Starting phenix.real_space_refine on Fri Aug 7 16:15:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13er_77024/08_2026/13er_77024.cif Found real_map, /net/cci-nas-00/data/ceres_data/13er_77024/08_2026/13er_77024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13er_77024/08_2026/13er_77024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13er_77024/08_2026/13er_77024.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13er_77024/08_2026/13er_77024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13er_77024/08_2026/13er_77024.map" } resolution = 3.22 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 7 9.91 5 S 116 5.16 5 C 14251 2.51 5 N 3802 2.21 5 O 4301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22477 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7321 Classifications: {'peptide': 918} Link IDs: {'PTRANS': 52, 'TRANS': 865} Chain breaks: 2 Chain: "B" Number of atoms: 7311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 917, 7311 Classifications: {'peptide': 917} Link IDs: {'PTRANS': 52, 'TRANS': 864} Chain breaks: 2 Chain: "C" Number of atoms: 7318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7318 Classifications: {'peptide': 918} Link IDs: {'PTRANS': 52, 'TRANS': 865} Chain breaks: 2 Chain: "G" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 520 Classifications: {'peptide': 62} Link IDs: {'PCIS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Planarities with less than four sites: {'CGU:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 4.77, per 1000 atoms: 0.21 Number of scatterers: 22477 At special positions: 0 Unit cell: (114.75, 118.15, 144.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 7 19.99 S 116 16.00 O 4301 8.00 N 3802 7.00 C 14251 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: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 41 sheets defined 19.1% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.812A pdb=" N TYR A 23 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.777A pdb=" N LYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 45 " --> pdb=" O ASN A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 45' 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 278 through 285 removed outlier: 3.554A pdb=" N THR A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 285' Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.507A pdb=" N GLY A 324 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 325 " --> pdb=" O MET A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.971A pdb=" N SER A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.996A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 511 through 517 Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.729A pdb=" N ASP A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 577 through 582 removed outlier: 4.667A pdb=" N ASN A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 773 through 786 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 903 through 908 removed outlier: 4.046A pdb=" N SER A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.544A pdb=" N TYR B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.878A pdb=" N TYR B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.870A 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 35 Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.503A pdb=" N LYS B 44 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE B 45 " --> pdb=" O ASN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 45' 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 320 through 325 removed outlier: 3.774A pdb=" N GLN B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.883A pdb=" N SER B 377 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.513A pdb=" N ILE B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 489 through 492 removed outlier: 3.523A pdb=" N LEU B 492 " --> pdb=" O ALA B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'B' and resid 511 through 517 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 611 through 616 Processing helix chain 'B' and resid 634 through 646 Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 773 through 786 Processing helix chain 'B' and resid 829 through 833 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.523A pdb=" N LEU C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.653A pdb=" N LYS C 44 " --> pdb=" O LEU C 41 " (cutoff:3.500A) 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 195 through 199 removed outlier: 3.876A pdb=" N GLY C 198 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 199 " --> pdb=" O VAL C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 199' Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.756A pdb=" N GLN C 325 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 474 through 488 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 493 through 497 Processing helix chain 'C' and resid 511 through 518 removed outlier: 3.586A pdb=" N ARG C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 526 removed outlier: 3.734A pdb=" N ASP C 526 " --> pdb=" O GLY C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 551 through 562 Processing helix chain 'C' and resid 599 through 604 removed outlier: 3.660A pdb=" N VAL C 603 " --> pdb=" O ASP C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 646 Processing helix chain 'C' and resid 716 through 721 Processing helix chain 'C' and resid 773 through 786 Processing helix chain 'C' and resid 898 through 901 Processing helix chain 'C' and resid 902 through 907 removed outlier: 3.644A pdb=" N ASN C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 23 through 32 removed outlier: 3.664A pdb=" N ALA G 30 " --> pdb=" O CGU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 47 Processing helix chain 'G' and resid 48 through 51 removed outlier: 3.914A pdb=" N ARG G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'G' and resid 53 through 61 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.114A pdb=" N ARG A 104 " --> pdb=" O ASP A 622 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 624 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP A 102 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A 626 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR A 100 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.114A pdb=" N ARG A 104 " --> pdb=" O ASP A 622 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 624 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP A 102 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A 626 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR A 100 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.918A pdb=" N ASP A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.835A pdb=" N GLU B 462 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 173 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 134 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY A 230 " --> pdb=" O TYR A 295 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLU A 297 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL A 232 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 12.313A pdb=" N MET A 272 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR B 439 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE A 274 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 188 through 190 Processing sheet with id=AA7, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AA8, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.680A pdb=" N GLN A 326 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AB1, first strand: chain 'A' and resid 409 through 410 removed outlier: 4.032A pdb=" N ILE A 409 " --> pdb=" O TRP A 535 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 473 removed outlier: 3.509A pdb=" N MET A 471 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B 471 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET C 471 " --> pdb=" O CYS C 422 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 133 through 137 removed outlier: 7.381A pdb=" N GLU A 462 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ALA C 175 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY A 464 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 274 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 292 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA C 228 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N TYR C 295 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY C 230 " --> pdb=" O TYR C 295 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLU C 297 " --> pdb=" O GLY C 230 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL C 232 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 652 through 655 Processing sheet with id=AB5, first strand: chain 'A' and resid 660 through 667 removed outlier: 4.086A pdb=" N GLY A 688 " --> pdb=" O GLU A 932 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 673 through 681 removed outlier: 4.106A pdb=" N SER A 680 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS A 910 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 911 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 736 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP A 913 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 734 " --> pdb=" O ASP A 913 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 915 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 732 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A 917 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 673 through 681 removed outlier: 4.106A pdb=" N SER A 680 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS A 910 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 911 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 736 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP A 913 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 734 " --> pdb=" O ASP A 913 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 915 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 732 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A 917 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 809 through 817 Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.932A pdb=" N ARG B 104 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B 624 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP B 102 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 626 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR B 100 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.753A pdb=" N TYR B 592 " --> pdb=" O PHE B 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 94 through 95 removed outlier: 3.738A pdb=" N LEU B 94 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 177 through 178 removed outlier: 3.541A pdb=" N GLU B 134 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 173 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.630A pdb=" N ALA B 228 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR B 295 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY B 230 " --> pdb=" O TYR B 295 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLU B 297 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 232 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE B 274 " --> pdb=" O VAL C 437 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 188 through 191 Processing sheet with id=AC6, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.270A pdb=" N GLN B 326 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AC8, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 655 removed outlier: 3.573A pdb=" N GLN B 652 " --> pdb=" O VAL B 939 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 660 through 667 removed outlier: 4.095A pdb=" N GLY B 688 " --> pdb=" O GLU B 932 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 673 through 681 removed outlier: 4.415A pdb=" N SER B 680 " --> pdb=" O HIS B 910 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N HIS B 910 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 732 " --> pdb=" O PHE B 754 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 810 through 817 Processing sheet with id=AD4, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.773A pdb=" N ARG C 104 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 624 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP C 102 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU C 626 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR C 100 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.773A pdb=" N ARG C 104 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 624 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP C 102 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU C 626 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR C 100 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.762A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 82 " --> pdb=" O TRP C 594 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP C 594 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 94 through 95 Processing sheet with id=AD8, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.644A pdb=" N GLY C 190 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.846A pdb=" N GLN C 326 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 409 through 410 removed outlier: 3.619A pdb=" N ILE C 409 " --> pdb=" O TRP C 535 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP C 535 " --> pdb=" O ILE C 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 652 through 655 Processing sheet with id=AE3, first strand: chain 'C' and resid 660 through 667 removed outlier: 3.536A pdb=" N TYR C 928 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 692 " --> pdb=" O TYR C 928 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C 688 " --> pdb=" O GLU C 932 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 673 through 681 removed outlier: 4.080A pdb=" N SER C 680 " --> pdb=" O HIS C 910 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS C 910 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASP C 913 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE C 734 " --> pdb=" O ASP C 913 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 915 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL C 732 " --> pdb=" O THR C 915 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU C 917 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 809 through 817 610 hydrogen bonds defined for protein. 1569 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: 5.27 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7379 1.34 - 1.46: 5371 1.46 - 1.58: 10093 1.58 - 1.70: 0 1.70 - 1.81: 207 Bond restraints: 23050 Sorted by residual: bond pdb=" C GLY B 254 " pdb=" N GLY B 255 " ideal model delta sigma weight residual 1.332 1.324 0.008 5.00e-03 4.00e+04 2.68e+00 bond pdb=" C LEU B 124 " pdb=" N ALA B 125 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.47e-02 4.63e+03 1.67e+00 bond pdb=" C ASP B 746 " pdb=" N ARG B 747 " ideal model delta sigma weight residual 1.332 1.316 0.017 1.40e-02 5.10e+03 1.41e+00 bond pdb=" C VAL A 857 " pdb=" N PRO A 858 " ideal model delta sigma weight residual 1.335 1.345 -0.010 8.70e-03 1.32e+04 1.30e+00 bond pdb=" C VAL C 50 " pdb=" N ALA C 51 " ideal model delta sigma weight residual 1.331 1.354 -0.023 2.07e-02 2.33e+03 1.27e+00 ... (remaining 23045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 30665 1.46 - 2.93: 580 2.93 - 4.39: 90 4.39 - 5.86: 17 5.86 - 7.32: 2 Bond angle restraints: 31354 Sorted by residual: angle pdb=" C VAL B 196 " pdb=" N ALA B 197 " pdb=" CA ALA B 197 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.95e+00 angle pdb=" C PHE C 569 " pdb=" N HIS C 570 " pdb=" CA HIS C 570 " ideal model delta sigma weight residual 122.62 126.48 -3.86 1.63e+00 3.76e-01 5.60e+00 angle pdb=" C GLY B 254 " pdb=" N GLY B 255 " pdb=" CA GLY B 255 " ideal model delta sigma weight residual 122.29 120.19 2.10 8.90e-01 1.26e+00 5.56e+00 angle pdb=" CA TRP B 742 " pdb=" CB TRP B 742 " pdb=" CG TRP B 742 " ideal model delta sigma weight residual 113.60 109.16 4.44 1.90e+00 2.77e-01 5.45e+00 angle pdb=" C ASN B 902 " pdb=" N LEU B 903 " pdb=" CA LEU B 903 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 ... (remaining 31349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 12956 16.71 - 33.42: 564 33.42 - 50.12: 114 50.12 - 66.83: 24 66.83 - 83.54: 6 Dihedral angle restraints: 13664 sinusoidal: 5421 harmonic: 8243 Sorted by residual: dihedral pdb=" CA PHE C 209 " pdb=" C PHE C 209 " pdb=" N GLN C 210 " pdb=" CA GLN C 210 " ideal model delta harmonic sigma weight residual -180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA PHE B 209 " pdb=" C PHE B 209 " pdb=" N GLN B 210 " pdb=" CA GLN B 210 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE A 209 " pdb=" C PHE A 209 " pdb=" N GLN A 210 " pdb=" CA GLN A 210 " ideal model delta harmonic sigma weight residual 180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 13661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2026 0.032 - 0.064: 822 