET cc_start: 0.8209 (mtt) cc_final: 0.7776 (mtp) REVERT: A 288 GLU cc_start: 0.7597 (pt0) cc_final: 0.7302 (pt0) REVERT: A 295 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8331 (p) REVERT: A 386 SER cc_start: 0.7775 (p) cc_final: 0.7355 (m) REVERT: A 399 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7496 (mm) REVERT: A 574 GLU cc_start: 0.7791 (tt0) cc_final: 0.7259 (tm-30) REVERT: A 612 PHE cc_start: 0.8561 (t80) cc_final: 0.8163 (t80) REVERT: A 622 LEU cc_start: 0.8108 (tp) cc_final: 0.7870 (tt) REVERT: A 623 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: A 630 THR cc_start: 0.8418 (p) cc_final: 0.8181 (p) REVERT: A 632 ASP cc_start: 0.7813 (m-30) cc_final: 0.7556 (m-30) REVERT: A 637 ASP cc_start: 0.7785 (t0) cc_final: 0.7475 (t70) REVERT: A 644 MET cc_start: 0.7754 (tpp) cc_final: 0.7543 (mmp) REVERT: A 663 ASN cc_start: 0.8307 (t0) cc_final: 0.8009 (t0) REVERT: A 668 ARG cc_start: 0.6484 (mtm-85) cc_final: 0.5967 (mtm-85) REVERT: A 692 VAL cc_start: 0.8429 (m) cc_final: 0.7985 (t) REVERT: A 716 MET cc_start: 0.7560 (tpp) cc_final: 0.7183 (mmm) REVERT: A 727 ASP cc_start: 0.7895 (t0) cc_final: 0.7452 (t0) REVERT: A 734 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: A 774 TYR cc_start: 0.8151 (p90) cc_final: 0.7686 (p90) REVERT: A 928 ILE cc_start: 0.8486 (mm) cc_final: 0.8055 (mm) REVERT: C 29 VAL cc_start: 0.7310 (p) cc_final: 0.6930 (m) REVERT: C 31 PHE cc_start: 0.8268 (t80) cc_final: 0.7882 (t80) REVERT: C 33 ARG cc_start: 0.7174 (mtm180) cc_final: 0.6748 (mtm110) REVERT: C 49 THR cc_start: 0.8149 (m) cc_final: 0.7801 (p) REVERT: C 58 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7904 (m) REVERT: C 60 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6695 (mtm180) REVERT: C 137 VAL cc_start: 0.8252 (t) cc_final: 0.8015 (p) REVERT: C 161 ASN cc_start: 0.8370 (t0) cc_final: 0.8071 (t0) REVERT: C 277 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6911 (mp0) REVERT: C 294 VAL cc_start: 0.8555 (t) cc_final: 0.8310 (p) REVERT: C 330 MET cc_start: 0.8160 (mtp) cc_final: 0.7903 (mtm) REVERT: C 437 ASN cc_start: 0.7831 (m-40) cc_final: 0.7507 (t0) REVERT: C 453 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: C 510 ILE cc_start: 0.7609 (tp) cc_final: 0.7406 (tt) REVERT: C 540 MET cc_start: 0.8421 (mtt) cc_final: 0.8109 (mtt) REVERT: C 570 SER cc_start: 0.8093 (m) cc_final: 0.7634 (p) REVERT: C 571 TYR cc_start: 0.8063 (m-80) cc_final: 0.7757 (m-80) REVERT: C 622 LEU cc_start: 0.7918 (tp) cc_final: 0.7643 (tt) REVERT: C 630 THR cc_start: 0.8395 (p) cc_final: 0.8046 (p) REVERT: C 632 ASP cc_start: 0.7805 (m-30) cc_final: 0.7416 (m-30) REVERT: C 640 SER cc_start: 0.7845 (t) cc_final: 0.7645 (t) REVERT: C 716 MET cc_start: 0.7689 (tpp) cc_final: 0.7169 (mpp) REVERT: C 727 ASP cc_start: 0.7877 (t0) cc_final: 0.7306 (t0) REVERT: C 747 ASN cc_start: 0.8252 (m-40) cc_final: 0.7979 (m110) REVERT: C 800 GLU cc_start: 0.8018 (mp0) cc_final: 0.7816 (mp0) REVERT: C 916 ASP cc_start: 0.7726 (t0) cc_final: 0.7338 (t0) REVERT: C 919 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6988 (ttm-80) REVERT: C 929 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7067 (pp20) outliers start: 115 outliers final: 88 residues processed: 625 average time/residue: 0.1913 time to fit residues: 175.7301 Evaluate side-chains 658 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 556 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 711 LYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 921 HIS Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 935 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 228 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 242 optimal weight: 0.3980 chunk 233 optimal weight: 0.0870 chunk 144 optimal weight: 0.9980 chunk 222 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN B 888 ASN A 726 ASN C 405 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.089857 restraints weight = 34214.990| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.03 r_work: 0.2917 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22725 Z= 0.114 Angle : 0.525 7.372 30954 Z= 0.278 Chirality : 0.044 0.161 3294 Planarity : 0.004 0.047 4089 Dihedral : 5.061 56.831 3090 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.40 % Allowed : 23.70 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.15), residues: 2769 helix: 0.25 (0.29), residues: 348 sheet: -0.01 (0.20), residues: 630 loop : -0.82 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 668 TYR 0.013 0.001 TYR A 495 PHE 0.014 0.001 PHE B 672 TRP 0.013 0.001 TRP B 723 HIS 0.006 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00256 (22725) covalent geometry : angle 0.52474 (30954) hydrogen bonds : bond 0.03577 ( 623) hydrogen bonds : angle 5.50898 ( 1788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 560 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7502 (mp0) cc_final: 0.6993 (mp0) REVERT: B 81 LYS cc_start: 0.8393 (tppp) cc_final: 0.8135 (ttpt) REVERT: B 190 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: B 192 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 