0.064 - 0.096: 325 0.096 - 0.128: 149 0.128 - 0.160: 19 Chirality restraints: 3341 Sorted by residual: chirality pdb=" CA THR B 954 " pdb=" N THR B 954 " pdb=" C THR B 954 " pdb=" CB THR B 954 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA THR A 954 " pdb=" N THR A 954 " pdb=" C THR A 954 " pdb=" CB THR A 954 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA THR C 954 " pdb=" N THR C 954 " pdb=" C THR C 954 " pdb=" CB THR C 954 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 3338 not shown) Planarity restraints: 4129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 212 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO C 213 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 213 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 213 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 674 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 675 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 675 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 675 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 810 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO C 811 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 811 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 811 " 0.023 5.00e-02 4.00e+02 ... (remaining 4126 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1790 2.74 - 3.28: 21288 3.28 - 3.82: 34692 3.82 - 4.36: 42431 4.36 - 4.90: 75145 Nonbonded interactions: 175346 Sorted by model distance: nonbonded pdb=" OE1 GLN B 575 " pdb=" OH TYR B 592 " model vdw 2.196 3.040 nonbonded pdb="OE12 CGU G 16 " pdb="CA CA G 604 " model vdw 2.197 2.510 nonbonded pdb="OE21 CGU G 7 " pdb="CA CA G 602 " model vdw 2.206 2.510 nonbonded pdb=" OG1 THR C 237 " pdb=" OD1 ASP C 298 " model vdw 2.217 3.040 nonbonded pdb="OE22 CGU G 29 " pdb="CA CA G 601 " model vdw 2.221 2.510 ... (remaining 175341 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 449 or resid 451 through 957)) selection = (chain 'B' and resid 7 through 957) selection = (chain 'C' and (resid 7 through 449 or resid 451 through 957)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.320 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23050 Z= 0.183 Angle : 0.521 7.324 31354 Z= 0.282 Chirality : 0.044 0.160 3341 Planarity : 0.004 0.048 4129 Dihedral : 10.202 83.540 8390 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 3.59 % Allowed : 6.11 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.16), residues: 2772 helix: 1.43 (0.32), residues: 326 sheet: 0.07 (0.20), residues: 640 loop : -1.24 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 814 TYR 0.017 0.001 TYR B 928 PHE 0.012 0.002 PHE B 792 TRP 0.014 0.001 TRP B 535 HIS 0.007 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (23050) covalent geometry : angle 0.52073 / 0.28 (31354) hydrogen bonds : bond 0.18080 / 11.98 ( 581) hydrogen bonds : angle 7.16371 / 4.91 ( 1569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 755 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.6887 (mmt) cc_final: 0.6509 (mmt) REVERT: A 7 MET cc_start: 0.6917 (mmm) cc_final: 0.6633 (mmm) REVERT: A 12 TYR cc_start: 0.8722 (t80) cc_final: 0.8278 (t80) REVERT: A 180 ILE cc_start: 0.8206 (mt) cc_final: 0.7981 (mt) REVERT: A 189 ILE cc_start: 0.6563 (mm) cc_final: 0.6338 (mt) REVERT: A 347 TYR cc_start: 0.8550 (m-80) cc_final: 0.8291 (m-80) REVERT: A 547 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7247 (p0) REVERT: A 785 TYR cc_start: 0.8169 (m-80) cc_final: 0.7788 (m-10) REVERT: A 818 ASP cc_start: 0.8100 (t0) cc_final: 0.7699 (t0) REVERT: A 830 ILE cc_start: 0.8205 (mp) cc_final: 0.7842 (tp) REVERT: A 947 ILE cc_start: 0.8704 (mt) cc_final: 0.8456 (tt) REVERT: B 41 LEU cc_start: 0.8105 (mt) cc_final: 0.7874 (mp) REVERT: B 83 ARG cc_start: 0.8711 (ttt-90) cc_final: 0.8409 (ttp80) REVERT: B 136 GLU cc_start: 0.1959 (tm-30) cc_final: 0.1434 (tm-30) REVERT: B 171 VAL cc_start: 0.8468 (t) cc_final: 0.8142 (p) REVERT: B 183 THR cc_start: 0.7009 (p) cc_final: 0.6808 (p) REVERT: B 185 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 218 SER cc_start: 0.7447 (m) cc_final: 0.7185 (t) REVERT: B 305 ASP cc_start: 0.7983 (p0) cc_final: 0.7653 (p0) REVERT: B 335 ILE cc_start: 0.8695 (mt) cc_final: 0.8448 (mm) REVERT: B 348 ASN cc_start: 0.8568 (m110) cc_final: 0.8272 (m-40) REVERT: B 368 ASP cc_start: 0.8711 (t0) cc_final: 0.8354 (t0) REVERT: B 369 LEU cc_start: 0.8140 (mt) cc_final: 0.7898 (mp) REVERT: B 393 SER cc_start: 0.8745 (p) cc_final: 0.8488 (p) REVERT: B 403 ASP cc_start: 0.7284 (t0) cc_final: 0.6845 (t0) REVERT: B 405 ASP cc_start: 0.8111 (m-30) cc_final: 0.7877 (m-30) REVERT: B 417 GLU cc_start: 0.8181 (mp0) cc_final: 0.7884 (mp0) REVERT: B 487 ASN cc_start: 0.8353 (m-40) cc_final: 0.8133 (m-40) REVERT: B 600 VAL cc_start: 0.7854 (t) cc_final: 0.7624 (m) REVERT: B 624 ILE cc_start: 0.8433 (tt) cc_final: 0.8088 (pt) REVERT: B 706 TYR cc_start: 0.8065 (t80) cc_final: 0.7841 (t80) REVERT: B 799 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8110 (ttmm) REVERT: B 883 ARG cc_start: 0.7798 (mtm180) cc_final: 0.7449 (ptp-110) REVERT: B 941 GLN cc_start: 0.7983 (pt0) cc_final: 0.7694 (mt0) REVERT: C 235 LYS cc_start: 0.7502 (pttt) cc_final: 0.7082 (pttm) REVERT: C 256 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: C 403 ASP cc_start: 0.7264 (t0) cc_final: 0.7027 (t0) REVERT: C 506 SER cc_start: 0.8358 (m) cc_final: 0.7986 (p) REVERT: C 527 CYS cc_start: 0.7596 (t) cc_final: 0.7268 (m) REVERT: C 558 SER cc_start: 0.8489 (t) cc_final: 0.8147 (p) REVERT: C 659 SER cc_start: 0.8651 (m) cc_final: 0.8427 (p) REVERT: C 730 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8438 (mttp) REVERT: C 745 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7817 (p0) REVERT: C 758 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7917 (tpp80) REVERT: C 818 ASP cc_start: 0.7846 (t0) cc_final: 0.7178 (t0) REVERT: C 821 LYS cc_start: 0.7653 (mttt) cc_final: 0.7354 (mttp) REVERT: C 826 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8420 (mm110) REVERT: C 935 ASP cc_start: 0.8291 (t0) cc_final: 0.8019 (t0) REVERT: C 939 VAL cc_start: 0.8526 (t) cc_final: 0.8292 (p) outliers start: 87 outliers final: 34 residues processed: 814 average time/residue: 0.1706 time to fit residues: 212.6753 Evaluate side-chains 659 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 622 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 848 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 370 GLN A 461 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 582 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN B 510 ASN B 575 GLN C 256 GLN C 325 GLN C 601 ASN C 726 ASN C 851 GLN C 940 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092100 restraints weight = 35283.740| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.29 r_work: 0.3002 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23050 Z= 0.164 Angle : 0.557 8.693 31354 Z= 0.296 Chirality : 0.045 0.219 3341 Planarity : 0.004 0.048 4129 Dihedral : 6.865 87.737 3211 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 3.02 % Allowed : 13.22 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.16), residues: 2772 helix: 1.05 (0.30), residues: 352 sheet: 0.16 (0.21), residues: 610 loop : -1.33 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 807 TYR 0.024 0.002 TYR C 23 PHE 0.019 0.002 PHE C 457 TRP 0.011 0.001 TRP B 742 HIS 0.006 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (23050) covalent geometry : angle 0.55674 / 0.30 (31354) hydrogen bonds : bond 0.04406 / 2.96 ( 581) hydrogen bonds : angle 5.72760 / 3.93 ( 1569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 640 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6705 (mmm) cc_final: 0.6337 (mmm) REVERT: A 288 ILE cc_start: 0.8081 (pt) cc_final: 0.7850 (pt) REVERT: A 344 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8376 (tt) REVERT: A 438 LYS cc_start: 0.7780 (tttm) cc_final: 0.7235 (mtmt) REVERT: A 467 ASN cc_start: 0.8580 (m110) cc_final: 0.8316 (m-40) REVERT: A 547 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7742 (m-40) REVERT: A 730 LYS cc_start: 0.8692 (tttt) cc_final: 0.8478 (mttp) REVERT: A 740 VAL cc_start: 0.8063 (t) cc_final: 0.7683 (m) REVERT: A 785 TYR cc_start: 0.8409 (m-80) cc_final: 0.7981 (m-10) REVERT: A 899 LEU cc_start: 0.8815 (mt) cc_final: 0.8603 (mt) REVERT: B 41 LEU cc_start: 0.8487 (mt) cc_final: 0.8163 (mp) REVERT: B 168 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7633 (mtpp) REVERT: B 185 