406 TYR cc_start: 0.8432 (m-80) cc_final: 0.8160 (m-10) REVERT: B 475 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: B 583 MET cc_start: 0.8552 (mmm) cc_final: 0.8001 (mmm) REVERT: B 623 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6894 (pm20) REVERT: B 630 THR cc_start: 0.8284 (p) cc_final: 0.8042 (p) REVERT: B 658 SER cc_start: 0.8195 (t) cc_final: 0.7737 (m) REVERT: B 716 MET cc_start: 0.7586 (tpp) cc_final: 0.7099 (mmm) REVERT: B 734 GLU cc_start: 0.7801 (pm20) cc_final: 0.7595 (pm20) REVERT: B 823 TYR cc_start: 0.8704 (t80) cc_final: 0.8437 (t80) REVERT: B 832 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6807 (tt0) REVERT: A 6 MET cc_start: 0.5453 (ttt) cc_final: 0.5092 (tpp) REVERT: A 58 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7825 (m) REVERT: A 74 GLU cc_start: 0.7400 (tp30) cc_final: 0.7069 (tp30) REVERT: A 81 LYS cc_start: 0.8383 (tppp) cc_final: 0.8167 (tttm) REVERT: A 151 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8197 (m) REVERT: A 181 LYS cc_start: 0.8024 (tptp) cc_final: 0.7696 (mptp) REVERT: A 190 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: A 198 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6932 (mm-30) REVERT: A 221 MET cc_start: 0.8203 (mtt) cc_final: 0.7932 (mtp) REVERT: A 288 GLU cc_start: 0.7609 (pt0) cc_final: 0.7317 (pt0) REVERT: A 370 LEU cc_start: 0.8377 (mt) cc_final: 0.8177 (mp) REVERT: A 399 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7484 (mm) REVERT: A 437 ASN cc_start: 0.7870 (m-40) cc_final: 0.7496 (t0) REVERT: A 438 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8477 (m) REVERT: A 574 GLU cc_start: 0.7756 (tt0) cc_final: 0.7286 (tm-30) REVERT: A 612 PHE cc_start: 0.8564 (t80) cc_final: 0.8176 (t80) REVERT: A 623 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: A 630 THR cc_start: 0.8297 (p) cc_final: 0.8025 (p) REVERT: A 637 ASP cc_start: 0.7796 (t0) cc_final: 0.7490 (t70) REVERT: A 644 MET cc_start: 0.7764 (tpp) cc_final: 0.7532 (mmp) REVERT: A 663 ASN cc_start: 0.8294 (t0) cc_final: 0.7972 (t0) REVERT: A 692 VAL cc_start: 0.8414 (m) cc_final: 0.7917 (t) REVERT: A 716 MET cc_start: 0.7529 (tpp) cc_final: 0.7132 (mmm) REVERT: A 727 ASP cc_start: 0.7884 (t0) cc_final: 0.7431 (t0) REVERT: A 734 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: A 774 TYR cc_start: 0.8068 (p90) cc_final: 0.7736 (p90) REVERT: A 928 ILE cc_start: 0.8467 (mm) cc_final: 0.8038 (mm) REVERT: C 31 PHE cc_start: 0.8285 (t80) cc_final: 0.7850 (t80) REVERT: C 33 ARG cc_start: 0.7150 (mtm180) cc_final: 0.6735 (mtm110) REVERT: C 49 THR cc_start: 0.8112 (m) cc_final: 0.7830 (p) REVERT: C 58 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7941 (m) REVERT: C 60 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6666 (mtm180) REVERT: C 74 GLU cc_start: 0.7431 (tp30) cc_final: 0.7163 (tp30) REVERT: C 75 ASP cc_start: 0.7462 (m-30) cc_final: 0.7102 (m-30) REVERT: C 157 MET cc_start: 0.7767 (ttt) cc_final: 0.7544 (tpp) REVERT: C 161 ASN cc_start: 0.8299 (t0) cc_final: 0.7995 (t0) REVERT: C 277 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6829 (mp0) REVERT: C 294 VAL cc_start: 0.8562 (t) cc_final: 0.8297 (p) REVERT: C 330 MET cc_start: 0.8124 (mtp) cc_final: 0.7881 (mtm) REVERT: C 437 ASN cc_start: 0.7939 (m-40) cc_final: 0.7696 (t0) REVERT: C 453 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: C 484 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7916 (mt) REVERT: C 490 THR cc_start: 0.7855 (p) cc_final: 0.7632 (m) REVERT: C 510 ILE cc_start: 0.7605 (tp) cc_final: 0.7370 (tt) REVERT: C 570 SER cc_start: 0.8089 (m) cc_final: 0.7599 (p) REVERT: C 571 TYR cc_start: 0.7985 (m-80) cc_final: 0.7655 (m-80) REVERT: C 622 LEU cc_start: 0.7922 (tp) cc_final: 0.7652 (tt) REVERT: C 630 THR cc_start: 0.8362 (p) cc_final: 0.8001 (p) REVERT: C 632 ASP cc_start: 0.7675 (m-30) cc_final: 0.7177 (m-30) REVERT: C 637 ASP cc_start: 0.7395 (t0) cc_final: 0.7166 (t70) REVERT: C 640 SER cc_start: 0.7800 (t) cc_final: 0.7589 (t) REVERT: C 716 MET cc_start: 0.7669 (tpp) cc_final: 0.7141 (mpp) REVERT: C 727 ASP cc_start: 0.7827 (t0) cc_final: 0.7237 (t0) REVERT: C 747 ASN cc_start: 0.8225 (m-40) cc_final: 0.7978 (m110) REVERT: C 779 TYR cc_start: 0.7804 (p90) cc_final: 0.7538 (p90) REVERT: C 800 GLU cc_start: 0.8075 (mp0) cc_final: 0.7865 (mp0) REVERT: C 916 ASP cc_start: 0.7674 (t0) cc_final: 0.7315 (t0) REVERT: C 919 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6935 (ttm-80) REVERT: C 929 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7044 (pp20) outliers start: 106 outliers final: 70 residues processed: 615 average time/residue: 0.1925 time to fit residues: 173.8776 Evaluate side-chains 636 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 552 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 728 ARG Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 711 LYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 149 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 214 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 187 optimal weight: 0.0170 chunk 167 