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8151 (mt-10) REVERT: B 218 SER cc_start: 0.8654 (m) cc_final: 0.8263 (t) REVERT: B 288 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7375 (mm) REVERT: B 289 GLN cc_start: 0.8116 (mp10) cc_final: 0.7910 (mp10) REVERT: B 348 ASN cc_start: 0.8467 (m110) cc_final: 0.8044 (m-40) REVERT: B 368 ASP cc_start: 0.7913 (t0) cc_final: 0.7557 (t0) REVERT: B 369 LEU cc_start: 0.8645 (mt) cc_final: 0.8372 (mp) REVERT: B 393 SER cc_start: 0.8767 (p) cc_final: 0.8455 (p) REVERT: B 417 GLU cc_start: 0.8067 (mp0) cc_final: 0.7731 (mp0) REVERT: B 472 GLU cc_start: 0.7777 (tt0) cc_final: 0.7326 (tt0) REVERT: B 555 ARG cc_start: 0.8672 (ttp-170) cc_final: 0.8369 (mtm110) REVERT: B 624 ILE cc_start: 0.8552 (tt) cc_final: 0.8324 (pt) REVERT: B 706 TYR cc_start: 0.8816 (t80) cc_final: 0.8417 (t80) REVERT: B 799 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8439 (ttmm) REVERT: B 801 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7768 (mmm160) REVERT: B 864 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8388 (mtpp) REVERT: B 905 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7677 (p90) REVERT: B 941 GLN cc_start: 0.8823 (pt0) cc_final: 0.8493 (mt0) REVERT: C 65 THR cc_start: 0.8313 (m) cc_final: 0.8021 (p) REVERT: C 96 MET cc_start: 0.8165 (mmt) cc_final: 0.7635 (mmt) REVERT: C 203 ILE cc_start: 0.8425 (mt) cc_final: 0.8139 (pt) REVERT: C 207 LYS cc_start: 0.8926 (pttt) cc_final: 0.8627 (ptmt) REVERT: C 298 ASP cc_start: 0.7679 (t0) cc_final: 0.7422 (t0) REVERT: C 320 LYS cc_start: 0.8295 (tttt) cc_final: 0.8036 (tttm) REVERT: C 403 ASP cc_start: 0.7955 (t0) cc_final: 0.7721 (t0) REVERT: C 506 SER cc_start: 0.9057 (m) cc_final: 0.8704 (p) REVERT: C 507 ASP cc_start: 0.8371 (p0) cc_final: 0.8149 (p0) REVERT: C 559 MET cc_start: 0.8413 (mtp) cc_final: 0.8199 (mtt) REVERT: C 659 SER cc_start: 0.8802 (m) cc_final: 0.8592 (p) REVERT: C 687 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8560 (mtm110) REVERT: C 730 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8448 (mttp) REVERT: C 818 ASP cc_start: 0.8146 (t0) cc_final: 0.7742 (t0) REVERT: C 821 LYS cc_start: 0.8936 (mttt) cc_final: 0.8374 (mttp) REVERT: C 919 ASP cc_start: 0.8012 (m-30) cc_final: 0.7604 (m-30) REVERT: C 932 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7506 (mm-30) REVERT: C 935 ASP cc_start: 0.7441 (t0) cc_final: 0.7137 (t0) REVERT: C 939 VAL cc_start: 0.8317 (t) cc_final: 0.7996 (p) outliers start: 73 outliers final: 51 residues processed: 680 average time/residue: 0.1737 time to fit residues: 179.5954 Evaluate side-chains 657 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 602 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 180 optimal weight: 2.9990 chunk 156 optimal weight: 0.0470 chunk 211 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 210 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN A 370 GLN A 467 ASN A 582 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 662 ASN C 359 GLN C 412 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093767 restraints weight = 35159.694| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.31 r_work: 0.2999 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23050 Z= 0.094 Angle : 0.500 8.586 31354 Z= 0.263 Chirality : 0.043 0.198 3341 Planarity : 0.004 0.045 4129 Dihedral : 6.422 88.596 3190 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.48 % Favored : 94.48 % Rotamer: Outliers : 3.35 % Allowed : 14.91 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.16), residues: 2772 helix: 1.17 (0.30), residues: 352 sheet: 0.25 (0.21), residues: 606 loop : -1.30 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 83 TYR 0.018 0.001 TYR C 23 PHE 0.019 0.001 PHE A 31 TRP 0.011 0.001 TRP B 742 HIS 0.004 0.001 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (23050) covalent geometry : angle 0.50006 / 0.26 (31354) hydrogen bonds : bond 0.03256 / 2.19 ( 581) hydrogen bonds : angle 5.41134 / 3.70 ( 1569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 619 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6553 (mmm) cc_final: 0.6273 (mmm) REVERT: A 9 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7528 (tp-100) REVERT: A 438 LYS cc_start: 0.7692 (tttm) cc_final: 0.7143 (mtmt) REVERT: A 611 ASP cc_start: 0.8136 (t0) cc_final: 0.7789 (t0) REVERT: A 730 LYS cc_start: 0.8658 (tttt) cc_final: 0.8446 (mttp) REVERT: A 740 VAL cc_start: 0.8019 (t) cc_final: 0.7617 (m) REVERT: A 753 GLU cc_start: 0.8173 (pm20) cc_final: 0.7793 (pm20) REVERT: A 758 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8335 (tpp80) REVERT: A 785 TYR cc_start: 0.8364 (m-80) cc_final: 0.7915 (m-10) REVERT: B 38 TYR cc_start: 0.8020 (p90) cc_final: 0.7597 (p90) REVERT: B 41 LEU cc_start: 0.8450 (mt) cc_final: 0.8141 (mp) REVERT: B 73 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7742 (ttt-90) REVERT: B 113 PHE cc_start: 0.8516 (t80) cc_final: 0.8200 (t80) REVERT: B 134 GLU cc_start: 0.8246 (pt0) cc_final: 0.7792 (mt-10) REVERT: B 167 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7681 (ptpt) REVERT: B 168 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7612 (mtpp) REVERT: B 185 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8200 (mt-10) REVERT: B 218 SER cc_start: 0.8572 (m) cc_final: 0.8188 (t) REVERT: B 289 GLN cc_start: 0.8132 (mp10) cc_final: 0.7923 (mp10) REVERT: B 313 LYS cc_start: 0.7986 (ptpp) cc_final: 0.7740 (pttp) REVERT: B 348 ASN cc_start: 0.8449 (m110) cc_final: 0.8034 (m-40) REVERT: B 368 ASP cc_start: 0.7985 (t0) cc_final: 0.7597 (t0) REVERT: B 369 LEU cc_start: 0.8668 (mt) cc_final: 0.8408 (mp) REVERT: B 393 SER cc_start: 0.8764 (p) cc_final: 0.8422 (p) REVERT: B 417 GLU cc_start: 0.8086 (mp0) cc_final: 0.7734 (mp0) REVERT: B 472 GLU cc_start: 0.7760 (tt0) cc_final: 0.7260 (tt0) REVERT: B 624 ILE cc_start: 0.8509 (tt) cc_final: 0.8274 (pt) REVERT: B 646 ARG cc_start: 0.8259 (mmt90) cc_final: 0.8029 (mmt90) REVERT: B 687 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.7849 (mtm-85) REVERT: B 694 LEU cc_start: 0.8116 (mt) cc_final: 0.7911 (mt) REVERT: B 706 TYR cc_start: 0.8788 (t80) cc_final: 0.8301 (t80) REVERT: B 801 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7887 (mmm160) REVERT: B 853 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7312 (t80) REVERT: B 864 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8322 (mtpp) REVERT: B 865 THR cc_start: 0.8819 (t) cc_final: 0.8457 (t) REVERT: B 899 LEU cc_start: 0.8753 (mt) cc_final: 0.8546 (tp) REVERT: B 905 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7608 (p90) REVERT: B 953 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7945 (ttp80) REVERT: C 30 GLN cc_start: 0.7321 (tm-30) cc_final: 0.7108 (tm-30) REVERT: C 203 ILE cc_start: 0.8434 (mt) cc_final: 0.8213 (pt) REVERT: C 207 LYS cc_start: 0.8834 (pttt) cc_final: 0.8556 (ptmt) REVERT: C 212 GLU cc_start: 0.7918 (mp0) cc_final: 0.7706 (mp0) REVERT: C 302 GLU cc_start: 0.8280 (pt0) cc_final: 0.7943 (pt0) REVERT: C 368 ASP cc_start: 0.8352 (t0) cc_final: 0.8141 (m-30) REVERT: C 453 LYS cc_start: 0.7750 (mtpm) cc_final: 0.7435 (mtpm) REVERT: C 506 SER cc_start: 0.9052 (m) cc_final: 0.8688 (p) REVERT: C 507 ASP cc_start: 0.8419 (p0) cc_final: 0.8184 (p0) REVERT: C 621 PHE cc_start: 0.8183 (m-80) cc_final: 0.7935 (m-80) REVERT: C 687 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8426 (mtm110) REVERT: C 730 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8420 (mttp) REVERT: C 793 TYR cc_start: 0.8731 (p90) cc_final: 0.8518 (p90) REVERT: C 818 ASP cc_start: 0.8162 (t0) cc_final: 0.7749 (t0) REVERT: C 821 LYS cc_start: 0.8927 (mttt) cc_final: 0.7844 (mttp) REVERT: C 823 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8364 (mmtt) REVERT: C 889 ASN cc_start: 0.8480 (p0) cc_final: 0.8003 (p0) REVERT: C 891 MET cc_start: 0.8829 (mtp) cc_final: 0.8226 (mtp) REVERT: C 935 ASP cc_start: 0.7384 (t0) cc_final: 0.7119 (t0) REVERT: C 939 VAL cc_start: 0.8296 (t) cc_final: 0.7996 (p) outliers start: 81 outliers final: 45 residues processed: 665 average time/residue: 0.1759 time to fit residues: 177.7452 Evaluate side-chains 645 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 597 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 86 optimal weight: 7.9990 chunk 90 optimal weight: 0.4980 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 134 optimal weight: 0.0870 chunk 260 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 47 ASN C 940 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.091379 restraints