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN C 636 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089797 restraints weight = 34721.542| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.06 r_work: 0.2923 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22725 Z= 0.112 Angle : 0.519 6.737 30954 Z= 0.275 Chirality : 0.044 0.159 3294 Planarity : 0.004 0.047 4089 Dihedral : 4.840 57.590 3083 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.48 % Allowed : 23.45 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.16), residues: 2769 helix: 0.32 (0.29), residues: 345 sheet: 0.02 (0.20), residues: 630 loop : -0.77 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 242 TYR 0.018 0.001 TYR A 84 PHE 0.014 0.001 PHE B 672 TRP 0.013 0.001 TRP B 723 HIS 0.005 0.001 HIS A 708 Details of bonding type rmsd covalent geometry : bond 0.00258 (22725) covalent geometry : angle 0.51887 (30954) hydrogen bonds : bond 0.03466 ( 623) hydrogen bonds : angle 5.41657 ( 1788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 553 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7475 (mp0) cc_final: 0.6952 (mp0) REVERT: B 81 LYS cc_start: 0.8333 (tppp) cc_final: 0.8075 (ttpt) REVERT: B 190 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: B 192 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7234 (mm-30) REVERT: B 406 TYR cc_start: 0.8430 (m-80) cc_final: 0.8172 (m-10) REVERT: B 475 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: B 583 MET cc_start: 0.8558 (mmm) cc_final: 0.7974 (mmm) REVERT: B 623 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6900 (pm20) REVERT: B 630 THR cc_start: 0.8268 (p) cc_final: 0.8034 (p) REVERT: B 658 SER cc_start: 0.8203 (t) cc_final: 0.7753 (m) REVERT: B 734 GLU cc_start: 0.7707 (pm20) cc_final: 0.7482 (pm20) REVERT: B 823 TYR cc_start: 0.8691 (t80) cc_final: 0.8391 (t80) REVERT: B 828 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7537 (ttm) REVERT: B 832 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 58 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7850 (m) REVERT: A 74 GLU cc_start: 0.7433 (tp30) cc_final: 0.7083 (tp30) REVERT: A 81 LYS cc_start: 0.8398 (tppp) cc_final: 0.8151 (tttm) REVERT: A 83 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7320 (tpt-90) REVERT: A 151 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8182 (m) REVERT: A 181 LYS cc_start: 0.8026 (tptp) cc_final: 0.7692 (mptp) REVERT: A 190 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: A 198 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6950 (mm-30) REVERT: A 221 MET cc_start: 0.8199 (mtt) cc_final: 0.7914 (mtp) REVERT: A 242 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7375 (ttp80) REVERT: A 370 LEU cc_start: 0.8358 (mt) cc_final: 0.8153 (mp) REVERT: A 386 SER cc_start: 0.7629 (p) cc_final: 0.7269 (m) REVERT: A 399 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7480 (mm) REVERT: A 437 ASN cc_start: 0.7878 (m-40) cc_final: 0.7486 (t0) REVERT: A 574 GLU cc_start: 0.7726 (tt0) cc_final: 0.7218 (tm-30) REVERT: A 623 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: A 630 THR cc_start: 0.8305 (p) cc_final: 0.8039 (p) REVERT: A 637 ASP cc_start: 0.7775 (t0) cc_final: 0.7472 (t70) REVERT: A 639 LEU cc_start: 0.8605 (tp) cc_final: 0.8381 (tp) REVERT: A 644 MET cc_start: 0.7789 (tpp) cc_final: 0.7553 (mmp) REVERT: A 663 ASN cc_start: 0.8276 (t0) cc_final: 0.7948 (t0) REVERT: A 692 VAL cc_start: 0.8421 (m) cc_final: 0.7923 (t) REVERT: A 716 MET cc_start: 0.7564 (tpp) cc_final: 0.7144 (mmm) REVERT: A 727 ASP cc_start: 0.7893 (t0) cc_final: 0.7430 (t0) REVERT: A 734 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: A 774 TYR cc_start: 0.8060 (p90) cc_final: 0.7738 (p90) REVERT: A 928 ILE cc_start: 0.8440 (mm) cc_final: 0.8109 (mm) REVERT: C 31 PHE cc_start: 0.8247 (t80) cc_final: 0.7922 (t80) REVERT: C 33 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6738 (mtm110) REVERT: C 49 THR cc_start: 0.8100 (m) cc_final: 0.7827 (p) REVERT: C 58 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.8002 (m) REVERT: C 74 GLU cc_start: 0.7467 (tp30) cc_final: 0.7115 (tp30) REVERT: C 75 ASP cc_start: 0.7471 (m-30) cc_final: 0.7026 (m-30) REVERT: C 157 MET cc_start: 0.7770 (ttt) cc_final: 0.7554 (tpp) REVERT: C 161 ASN cc_start: 0.8253 (t0) cc_final: 0.7964 (t0) REVERT: C 189 TYR cc_start: 0.8130 (p90) cc_final: 0.7829 (p90) REVERT: C 277 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6892 (mp0) REVERT: C 294 VAL cc_start: 0.8559 (t) cc_final: 0.8293 (p) REVERT: C 330 MET cc_start: 0.8112 (mtp) cc_final: 0.7866 (mtt) REVERT: C 437 ASN cc_start: 0.7965 (m-40) cc_final: 0.7718 (t0) REVERT: C 453 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: C 490 THR cc_start: 0.7846 (p) cc_final: 0.7617 (m) REVERT: C 510 ILE cc_start: 0.7609 (tp) cc_final: 0.7371 (tt) REVERT: C 570 SER cc_start: 0.8119 (m) cc_final: 0.7661 (p) REVERT: C 571 TYR cc_start: 0.7974 (m-80) cc_final: 0.7628 (m-80) REVERT: C 622 LEU cc_start: 0.7914 (tp) cc_final: 0.7642 (tt) REVERT: C 630 THR cc_start: 0.8354 (p) cc_final: 0.7985 (p) REVERT: C 632 ASP cc_start: 0.7709 (m-30) cc_final: 0.7214 (m-30) REVERT: C 637 ASP cc_start: 0.7381 (t0) cc_final: 0.7165 (t70) REVERT: C 716 MET cc_start: 0.7684 (tpp) cc_final: 0.7159 (mpp) REVERT: C 718 ASP cc_start: 0.7674 (m-30) cc_final: 0.7312 (m-30) REVERT: C 727 ASP cc_start: 0.7813 (t0) cc_final: 0.7235 (t0) REVERT: C 747 ASN cc_start: 0.8223 (m-40) cc_final: 0.7995 (m110) REVERT: C 860 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7345 (mtm180) REVERT: C 916 ASP cc_start: 0.7657 (t0) cc_final: 0.7326 (t0) REVERT: C 929 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7053 (pp20) outliers start: 108 outliers final: 82 residues processed: 604 average time/residue: 0.1837 time to fit residues: 163.1396 Evaluate side-chains 642 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 545 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 711 LYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 860 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 203 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.089125 restraints weight = 34325.863| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.02 r_work: 0.2904 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22725 Z= 0.198 Angle : 0.569 6.677 30954 Z= 0.302 Chirality : 0.046 0.160 3294 Planarity : 0.005 0.055 4089 Dihedral : 5.063 57.267 3082 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.36 % Allowed : 24.08 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.15), residues: 2769 helix: 0.23 (0.29), residues: 345 sheet: -0.07 (0.20), residues: 615 loop : -0.87 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 925 TYR 0.026 0.002 TYR A 84 PHE 0.020 0.002 PHE B 672 TRP 0.017 0.002 TRP B 723 HIS 0.006 0.001 HIS B 815 Details of bonding type rmsd covalent geometry : bond 0.00457 (22725) covalent geometry : angle 0.56856 (30954) hydrogen bonds : bond 0.03984 ( 623) hydrogen bonds : angle 5.50240 ( 1788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 563 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7573 (mp0) cc_final: 0.7099 (mp0) REVERT: B 81 LYS cc_start: 0.8384 (tppp) cc_final: 0.8127 (ttpt) REVERT: B 190 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: B 192 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7208 (mm-30) REVERT: B 395 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: B 475 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: B 583 MET cc_start: 0.8550 (mmm) cc_final: 0.7986 (mmm) REVERT: B 623 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: B 630 THR cc_start: 0.8281 (p) cc_final: 0.8034 (p) REVERT: B 658 SER cc_start: 0.8213 (t) cc_final: 0.7799 (m) REVERT: B 716 MET cc_start: 0.7664 (tpp) cc_final: 0.6974 (mpp) REVERT: B 734 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: B 823 TYR cc_start: 0.8709 (t80) cc_final: 0.8371 (t80) REVERT: A 14 HIS cc_start: 0.8274 (m-70) cc_final: 0.7886 (m90) REVERT: A 58 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7823 (m) REVERT: A 74 GLU cc_start: 0.7428 (tp30) cc_final: 0.7048 (tp30) REVERT: A 81 LYS cc_start: 0.8406 (tppp) cc_final: 0.8084 (tttm) REVERT: A 151 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8263 (m) REVERT: A 181 LYS cc_start: 0.8042 (tptp) cc_final: 0.7718 (mptp) REVERT: A 190 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: A 221 MET cc_start: 0.8231 (mtt) cc_final: 0.7941 (mtp) REVERT: A 288 GLU cc_start: 0.7687 (pt0) cc_final: 0.7401 (pt0) REVERT: A 294 VAL cc_start: 0.8763 (t) cc_final: 0.8439 (p) REVERT: A 386 SER cc_start: 0.7718 (p) cc_final: 0.7341 (m) REVERT: A 399 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 437 ASN cc_start: 0.7898 (m-40) cc_final: 0.7387 (t0) REVERT: A 574 GLU cc_start: 0.7758 (tt0) cc_final: 0.7243 (tm-30) REVERT: A 623 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: A 630 THR cc_start: 0.8356 (p) cc_final: 0.8108 (p) REVERT: A 637 ASP cc_start: 0.7824 (t0) cc_final: 0.7500 (t70) REVERT: A 663 ASN cc_start: 0.8278 (t0) cc_final: 0.7975 (t0) REVERT: A 692 VAL cc_start: 0.8448 (m) cc_final: 0.7943 (t) REVERT: A 716 MET cc_start: 0.7589 (tpp) cc_final: 0.7181 (mmm) REVERT: A 727 ASP cc_start: 0.7906 (t0) cc_final: 0.7455 (t0) REVERT: A 734 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: A 774 TYR cc_start: 0.8050 (p90) cc_final: 0.7733 (p90) REVERT: A 919 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7731 (ttt-90) REVERT: A 928 ILE cc_start: 0.8477 (mm) cc_final: 0.8181 (mm) REVERT: C 31 PHE cc_start: 0.8316 (t80) cc_final: 0.7999 (t80) REVERT: C 33 ARG cc_start: 0.7154 (mtm180) cc_final: 0.6728 (mtm110) REVERT: C 49 THR cc_start: 0.8134 (m) cc_final: 0.7780 (p) REVERT: C 58 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7963 (m) REVERT: C 60 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6729 (mtm180) REVERT: C 74 GLU cc_start: 0.7546 (tp30) cc_final: 0.7345 (tp30) REVERT: C 81 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8260 (tttm) REVERT: C 137 VAL cc_start: 0.8272 (t) cc_final: 0.8058 (p) REVERT: C 157 MET cc_start: 0.7769 (ttt) cc_final: 0.7547 (tpp) REVERT: C 161 ASN cc_start: 0.8291 (t0) cc_final: 0.8012 (t0) REVERT: C 277 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6973 (mp0) REVERT: C 294 VAL cc_start: 0.8534 (t) cc_final: 0.8289 (p) REVERT: C 437 ASN cc_start: 0.7993 (m-40) cc_final: 0.7742 (t0) REVERT: C 490 THR cc_start: 0.7842 (p) cc_final: 0.7606 (m) REVERT: C 510 ILE cc_start: 0.7606 (tp) cc_final: 0.7368 (tt) REVERT: C 570 SER cc_start: 0.8149 (m) cc_final: 0.7696 (p) REVERT: C 571 TYR cc_start: 0.8066 (m-80) cc_final: 0.7623 (m-80) REVERT: C 622 LEU cc_start: 0.7956 (tp) cc_final: 0.7684 (tt) REVERT: C 630 THR cc_start: 0.8361 (p) cc_final: 0.7949 (p) REVERT: C 632 ASP cc_start: 0.7715 (m-30) cc_final: 0.7369 (m-30) REVERT: C 637 ASP cc_start: 0.7357 (t0) cc_final: 0.7133 (t70) REVERT: C 687 PHE cc_start: 0.8245 (t80) cc_final: 0.8018 (t80) REVERT: C 716 MET cc_start: 0.7697 (tpp) cc_final: 0.7162 (mpp) REVERT: C 718 ASP cc_start: 0.7701 (m-30) cc_final: 0.7387 (m-30) REVERT: C 727 ASP cc_start: 0.7863 (t0) cc_final: 0.7313 (t0) REVERT: C 777 GLU cc_start: 0.7022 (tp30) cc_final: 0.6686 (tp30) REVERT: C 800 GLU cc_start: 0.8037 (mp0) cc_final: 0.7808 (mp0) REVERT: C 916 ASP cc_start: 0.7610 (t0) cc_final: 0.7244 (t0) REVERT: C 929 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7065 (pp20) outliers start: 105 outliers final: 81 residues processed: 611 average time/residue: 0.1886 time to fit residues: 170.5302 Evaluate side-chains 647 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 553 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 711 LYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 845 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 0.2980 chunk 173 optimal weight: 0.2980 chunk 108 optimal weight: 0.0020 chunk 242 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 0.0050 chunk 223 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 chunk 265 optimal weight: 0.0670 chunk 89 optimal weight: 0.5980 overall best weight: 0.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 220 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 ASN A 303 ASN ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 643 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.091508 restraints weight = 34335.911| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.02 r_work: 0.2946 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22725 Z= 0.093 Angle : 0.514 8.177 30954 Z= 0.271 Chirality : 0.043 0.175 3294 Planarity : 0.004 0.043 4089 Dihedral : 4.685 59.634 3082 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.57 % Allowed : 25.20 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.16), residues: 2769 helix: 0.59 (0.30), residues: 327 sheet: 0.04 (0.20), residues: 612 loop : -0.78 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 925 TYR 0.018 0.001 TYR A 84 PHE 0.012 0.001 PHE C 672 TRP 0.013 0.001 TRP B 723 HIS 0.005 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00209 (22725) covalent geometry : angle 0.51374 (30954) hydrogen bonds : bond 0.03244 ( 623) hydrogen bonds : angle 5.36206 ( 1788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 553 time to evaluate : 0.793 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: B 22 GLU cc_start: 0.7560 (mp0) cc_final: 0.7090 (mp0) REVERT: B 81 LYS cc_start: 0.8314 (tppp) cc_final: 0.8105 (ttpt) REVERT: B 190 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: B 192 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 395 GLU cc_start: 0.7231 (tp30) cc_final: 0.6966 (tp30) REVERT: B 406 TYR cc_start: 0.8405 (m-80) cc_final: 0.8156 (m-10) REVERT: B 475 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7880 (t0) REVERT: B 583 MET cc_start: 0.8548 (mmm) cc_final: 0.7986 (mmm) REVERT: B 623 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: B 630 THR cc_start: 0.8247 (p) cc_final: 0.7997 (p) REVERT: B 644 MET cc_start: 0.7897 (tpp) cc_final: 0.7696 (mmp) REVERT: B 734 GLU cc_start: 0.7717 (pm20) cc_final: 0.7489 (pm20) REVERT: B 823 TYR cc_start: 0.8672 (t80) cc_final: 0.8463 (t80) REVERT: B 860 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6929 (mtm180) REVERT: B 861 THR cc_start: 0.7910 (t) cc_final: 0.7655 (p) REVERT: A 58 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7858 (m) REVERT: A 74 GLU cc_start: 0.7459 (tp30) cc_final: 0.7072 (tp30) REVERT: A 81 LYS cc_start: 0.8358 (tppp) cc_final: 0.8086 (tttm) REVERT: A 83 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7300 (tpt-90) REVERT: A 151 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8017 (m) REVERT: A 181 LYS cc_start: 0.8038 (tptp) cc_final: 0.7704 (mptp) REVERT: A 221 MET cc_start: 0.8172 (mtt) cc_final: 0.7941 (mtp) REVERT: A 288 GLU cc_start: 0.7631 (pt0) cc_final: 0.7353 (pt0) REVERT: A 370 LEU cc_start: 0.8340 (mt) cc_final: 0.8132 (mp) REVERT: A 386 SER cc_start: 0.7577 (p) cc_final: 0.7186 (m) REVERT: A 399 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7452 (mm) REVERT: A 437 ASN cc_start: 0.7879 (m-40) cc_final: 0.7402 (t0) REVERT: A 463 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7968 (p) REVERT: A 574 GLU cc_start: 0.7653 (tt0) cc_final: 0.7257 (tm-30) REVERT: A 623 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: A 630 THR cc_start: 0.8340 (p) cc_final: 0.8092 (p) REVERT: A 637 ASP cc_start: 0.7804 (t0) cc_final: 0.7473 (t70) REVERT: A 663 ASN cc_start: 0.8253 (t0) cc_final: 0.7941 (t0) REVERT: A 692 VAL cc_start: 0.8380 (m) cc_final: 0.7867 (t) REVERT: A 727 ASP cc_start: 0.7895 (t0) cc_final: 0.7430 (t0) REVERT: A 734 GLU cc_start: 0.7493 (pm20) cc_final: 0.7210 (pm20) REVERT: A 774 TYR cc_start: 0.8045 (p90) cc_final: 0.7816 (p90) REVERT: A 860 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7149 (mtm180) REVERT: A 928 ILE cc_start: 0.8429 (mm) cc_final: 0.8157 (mm) REVERT: C 31 PHE cc_start: 0.8318 (t80) cc_final: 0.8015 (t80) REVERT: C 33 ARG cc_start: 0.7167 (mtm180) cc_final: 0.6734 (mtm110) REVERT: C 49 THR cc_start: 0.8080 (m) cc_final: 0.7809 (p) REVERT: C 74 GLU cc_start: 0.7511 (tp30) cc_final: 0.7173 (tp30) REVERT: C 75 ASP cc_start: 0.7437 (m-30) cc_final: 0.6922 (m-30) REVERT: C 85 THR cc_start: 0.8703 (m) cc_final: 0.8416 (t) REVERT: C 161 ASN cc_start: 0.8167 (t0) cc_final: 0.7884 (t0) REVERT: C 277 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6881 (mp0) REVERT: C 294 VAL cc_start: 0.8551 (t) cc_final: 0.8297 (p) REVERT: C 437 ASN cc_start: 0.7930 (m-40) cc_final: 0.7700 (t0) REVERT: C 490 THR cc_start: 0.7774 (p) cc_final: 0.7563 (m) REVERT: C 510 ILE cc_start: 0.7536 (tp) cc_final: 0.7283 (tt) REVERT: C 570 SER cc_start: 0.8140 (m) cc_final: 0.7647 (p) REVERT: C 571 TYR cc_start: 0.7920 (m-80) cc_final: 0.7686 (m-10) REVERT: C 622 LEU cc_start: 0.7959 (tp) cc_final: 0.7667 (tt) REVERT: C 630 THR cc_start: 0.8431 (p) cc_final: 0.8140 (p) REVERT: C 632 ASP cc_start: 0.7597 (m-30) cc_final: 0.7133 (m-30) REVERT: C 637 ASP cc_start: 0.7251 (t0) cc_final: 0.7021 (t70) REVERT: C 716 MET cc_start: 0.7708 (tpp) cc_final: 0.7156 (mpp) REVERT: C 718 ASP cc_start: 0.7661 (m-30) cc_final: 0.7306 (m-30) REVERT: C 727 ASP cc_start: 0.7816 (t0) cc_final: 0.7607 (t0) REVERT: C 747 ASN cc_start: 0.8204 (m-40) cc_final: 0.7846 (m-40) REVERT: C 777 GLU cc_start: 0.7088 (tp30) cc_final: 0.6714 (tp30) REVERT: C 853 GLN cc_start: 0.7993 (mt0) cc_final: 0.7720 (mt0) REVERT: C 860 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7358 (mtm180) REVERT: C 916 ASP cc_start: 0.7523 (t0) cc_final: 0.7147 (t0) outliers start: 86 outliers final: 62 residues processed: 598 average time/residue: 0.1887 time to fit residues: 166.3757 Evaluate side-chains 616 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 542 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 733 ASN Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 860 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 171 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 169 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 220 ASN B 238 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 HIS ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN C 643 ASN C 733 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.089185 restraints weight = 34595.608| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.05 r_work: 0.2909 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22725 Z= 0.160 Angle : 0.556 7.884 30954 Z= 0.292 Chirality : 0.045 0.239 3294 Planarity : 0.005 0.050 4089 Dihedral : 4.741 58.615 3079 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.49 % Allowed : 25.49 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 2769 helix: 0.61 (0.30), residues: 327 sheet: -0.01 (0.20), residues: 612 loop : -0.82 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 925 TYR 0.022 0.001 TYR A 84 PHE 0.017 0.001 PHE B 672 TRP 0.017 0.002 TRP B 723 HIS 0.006 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00369 (22725) covalent geometry : angle 0.55569 (30954) hydrogen bonds : bond 0.03697 ( 623) hydrogen bonds : angle 5.39474 ( 1788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 540 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7604 (mp0) cc_final: 0.7004 (mp0) REVERT: B 81 LYS cc_start: 0.8361 (tppp) cc_final: 0.8112 (ttpt) REVERT: B 190 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: B 192 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 475 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: B 583 MET cc_start: 0.8531 (mmm) cc_final: 0.8121 (mmt) REVERT: B 623 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6948 (pm20) REVERT: B 630 THR cc_start: 0.8250 (p) cc_final: 0.8006 (p) REVERT: B 716 MET cc_start: 0.7737 (tpp) cc_final: 0.7128 (mpp) REVERT: B 734 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: B 823 TYR cc_start: 0.8698 (t80) cc_final: 0.8441 (t80) REVERT: A 14 HIS cc_start: 0.8261 (m-70) cc_final: 0.7873 (m90) REVERT: A 58 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7846 (m) REVERT: A 74 GLU cc_start: 0.7430 (tp30) cc_final: 0.7012 (tp30) REVERT: A 81 LYS cc_start: 0.8356 (tppp) cc_final: 0.7986 (tttm) REVERT: A 83 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7244 (tpt-90) REVERT: A 151 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8238 (m) REVERT: A 181 LYS cc_start: 0.8061 (tptp) cc_final: 0.7719 (mptp) REVERT: A 221 MET cc_start: 0.8219 (mtt) cc_final: 0.7964 (mtp) REVERT: A 288 GLU cc_start: 0.7705 (pt0) cc_final: 0.7418 (pt0) REVERT: A 294 VAL cc_start: 0.8753 (t) cc_final: 0.8393 (p) REVERT: A 370 LEU cc_start: 0.8377 (mt) cc_final: 0.8173 (mp) REVERT: A 386 SER cc_start: 0.7676 (p) cc_final: 0.7326 (m) REVERT: A 399 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 437 ASN cc_start: 0.7926 (m-40) cc_final: 0.7365 (t0) REVERT: A 463 SER cc_start: 0.8271 (m) cc_final: 0.7993 (p) REVERT: A 574 GLU cc_start: 0.7698 (tt0) cc_final: 0.7111 (tm-30) REVERT: A 623 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: A 630 THR cc_start: 0.8365 (p) cc_final: 0.8117 (p) REVERT: A 637 ASP cc_start: 0.7836 (t0) cc_final: 0.7493 (t70) REVERT: A 663 ASN cc_start: 0.8261 (t0) cc_final: 0.7959 (t0) REVERT: A 692 VAL cc_start: 0.8445 (m) cc_final: 0.7915 (t) REVERT: A 716 MET cc_start: 0.7587 (tpp) cc_final: 0.7153 (mmm) REVERT: A 727 ASP cc_start: 0.7868 (t0) cc_final: 0.7438 (t0) REVERT: A 734 GLU cc_start: 0.7588 (pm20) cc_final: 0.7284 (pm20) REVERT: A 774 TYR cc_start: 0.8069 (p90) cc_final: 0.7836 (p90) REVERT: A 919 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7702 (ttt-90) REVERT: A 928 ILE cc_start: 0.8451 (mm) cc_final: 0.8109 (mm) REVERT: C 31 PHE cc_start: 0.8311 (t80) cc_final: 0.8013 (t80) REVERT: C 33 ARG cc_start: 0.7160 (mtm180) cc_final: 0.6723 (mtm110) REVERT: C 49 THR cc_start: 0.8097 (m) cc_final: 0.7774 (p) REVERT: C 74 GLU cc_start: 0.7546 (tp30) cc_final: 0.7282 (tp30) REVERT: C 81 LYS cc_start: 0.8458 (tttm) cc_final: 0.8221 (tttm) REVERT: C 85 THR cc_start: 0.8724 (m) cc_final: 0.8440 (t) REVERT: C 157 MET cc_start: 0.8008 (tpp) cc_final: 0.7448 (tpp) REVERT: C 161 ASN cc_start: 0.8189 (t0) cc_final: 0.7916 (t0) REVERT: C 277 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6945 (mp0) REVERT: C 294 VAL cc_start: 0.8547 (t) cc_final: 0.8296 (p) REVERT: C 437 ASN cc_start: 0.7975 (m-40) cc_final: 0.7744 (t0) REVERT: C 490 THR cc_start: 0.7812 (p) cc_final: 0.7582 (m) REVERT: C 510 ILE cc_start: 0.7572 (tp) cc_final: 0.7328 (tt) REVERT: C 570 SER cc_start: 0.8142 (m) cc_final: 0.7723 (p) REVERT: C 571 TYR cc_start: 0.8000 (m-80) cc_final: 0.7466 (m-80) REVERT: C 622 LEU cc_start: 0.7950 (tp) cc_final: 0.7676 (tt) REVERT: C 630 THR cc_start: 0.8332 (p) cc_final: 0.8037 (p) REVERT: C 632 ASP cc_start: 0.7571 (m-30) cc_final: 0.7183 (m-30) REVERT: C 637 ASP cc_start: 0.7304 (t0) cc_final: 0.6915 (t70) REVERT: C 716 MET cc_start: 0.7721 (tpp) cc_final: 0.7165 (mpp) REVERT: C 718 ASP cc_start: 0.7703 (m-30) cc_final: 0.7350 (m-30) REVERT: C 747 ASN cc_start: 0.8332 (m-40) cc_final: 0.8086 (m110) REVERT: C 777 GLU cc_start: 0.7144 (tp30) cc_final: 0.6792 (tp30) REVERT: C 916 ASP cc_start: 0.7547 (t0) cc_final: 0.7128 (t0) outliers start: 84 outliers final: 70 residues processed: 587 average time/residue: 0.1809 time to fit residues: 156.2387 Evaluate side-chains 614 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 535 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 114 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 226 optimal weight: 0.0870 chunk 133 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 220 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 HIS ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN C 643 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090679 restraints weight = 34244.693| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.99 r_work: 0.2928 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22725 Z= 0.146 Angle : 0.551 9.005 30954 Z= 0.290 Chirality : 0.045 0.236 3294 Planarity : 0.004 0.048 4089 Dihedral : 4.725 56.612 3077 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.24 % Allowed : 25.90 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.15), residues: 2769 helix: 0.54 (0.30), residues: 327 sheet: -0.07 (0.20), residues: 612 loop : -0.82 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 668 TYR 0.021 0.001 TYR A 84 PHE 0.016 0.001 PHE B 672 TRP 0.015 0.002 TRP B 723 HIS 0.006 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00339 (22725) covalent geometry : angle 0.55109 (30954) hydrogen bonds : bond 0.03597 ( 623) hydrogen bonds : angle 5.36804 ( 1788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5538 Ramachandran restraints generated. 