weight = 35369.780| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.29 r_work: 0.2989 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23050 Z= 0.202 Angle : 0.563 8.820 31354 Z= 0.298 Chirality : 0.046 0.215 3341 Planarity : 0.004 0.047 4129 Dihedral : 6.454 88.742 3177 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 3.76 % Allowed : 15.37 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2772 helix: 1.11 (0.30), residues: 352 sheet: 0.13 (0.21), residues: 618 loop : -1.34 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 73 TYR 0.023 0.002 TYR C 23 PHE 0.016 0.002 PHE A 886 TRP 0.009 0.001 TRP C 135 HIS 0.009 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (23050) covalent geometry : angle 0.56331 / 0.30 (31354) hydrogen bonds : bond 0.04306 / 2.88 ( 581) hydrogen bonds : angle 5.44387 / 3.73 ( 1569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 612 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6574 (mmm) cc_final: 0.6275 (mmm) REVERT: A 344 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 438 LYS cc_start: 0.7779 (tttm) cc_final: 0.7228 (mtmt) REVERT: A 593 GLU cc_start: 0.8054 (tt0) cc_final: 0.7851 (tp30) REVERT: A 627 TYR cc_start: 0.8146 (m-10) cc_final: 0.7923 (m-10) REVERT: A 740 VAL cc_start: 0.8077 (t) cc_final: 0.7684 (m) REVERT: A 753 GLU cc_start: 0.8208 (pm20) cc_final: 0.7822 (pm20) REVERT: A 755 GLU cc_start: 0.8406 (tt0) cc_final: 0.8045 (tt0) REVERT: A 785 TYR cc_start: 0.8409 (m-80) cc_final: 0.7922 (m-10) REVERT: B 38 TYR cc_start: 0.8053 (p90) cc_final: 0.7586 (p90) REVERT: B 41 LEU cc_start: 0.8496 (mt) cc_final: 0.8158 (mp) REVERT: B 73 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7836 (ttt-90) REVERT: B 134 GLU cc_start: 0.8444 (pt0) cc_final: 0.8243 (pt0) REVERT: B 167 LYS cc_start: 0.7932 (ptpt) cc_final: 0.7605 (ptpt) REVERT: B 168 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7632 (mtpp) REVERT: B 185 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 218 SER cc_start: 0.8629 (m) cc_final: 0.8239 (t) REVERT: B 288 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7414 (mm) REVERT: B 289 GLN cc_start: 0.8216 (mp10) cc_final: 0.7977 (mp10) REVERT: B 297 GLU cc_start: 0.7972 (pt0) cc_final: 0.7657 (pt0) REVERT: B 305 ASP cc_start: 0.8004 (p0) cc_final: 0.7650 (p0) REVERT: B 313 LYS cc_start: 0.8019 (ptpp) cc_final: 0.7739 (pttp) REVERT: B 348 ASN cc_start: 0.8501 (m110) cc_final: 0.8020 (m-40) REVERT: B 368 ASP cc_start: 0.7946 (t0) cc_final: 0.7543 (t0) REVERT: B 369 LEU cc_start: 0.8742 (mt) cc_final: 0.8420 (mp) REVERT: B 393 SER cc_start: 0.8750 (p) cc_final: 0.8433 (p) REVERT: B 417 GLU cc_start: 0.8107 (mp0) cc_final: 0.7725 (mp0) REVERT: B 472 GLU cc_start: 0.7805 (tt0) cc_final: 0.7382 (tt0) REVERT: B 652 GLN cc_start: 0.8870 (mt0) cc_final: 0.8566 (mt0) REVERT: B 706 TYR cc_start: 0.8817 (t80) cc_final: 0.8390 (t80) REVERT: B 801 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7978 (mmm160) REVERT: B 853 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.7287 (t80) REVERT: B 864 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8448 (mtpp) REVERT: B 899 LEU cc_start: 0.8794 (mt) cc_final: 0.8459 (tp) REVERT: B 905 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7634 (p90) REVERT: B 953 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7597 (mtm-85) REVERT: C 30 GLN cc_start: 0.7337 (tm-30) cc_final: 0.7119 (tm-30) REVERT: C 81 LYS cc_start: 0.8309 (ptmm) cc_final: 0.8066 (ptmt) REVERT: C 203 ILE cc_start: 0.8484 (mt) cc_final: 0.8226 (pt) REVERT: C 207 LYS cc_start: 0.8915 (pttt) cc_final: 0.8649 (ptmt) REVERT: C 208 THR cc_start: 0.9120 (m) cc_final: 0.8725 (p) REVERT: C 268 SER cc_start: 0.8408 (t) cc_final: 0.8159 (t) REVERT: C 298 ASP cc_start: 0.7677 (t0) cc_final: 0.7466 (t0) REVERT: C 320 LYS cc_start: 0.8288 (tttt) cc_final: 0.8017 (tttm) REVERT: C 453 LYS cc_start: 0.7809 (mtpm) cc_final: 0.7458 (mtpm) REVERT: C 506 SER cc_start: 0.9063 (m) cc_final: 0.8707 (p) REVERT: C 507 ASP cc_start: 0.8414 (p0) cc_final: 0.8170 (p0) REVERT: C 730 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8442 (mttm) REVERT: C 818 ASP cc_start: 0.8183 (t0) cc_final: 0.7728 (t0) REVERT: C 821 LYS cc_start: 0.8914 (mttt) cc_final: 0.8328 (mttp) REVERT: C 891 MET cc_start: 0.8746 (mtp) cc_final: 0.8416 (mtp) REVERT: C 932 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7499 (mm-30) REVERT: C 935 ASP cc_start: 0.7434 (t0) cc_final: 0.7164 (t0) REVERT: C 939 VAL cc_start: 0.8366 (t) cc_final: 0.8030 (p) outliers start: 91 outliers final: 76 residues processed: 660 average time/residue: 0.1747 time to fit residues: 175.7126 Evaluate side-chains 676 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 595 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 673 ASN Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 724 TYR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN A 582 ASN B 43 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN C 47 ASN C 940 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.090757 restraints weight = 35126.645| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.34 r_work: 0.2984 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23050 Z= 0.191 Angle : 0.562 9.919 31354 Z= 0.297 Chirality : 0.045 0.225 3341 Planarity : 0.004 0.047 4129 Dihedral : 6.522 89.322 3177 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 4.21 % Allowed : 15.41 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.16), residues: 2772 helix: 0.98 (0.29), residues: 358 sheet: 0.07 (0.21), residues: 617 loop : -1.40 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 83 TYR 0.021 0.002 TYR C 23 PHE 0.017 0.002 PHE A 546 TRP 0.011 0.001 TRP C 135 HIS 0.008 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (23050) covalent geometry : angle 0.56162 / 0.30 (31354) hydrogen bonds : bond 0.04179 / 2.81 ( 581) hydrogen bonds : angle 5.44623 / 3.73 ( 1569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 589 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.6577 (mmm) cc_final: 0.6278 (mmm) REVERT: A 344 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8344 (tt) REVERT: A 416 ASP cc_start: 0.7745 (p0) cc_final: 0.7527 (p0) REVERT: A 438 LYS cc_start: 0.7764 (tttm) cc_final: 0.7221 (mtmt) REVERT: A 471 MET cc_start: 0.8540 (mtm) cc_final: 0.8183 (mtm) REVERT: A 740 VAL cc_start: 0.8043 (t) cc_final: 0.7647 (m) REVERT: A 749 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7963 (mt) REVERT: A 753 GLU cc_start: 0.8220 (pm20) cc_final: 0.7836 (pm20) REVERT: A 755 GLU cc_start: 0.8439 (tt0) cc_final: 0.8062 (tt0) REVERT: A 785 TYR cc_start: 0.8398 (m-80) cc_final: 0.7899 (m-10) REVERT: A 849 GLU cc_start: 0.8505 (pt0) cc_final: 0.8293 (pt0) REVERT: A 948 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 38 TYR cc_start: 0.8082 (p90) cc_final: 0.7631 (p90) REVERT: B 73 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7861 (ttt-90) REVERT: B 167 LYS cc_start: 0.7948 (ptpt) cc_final: 0.7586 (ptpt) REVERT: B 168 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7587 (mtpp) REVERT: B 185 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 218 SER cc_start: 0.8569 (m) cc_final: 0.8176 (t) REVERT: B 288 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7393 (mm) REVERT: B 289 GLN cc_start: 0.8258 (mp10) cc_final: 0.8008 (mp10) REVERT: B 297 GLU cc_start: 0.7984 (pt0) cc_final: 0.7387 (pt0) REVERT: B 305 ASP cc_start: 0.8027 (p0) cc_final: 0.7649 (p0) REVERT: B 311 LYS cc_start: 0.8865 (tttm) cc_final: 0.8579 (tttm) REVERT: B 313 LYS cc_start: 0.7983 (ptpp) cc_final: 0.7285 (pttp) REVERT: B 348 ASN cc_start: 0.8511 (m110) cc_final: 0.8035 (m-40) REVERT: B 368 ASP cc_start: 0.7957 (t0) cc_final: 0.7503 (t0) REVERT: B 369 LEU cc_start: 0.8764 (mt) cc_final: 0.8335 (mt) REVERT: B 372 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7834 (ttm-80) REVERT: B 393 SER cc_start: 0.8757 (p) cc_final: 0.8416 (p) REVERT: B 417 GLU cc_start: 0.8141 (mp0) cc_final: 0.7711 (mp0) REVERT: B 472 GLU cc_start: 0.7841 (tt0) cc_final: 0.7371 (tt0) REVERT: B 577 PHE cc_start: 0.8410 (t80) cc_final: 0.8205 (t80) REVERT: B 681 ARG cc_start: 0.8591 (ptp-110) cc_final: 0.8370 (ptm160) REVERT: B 687 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.8041 (mtm-85) REVERT: B 706 TYR cc_start: 0.8813 (t80) cc_final: 0.8392 (t80) REVERT: B 799 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8405 (mtmm) REVERT: B 853 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.7269 (t80) REVERT: B 864 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8412 (mtpp) REVERT: B 899 LEU cc_start: 0.8775 (mt) cc_final: 0.8462 (tp) REVERT: B 905 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7715 (p90) REVERT: B 941 GLN cc_start: 0.8827 (mt0) cc_final: 0.8556 (mt0) REVERT: B 953 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7436 (mtm-85) REVERT: C 30 GLN cc_start: 0.7351 (tm-30) cc_final: 0.7134 (tm-30) REVERT: C 81 LYS cc_start: 0.8293 (ptmm) cc_final: 0.8052 (ptmt) REVERT: C 203 ILE cc_start: 0.8483 (mt) cc_final: 0.8193 (pt) REVERT: C 207 LYS cc_start: 0.8915 (pttt) cc_final: 0.8656 (ptmt) REVERT: C 208 THR cc_start: 0.9126 (m) cc_final: 0.8733 (p) REVERT: C 268 SER cc_start: 0.8409 (t) cc_final: 0.8178 (t) REVERT: C 302 GLU cc_start: 0.8214 (pt0) cc_final: 0.7959 (tt0) REVERT: C 316 ASP cc_start: 0.8132 (t0) cc_final: 0.7854 (t0) REVERT: C 320 LYS cc_start: 0.8243 (tttt) cc_final: 0.7976 (tttm) REVERT: C 453 LYS cc_start: 0.7883 (mtpm) cc_final: 0.7548 (mtpm) REVERT: C 506 SER cc_start: 0.9083 (m) cc_final: 0.8720 (p) REVERT: C 507 ASP cc_start: 0.8409 (p0) cc_final: 0.8170 (p0) REVERT: C 730 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8418 (mttm) REVERT: C 818 ASP cc_start: 0.8188 (t0) cc_final: 0.7743 (t0) REVERT: C 821 LYS cc_start: 0.8903 (mttt) cc_final: 0.8300 (mttp) REVERT: C 891 MET cc_start: 0.8780 (mtp) cc_final: 0.8492 (mtp) REVERT: C 935 ASP cc_start: 0.7482 (t0) cc_final: 0.7178 (t0) REVERT: C 939 VAL cc_start: 0.8284 (t) cc_final: 0.7931 (p) outliers start: 102 outliers final: 80 residues processed: 648 average time/residue: 0.1560 time to fit residues: 153.7470 Evaluate side-chains 669 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 582 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 883 ARG Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 724 TYR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 160 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 47 ASN C 940 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.091442 restraints weight = 35044.090| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.39 r_work: 0.2951 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23050 Z= 0.137 Angle : 0.534 9.275 31354 Z= 0.281 Chirality : 0.044 0.215 3341 Planarity : 0.004 0.047 4129 Dihedral : 6.415 90.134 3177 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 4.38 % Allowed : 15.78 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2772 helix: 1.00 (0.29), residues: 364 sheet: 0.05 (0.20), residues: 621 loop : -1.37 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 73 TYR 0.019 0.001 TYR C 23 PHE 0.011 0.001 PHE B 686 TRP 0.011 0.001 TRP B 742 HIS 0.006 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (23050) covalent geometry : angle 0.53370 / 0.28 (31354) hydrogen bonds : bond 0.03684 / 2.48 ( 581) hydrogen bonds : angle 5.37110 / 3.67 ( 1569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 595 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6579 (mmm) cc_final: 0.6280 (mmm) REVERT: A 438 LYS cc_start: 0.7677 (tttm) cc_final: 0.7116 (mtmt) REVERT: A 740 VAL cc_start: 0.7965 (t) cc_final: 0.7554 (m) REVERT: A 749 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7903 (mt) REVERT: A 753 GLU cc_start: 0.8207 (pm20) cc_final: 0.7819 (pm20) REVERT: A 758 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8324 (mtt180) REVERT: A 785 TYR cc_start: 0.8363 (m-80) cc_final: 0.7880 (m-10) REVERT: A 948 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7876 (mt-10) REVERT: B 38 TYR cc_start: 0.8083 (p90) cc_final: 0.7617 (p90) REVERT: B 73 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7838 (ttt-90) REVERT: B 167 LYS cc_start: 0.7968 (ptpt) cc_final: 0.7583 (ptpt) REVERT: B 168 LYS cc_start: 0.7848 (mtmm) cc_final: 0.7536 (mtpp) REVERT: B 185 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8206 (mt-10) REVERT: B 218 SER cc_start: 0.8570 (m) cc_final: 0.8143 (t) REVERT: B 288 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7348 (mm) REVERT: B 289 GLN cc_start: 0.8236 (mp10) cc_final: 0.7981 (mp10) REVERT: B 297 GLU cc_start: 0.7961 (pt0) cc_final: 0.7353 (pt0) REVERT: B 311 LYS cc_start: 0.8832 (tttm) cc_final: 0.8544 (tttm) REVERT: B 313 LYS cc_start: 0.7962 (ptpp) cc_final: 0.7234 (pttp) REVERT: B 348 ASN cc_start: 0.8519 (m110) cc_final: 0.8046 (m-40) REVERT: B 368 ASP cc_start: 0.7968 (t0) cc_final: 0.7551 (t0) REVERT: B 369 LEU cc_start: 0.8728 (mt) cc_final: 0.8310 (mt) REVERT: B 372 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7833 (ttm-80) REVERT: B 387 ASP cc_start: 0.7546 (t0) cc_final: 0.7163 (t0) REVERT: B 389 THR cc_start: 0.8503 (m) cc_final: 0.8130 (p) REVERT: B 393 SER cc_start: 0.8779 (p) cc_final: 0.8411 (p) REVERT: B 417 GLU cc_start: 0.8167 (mp0) cc_final: 0.7724 (mp0) REVERT: B 472 GLU cc_start: 0.7874 (tt0) cc_final: 0.7367 (tt0) REVERT: B 645 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8168 (mm) REVERT: B 681 ARG cc_start: 0.8592 (ptp-110) cc_final: 0.8373 (ptm160) REVERT: B 687 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.8018 (mtm-85) REVERT: B 706 TYR cc_start: 0.8787 (t80) cc_final: 0.8353 (t80) REVERT: B 799 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8378 (mtmm) REVERT: B 853 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7297 (t80) REVERT: B 864 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8390 (mtpp) REVERT: B 886 PHE cc_start: 0.8542 (t80) cc_final: 0.8276 (t80) REVERT: B 899 LEU cc_start: 0.8750 (mt) cc_final: 0.8383 (tp) REVERT: B 905 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7577 (p90) REVERT: B 941 GLN cc_start: 0.8800 (mt0) cc_final: 0.8527 (mt0) REVERT: B 953 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7530 (mtm-85) REVERT: C 30 GLN cc_start: 0.7323 (tm-30) cc_final: 0.7109 (tm-30) REVERT: C 81 LYS cc_start: 0.8209 (ptmm) cc_final: 0.7990 (ptmt) REVERT: C 203 ILE cc_start: 0.8469 (mt) cc_final: 0.8172 (pt) REVERT: C 207 LYS cc_start: 0.8858 (pttt) cc_final: 0.8559 (ptmt) REVERT: C 208 THR cc_start: 0.9109 (m) cc_final: 0.8702 (p) REVERT: C 268 SER cc_start: 0.8397 (t) cc_final: 0.8044 (t) REVERT: C 316 ASP cc_start: 0.8150 (t0) cc_final: 0.7851 (t0) REVERT: C 453 LYS cc_start: 0.7895 (mtpm) cc_final: 0.7575 (mtpm) REVERT: C 506 SER cc_start: 0.9079 (m) cc_final: 0.8703 (p) REVERT: C 818 ASP cc_start: 0.8210 (t0) cc_final: 0.7744 (t0) REVERT: C 821 LYS cc_start: 0.8876 (mttt) cc_final: 0.8300 (mttp) REVERT: C 891 MET cc_start: 0.8796 (mtp) cc_final: 0.8493 (mtp) REVERT: C 935 ASP cc_start: 0.7541 (t0) cc_final: 0.7237 (t0) REVERT: C 939 VAL cc_start: 0.8285 (t) cc_final: 0.7943 (p) REVERT: G 5 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7624 (mp) outliers start: 106 outliers final: 83 residues processed: 657 average time/residue: 0.1468 time to fit residues: 147.9724 Evaluate side-chains 683 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 591 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 673 ASN Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 107 optimal weight: 8.9990 chunk 242 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 268 optimal weight: 0.0170 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN A 582 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 47 ASN C 940 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.091631 restraints weight = 35003.319| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.39 r_work: 0.2952 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23050 Z= 0.135 Angle : 0.533 8.995 31354 Z= 0.280 Chirality : 0.044 0.208 3341 Planarity : 0.004 0.046 4129 Dihedral : 6.377 90.902 3177 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 4.25 % Allowed : 16.40 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2772 helix: 1.09 (0.29), residues: 358 sheet: 0.08 (0.21), residues: 608 loop : -1.35 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 83 TYR 0.022 0.001 TYR A 80 PHE 0.029 0.001 PHE A 546 TRP 0.010 0.001 TRP C 135 HIS 0.006 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (23050) covalent geometry : angle 0.53266 / 0.28 (31354) hydrogen bonds : bond 0.03634 / 2.45 ( 581) hydrogen bonds : angle 5.35089 / 3.66 ( 1569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 596 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6580 (mmm) cc_final: 0.6279 (mmm) REVERT: A 13 MET cc_start: 0.8640 (mmm) cc_final: 0.8359 (tpp) REVERT: A 438 LYS cc_start: 0.7668 (tttm) cc_final: 0.7117 (mtmt) REVERT: A 740 VAL cc_start: 0.7960 (t) cc_final: 0.7546 (m) REVERT: A 749 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7920 (mt) REVERT: A 753 GLU cc_start: 0.8248 (pm20) cc_final: 0.7859 (pm20) REVERT: A 755 GLU cc_start: 0.8472 (tt0) cc_final: 0.8093 (tt0) REVERT: A 758 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8094 (mtt180) REVERT: A 785 TYR cc_start: 0.8384 (m-80) cc_final: 0.7922 (m-10) REVERT: A 849 GLU cc_start: 0.8520 (pt0) cc_final: 0.8296 (pt0) REVERT: A 948 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 38 TYR cc_start: 0.8061 (p90) cc_final: 0.7611 (p90) REVERT: B 73 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7842 (ttt-90) REVERT: B 167 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7539 (ptpt) REVERT: B 168 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7548 (mtpp) REVERT: B 185 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 218 SER cc_start: 0.8574 (m) cc_final: 0.8147 (t) REVERT: B 288 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7190 (mm) REVERT: B 289 GLN cc_start: 0.8238 (mp10) cc_final: 0.7946 (mp10) REVERT: B 297 GLU cc_start: 0.7959 (pt0) cc_final: 0.7725 (pt0) REVERT: B 311 LYS cc_start: 0.8832 (tttm) cc_final: 0.8554 (tttm) REVERT: B 313 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7198 (pttp) REVERT: B 348 ASN cc_start: 0.8539 (m110) cc_final: 0.8050 (m-40) REVERT: B 368 ASP cc_start: 0.7967 (t0) cc_final: 0.7555 (t0) REVERT: B 369 LEU cc_start: 0.8722 (mt) cc_final: 0.8319 (mt) REVERT: B 372 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7831 (ttm-80) REVERT: B 393 SER cc_start: 0.8794 (p) cc_final: 0.8415 (p) REVERT: B 417 GLU cc_start: 0.8164 (mp0) cc_final: 0.7710 (mp0) REVERT: B 472 GLU cc_start: 0.7907 (tt0) cc_final: 0.7403 (tt0) REVERT: B 645 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8172 (mm) REVERT: B 681 ARG cc_start: 0.8577 (ptp-110) cc_final: 0.8355 (ptm160) REVERT: B 687 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.8027 (mtm-85) REVERT: B 706 TYR cc_start: 0.8778 (t80) cc_final: 0.8336 (t80) REVERT: B 799 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (mtmm) REVERT: B 853 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.7282 (t80) REVERT: B 864 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8389 (mtpp) REVERT: B 865 THR cc_start: 0.8680 (t) cc_final: 0.8149 (t) REVERT: B 886 PHE cc_start: 0.8549 (t80) cc_final: 0.8329 (t80) REVERT: B 899 LEU cc_start: 0.8741 (mt) cc_final: 0.8404 (tp) REVERT: B 905 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7693 (p90) REVERT: B 941 GLN cc_start: 0.8800 (mt0) cc_final: 0.8519 (mt0) REVERT: B 953 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7536 (mtm-85) REVERT: C 30 GLN cc_start: 0.7303 (tm-30) cc_final: 0.7081 (tm-30) REVERT: C 81 LYS cc_start: 0.8159 (ptmm) cc_final: 0.7864 (ptmt) REVERT: C 203 ILE cc_start: 0.8463 (mt) cc_final: 0.8171 (pt) REVERT: C 207 LYS cc_start: 0.8853 (pttt) cc_final: 0.8557 (ptmt) REVERT: C 208 THR cc_start: 0.9093 (m) cc_final: 0.8677 (p) REVERT: C 268 SER cc_start: 0.8405 (t) cc_final: 0.8047 (t) REVERT: C 302 GLU cc_start: 0.8261 (pt0) cc_final: 0.7970 (tt0) REVERT: C 316 ASP cc_start: 0.8142 (t0) cc_final: 0.7854 (t0) REVERT: C 453 LYS cc_start: 0.7884 (mtpm) cc_final: 0.7567 (mtpm) REVERT: C 506 SER cc_start: 0.9085 (m) cc_final: 0.8702 (p) REVERT: C 818 ASP cc_start: 0.8212 (t0) cc_final: 0.7752 (t0) REVERT: C 821 LYS cc_start: 0.8846 (mttt) cc_final: 0.8266 (mttp) REVERT: C 891 MET cc_start: 0.8817 (mtp) cc_final: 0.8468 (mtp) REVERT: C 935 ASP cc_start: 0.7494 (t0) cc_final: 0.7212 (t0) REVERT: C 939 VAL cc_start: 0.8229 (t) cc_final: 0.7890 (p) REVERT: G 5 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7685 (mp) outliers start: 103 outliers final: 83 residues processed: 655 average time/residue: 0.1607 time to fit residues: 160.9894 Evaluate side-chains 679 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 587 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 883 ARG Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 41 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN B 18 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 47 ASN C 940 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.091841 restraints weight = 34792.300| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.25 r_work: 0.2943 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23050 Z= 0.171 Angle : 0.566 10.773 31354 Z= 0.297 Chirality : 0.045 0.208 3341 Planarity : 0.004 0.046 4129 Dihedral : 6.473 90.846 3177 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.20 % Favored : 93.76 % Rotamer: Outliers : 4.46 % Allowed : 16.77 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2772 helix: 1.04 (0.29), residues: 358 sheet: 0.11 (0.21), residues: 614 loop : -1.40 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 73 TYR 0.022 0.001 TYR A 346 PHE 0.028 0.002 PHE A 546 TRP 0.010 0.001 TRP C 135 HIS 0.008 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (23050) covalent geometry : angle 0.56567 / 0.30 (31354) hydrogen bonds : bond 0.03981 / 2.68 ( 581) hydrogen bonds : angle 5.38433 / 3.68 ( 1569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 599 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.6599 (mmm) cc_final: 0.6297 (mmm) REVERT: A 438 LYS cc_start: 0.7794 (tttm) cc_final: 0.7261 (mtmt) REVERT: A 740 VAL cc_start: 0.8099 (t) cc_final: 0.7699 (m) REVERT: A 749 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7987 (mt) REVERT: A 753 GLU cc_start: 0.8252 (pm20) cc_final: 0.7904 (pm20) REVERT: A 755 GLU cc_start: 0.8415 (tt0) cc_final: 0.8057 (tt0) REVERT: A 758 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8098 (mtt180) REVERT: A 785 TYR cc_start: 0.8397 (m-80) cc_final: 0.7953 (m-10) REVERT: A 948 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 38 TYR cc_start: 0.8070 (p90) cc_final: 0.7612 (p90) REVERT: B 73 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7840 (ttt-90) REVERT: B 167 LYS cc_start: 0.7943 (ptpt) cc_final: 0.7531 (ptpt) REVERT: B 168 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7622 (mtpp) REVERT: B 185 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8228 (mt-10) REVERT: B 218 SER cc_start: 0.8550 (m) cc_final: 0.8175 (t) REVERT: B 288 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7424 (mm) REVERT: B 289 GLN cc_start: 0.8323 (mp10) cc_final: 0.8020 (mp10) REVERT: B 311 LYS cc_start: 0.8810 (tttm) cc_final: 0.8550 (tttm) REVERT: B 313 LYS cc_start: 0.7953 (ptpp) cc_final: 0.7247 (pttp) REVERT: B 348 ASN cc_start: 0.8529 (m110) cc_final: 0.8057 (m-40) REVERT: B 368 ASP cc_start: 0.7968 (t0) cc_final: 0.7600 (t0) REVERT: B 369 LEU cc_start: 0.8778 (mt) cc_final: 0.8425 (mt) REVERT: B 372 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7886 (ttm-80) REVERT: B 393 SER cc_start: 0.8739 (p) cc_final: 0.8386 (p) REVERT: B 417 GLU cc_start: 0.8130 (mp0) cc_final: 0.7713 (mp0) REVERT: B 472 GLU cc_start: 0.7804 (tt0) cc_final: 0.7391 (tt0) REVERT: B 645 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8222 (mm) REVERT: B 681 ARG cc_start: 0.8622 (ptp-110) cc_final: 0.8399 (ptm160) REVERT: B 687 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.8087 (mtm-85) REVERT: B 706 TYR cc_start: 0.8808 (t80) cc_final: 0.8394 (t80) REVERT: B 799 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: B 802 MET cc_start: 0.8368 (ttt) cc_final: 0.8160 (ttp) REVERT: B 853 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.7254 (t80) REVERT: B 864 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8381 (mtpp) REVERT: B 865 THR cc_start: 0.8608 (t) cc_final: 0.8065 (t) REVERT: B 886 PHE cc_start: 0.8620 (t80) cc_final: 0.8378 (t80) REVERT: B 899 LEU cc_start: 0.8804 (mt) cc_final: 0.8464 (tp) REVERT: B 905 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7717 (p90) REVERT: B 941 GLN cc_start: 0.8845 (mt0) cc_final: 0.8568 (mt0) REVERT: B 953 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7573 (mtm-85) REVERT: C 30 GLN cc_start: 0.7375 (tm-30) cc_final: 0.7153 (tm-30) REVERT: C 81 LYS cc_start: 0.8245 (ptmm) cc_final: 0.7972 (ptmt) REVERT: C 207 LYS cc_start: 0.8886 (pttt) cc_final: 0.8633 (ptmt) REVERT: C 208 THR cc_start: 0.9119 (m) cc_final: 0.8735 (p) REVERT: C 268 SER cc_start: 0.8428 (t) cc_final: 0.8191 (t) REVERT: C 302 GLU cc_start: 0.8188 (pt0) cc_final: 0.7938 (tt0) REVERT: C 316 ASP cc_start: 0.8152 (t0) cc_final: 0.7873 (t0) REVERT: C 403 ASP cc_start: 0.7965 (t0) cc_final: 0.7661 (t0) REVERT: C 453 LYS cc_start: 0.7913 (mtpm) cc_final: 0.7653 (mtpm) REVERT: C 462 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7544 (mm-30) REVERT: C 506 SER cc_start: 0.9078 (m) cc_final: 