2769 Oldfield, 0 Emsley, 2769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 539 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7633 (mp0) cc_final: 0.6992 (mp0) REVERT: B 81 LYS cc_start: 0.8386 (tppp) cc_final: 0.8124 (ttpt) REVERT: B 190 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: B 192 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7156 (mm-30) REVERT: B 475 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7899 (t0) REVERT: B 583 MET cc_start: 0.8519 (mmm) cc_final: 0.8110 (mmt) REVERT: B 623 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: B 630 THR cc_start: 0.8248 (p) cc_final: 0.8005 (p) REVERT: B 716 MET cc_start: 0.7703 (tpp) cc_final: 0.7104 (mpp) REVERT: B 734 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: B 823 TYR cc_start: 0.8685 (t80) cc_final: 0.8438 (t80) REVERT: A 14 HIS cc_start: 0.8297 (m-70) cc_final: 0.7918 (m90) REVERT: A 58 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7853 (m) REVERT: A 74 GLU cc_start: 0.7444 (tp30) cc_final: 0.7033 (tp30) REVERT: A 81 LYS cc_start: 0.8356 (tppp) cc_final: 0.7998 (tttm) REVERT: A 83 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7259 (tpt-90) REVERT: A 96 MET cc_start: 0.8251 (mmp) cc_final: 0.7967 (mmm) REVERT: A 151 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8228 (m) REVERT: A 181 LYS cc_start: 0.8067 (tptp) cc_final: 0.7728 (mptp) REVERT: A 221 MET cc_start: 0.8217 (mtt) cc_final: 0.7964 (mtp) REVERT: A 288 GLU cc_start: 0.7673 (pt0) cc_final: 0.7404 (pt0) REVERT: A 294 VAL cc_start: 0.8757 (t) cc_final: 0.8418 (p) REVERT: A 370 LEU cc_start: 0.8376 (mt) cc_final: 0.8157 (mp) REVERT: A 386 SER cc_start: 0.7632 (p) cc_final: 0.7290 (m) REVERT: A 399 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7540 (mm) REVERT: A 437 ASN cc_start: 0.7897 (m-40) cc_final: 0.7522 (t0) REVERT: A 463 SER cc_start: 0.8254 (m) cc_final: 0.7985 (p) REVERT: A 574 GLU cc_start: 0.7648 (tt0) cc_final: 0.7130 (tm-30) REVERT: A 623 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: A 630 THR cc_start: 0.8380 (p) cc_final: 0.8137 (p) REVERT: A 637 ASP cc_start: 0.7770 (t0) cc_final: 0.7454 (t70) REVERT: A 663 ASN cc_start: 0.8267 (t0) cc_final: 0.7974 (t0) REVERT: A 692 VAL cc_start: 0.8393 (m) cc_final: 0.7921 (t) REVERT: A 716 MET cc_start: 0.7579 (tpp) cc_final: 0.7169 (mmm) REVERT: A 734 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: A 774 TYR cc_start: 0.8054 (p90) cc_final: 0.7825 (p90) REVERT: A 919 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7678 (ttt-90) REVERT: A 928 ILE cc_start: 0.8457 (mm) cc_final: 0.8133 (mm) REVERT: C 31 PHE cc_start: 0.8335 (t80) cc_final: 0.8038 (t80) REVERT: C 33 ARG cc_start: 0.7166 (mtm180) cc_final: 0.6723 (mtm110) REVERT: C 49 THR cc_start: 0.8054 (m) cc_final: 0.7760 (p) REVERT: C 74 GLU cc_start: 0.7536 (tp30) cc_final: 0.7282 (tp30) REVERT: C 81 LYS cc_start: 0.8475 (tttm) cc_final: 0.8215 (tttm) REVERT: C 85 THR cc_start: 0.8713 (m) cc_final: 0.8436 (t) REVERT: C 157 MET cc_start: 0.8011 (tpp) cc_final: 0.7723 (tpp) REVERT: C 161 ASN cc_start: 0.8180 (t0) cc_final: 0.7937 (t0) REVERT: C 277 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6916 (mp0) REVERT: C 294 VAL cc_start: 0.8541 (t) cc_final: 0.8305 (p) REVERT: C 437 ASN cc_start: 0.7994 (m-40) cc_final: 0.7755 (t0) REVERT: C 490 THR cc_start: 0.7807 (p) cc_final: 0.7576 (m) REVERT: C 510 ILE cc_start: 0.7555 (tp) cc_final: 0.7306 (tt) REVERT: C 570 SER cc_start: 0.8140 (m) cc_final: 0.7733 (p) REVERT: C 571 TYR cc_start: 0.7977 (m-80) cc_final: 0.7452 (m-80) REVERT: C 622 LEU cc_start: 0.7997 (tp) cc_final: 0.7717 (tt) REVERT: C 630 THR cc_start: 0.8447 (p) cc_final: 0.8162 (p) REVERT: C 632 ASP cc_start: 0.7557 (m-30) cc_final: 0.7097 (m-30) REVERT: C 637 ASP cc_start: 0.7287 (t0) cc_final: 0.6884 (t70) REVERT: C 639 LEU cc_start: 0.8632 (tp) cc_final: 0.8054 (tt) REVERT: C 716 MET cc_start: 0.7716 (tpp) cc_final: 0.7186 (mpp) REVERT: C 718 ASP cc_start: 0.7701 (m-30) cc_final: 0.7386 (m-30) REVERT: C 777 GLU cc_start: 0.7164 (tp30) cc_final: 0.6747 (tp30) REVERT: C 779 TYR cc_start: 0.7906 (p90) cc_final: 0.7482 (p90) REVERT: C 916 ASP cc_start: 0.7532 (t0) cc_final: 0.7100 (t0) REVERT: C 935 THR cc_start: 0.8522 (p) cc_final: 0.8296 (t) outliers start: 78 outliers final: 65 residues processed: 580 average time/residue: 0.1784 time to fit residues: 152.7837 Evaluate side-chains 615 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 540 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 874 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 188 optimal weight: 20.0000 chunk 18 optimal weight: 0.0770 chunk 268 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 220 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN C 576 ASN C 643 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.089339 restraints weight = 34617.507| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.99 r_work: 0.2892 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22725 Z= 0.233 Angle : 0.609 10.664 30954 Z= 0.321 Chirality : 0.047 0.245 3294 Planarity : 0.005 0.055 4089 Dihedral : 5.011 58.201 3076 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.65 % Allowed : 25.61 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 2769 helix: 0.14 (0.29), residues: 345 sheet: -0.20 (0.20), residues: 615 loop : -0.89 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 668 TYR 0.023 0.002 TYR A 84 PHE 0.020 0.002 PHE B 672 TRP 0.017 0.002 TRP B 723 HIS 0.006 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00537 (22725) covalent geometry : angle 0.60939 (30954) hydrogen bonds : bond 0.04124 ( 623) hydrogen bonds : angle 5.49163 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5707.33 seconds wall clock time: 98 minutes 26.63 seconds (5906.63 seconds total)