0.8742 (p) REVERT: C 611 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: C 670 ASN cc_start: 0.8767 (m110) cc_final: 0.8545 (m-40) REVERT: C 730 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8434 (mttp) REVERT: C 818 ASP cc_start: 0.8135 (t0) cc_final: 0.7743 (t0) REVERT: C 821 LYS cc_start: 0.8908 (mttt) cc_final: 0.8297 (mttp) REVERT: C 935 ASP cc_start: 0.7469 (t0) cc_final: 0.7243 (t0) REVERT: C 939 VAL cc_start: 0.8313 (t) cc_final: 0.7973 (p) REVERT: G 5 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7745 (mp) outliers start: 108 outliers final: 91 residues processed: 658 average time/residue: 0.1607 time to fit residues: 161.1368 Evaluate side-chains 685 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 584 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 673 ASN Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 883 ARG Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 128 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 209 optimal weight: 0.0980 chunk 210 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN A 582 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 940 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.106326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.090617 restraints weight = 35233.202| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.29 r_work: 0.2938 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23050 Z= 0.180 Angle : 0.574 9.754 31354 Z= 0.302 Chirality : 0.045 0.221 3341 Planarity : 0.004 0.070 4129 Dihedral : 6.517 91.302 3177 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 4.38 % Allowed : 17.22 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2772 helix: 1.01 (0.29), residues: 358 sheet: 0.09 (0.21), residues: 614 loop : -1.40 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 879 TYR 0.021 0.002 TYR A 80 PHE 0.027 0.002 PHE A 546 TRP 0.010 0.001 TRP C 135 HIS 0.008 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (23050) covalent geometry : angle 0.57423 / 0.30 (31354) hydrogen bonds : bond 0.04031 / 2.72 ( 581) hydrogen bonds : angle 5.40124 / 3.69 ( 1569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 586 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.6591 (mmm) cc_final: 0.6287 (mmm) REVERT: A 13 MET cc_start: 0.8742 (mmm) cc_final: 0.8471 (tpp) REVERT: A 438 LYS cc_start: 0.7778 (tttm) cc_final: 0.7242 (mtmt) REVERT: A 459 GLU cc_start: 0.7499 (tp30) cc_final: 0.6915 (tp30) REVERT: A 722 THR cc_start: 0.8372 (t) cc_final: 0.8062 (p) REVERT: A 740 VAL cc_start: 0.8063 (t) cc_final: 0.7659 (m) REVERT: A 749 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7984 (mt) REVERT: A 753 GLU cc_start: 0.8234 (pm20) cc_final: 0.7883 (pm20) REVERT: A 755 GLU cc_start: 0.8431 (tt0) cc_final: 0.8071 (tt0) REVERT: A 758 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8103 (mtt180) REVERT: A 785 TYR cc_start: 0.8385 (m-80) cc_final: 0.7942 (m-10) REVERT: A 948 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7895 (mt-10) REVERT: B 38 TYR cc_start: 0.8083 (p90) cc_final: 0.7626 (p90) REVERT: B 73 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7856 (ttt-90) REVERT: B 167 LYS cc_start: 0.7943 (ptpt) cc_final: 0.7521 (ptpt) REVERT: B 168 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7624 (mtpp) REVERT: B 185 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 218 SER cc_start: 0.8544 (m) cc_final: 0.8153 (t) REVERT: B 288 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7419 (mm) REVERT: B 289 GLN cc_start: 0.8324 (mp10) cc_final: 0.8019 (mp10) REVERT: B 311 LYS cc_start: 0.8821 (tttm) cc_final: 0.8545 (tttm) REVERT: B 313 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7216 (pttp) REVERT: B 348 ASN cc_start: 0.8538 (m110) cc_final: 0.8064 (m-40) REVERT: B 368 ASP cc_start: 0.7986 (t0) cc_final: 0.7628 (t0) REVERT: B 369 LEU cc_start: 0.8747 (mt) cc_final: 0.8378 (mt) REVERT: B 372 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7869 (ttm-80) REVERT: B 393 SER cc_start: 0.8761 (p) cc_final: 0.8400 (p) REVERT: B 417 GLU cc_start: 0.8147 (mp0) cc_final: 0.7720 (mp0) REVERT: B 472 GLU cc_start: 0.7833 (tt0) cc_final: 0.7410 (tt0) REVERT: B 645 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8211 (mm) REVERT: B 681 ARG cc_start: 0.8611 (ptp-110) cc_final: 0.8387 (ptm160) REVERT: B 687 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.8076 (mtm-85) REVERT: B 706 TYR cc_start: 0.8812 (t80) cc_final: 0.8391 (t80) REVERT: B 802 MET cc_start: 0.8296 (ttt) cc_final: 0.8045 (ttp) REVERT: B 853 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.7256 (t80) REVERT: B 864 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8392 (mtpp) REVERT: B 899 LEU cc_start: 0.8792 (mt) cc_final: 0.8426 (tp) REVERT: B 905 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7740 (p90) REVERT: B 941 GLN cc_start: 0.8848 (mt0) cc_final: 0.8574 (mt0) REVERT: B 944 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7679 (ttm110) REVERT: B 953 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7580 (mtm-85) REVERT: C 30 GLN cc_start: 0.7365 (tm-30) cc_final: 0.7133 (tm-30) REVERT: C 81 LYS cc_start: 0.8224 (ptmm) cc_final: 0.7947 (ptmt) REVERT: C 203 ILE cc_start: 0.8521 (mt) cc_final: 0.8221 (pt) REVERT: C 207 LYS cc_start: 0.8888 (pttt) cc_final: 0.8632 (ptmt) REVERT: C 208 THR cc_start: 0.9116 (m) cc_final: 0.8734 (p) REVERT: C 268 SER cc_start: 0.8434 (t) cc_final: 0.8190 (t) REVERT: C 302 GLU cc_start: 0.8213 (pt0) cc_final: 0.7953 (tt0) REVERT: C 316 ASP cc_start: 0.8180 (t0) cc_final: 0.7902 (t0) REVERT: C 403 ASP cc_start: 0.7959 (t0) cc_final: 0.7627 (t0) REVERT: C 453 LYS cc_start: 0.7927 (mtpm) cc_final: 0.7685 (mtpm) REVERT: C 462 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7547 (mm-30) REVERT: C 506 SER cc_start: 0.9085 (m) cc_final: 0.8737 (p) REVERT: C 611 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: C 670 ASN cc_start: 0.8777 (m110) cc_final: 0.8548 (m-40) REVERT: C 730 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8421 (mttm) REVERT: C 818 ASP cc_start: 0.8189 (t0) cc_final: 0.7772 (t0) REVERT: C 821 LYS cc_start: 0.8899 (mttt) cc_final: 0.8294 (mttp) REVERT: C 891 MET cc_start: 0.8800 (mtp) cc_final: 0.8559 (mtp) REVERT: C 935 ASP cc_start: 0.7507 (t0) cc_final: 0.7240 (t0) REVERT: C 939 VAL cc_start: 0.8319 (t) cc_final: 0.7977 (p) REVERT: G 5 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7757 (mp) outliers start: 106 outliers final: 93 residues processed: 644 average time/residue: 0.1637 time to fit residues: 160.1257 Evaluate side-chains 685 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 583 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 673 ASN Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 883 ARG Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 269 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 240 optimal weight: 0.0570 chunk 174 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 214 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 47 ASN C 940 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.091232 restraints weight = 35228.700| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.32 r_work: 0.2979 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23050 Z= 0.189 Angle : 0.583 9.600 31354 Z= 0.306 Chirality : 0.046 0.222 3341 Planarity : 0.004 0.048 4129 Dihedral : 6.579 91.731 3177 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.46 % Favored : 93.51 % Rotamer: Outliers : 4.42 % Allowed : 17.27 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2772 helix: 1.21 (0.30), residues: 340 sheet: 0.05 (0.21), residues: 617 loop : -1.39 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 73 TYR 0.022 0.002 TYR A 80 PHE 0.026 0.002 PHE A 546 TRP 0.016 0.001 TRP B 882 HIS 0.008 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (23050) covalent geometry : angle 0.58256 / 0.31 (31354) hydrogen bonds : bond 0.04136 / 2.79 ( 581) hydrogen bonds : angle 5.44169 / 3.72 ( 1569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5544 Ramachandran restraints generated. 2772 Oldfield, 0 Emsley, 2772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 591 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.6590 (mmm) cc_final: 0.6279 (mmm) REVERT: A 289 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7899 (mm-40) REVERT: A 438 LYS cc_start: 0.7758 (tttm) cc_final: 0.7210 (mtmt) REVERT: A 459 GLU cc_start: 0.7534 (tp30) cc_final: 0.6933 (tp30) REVERT: A 722 THR cc_start: 0.8396 (t) cc_final: 0.8083 (p) REVERT: A 740 VAL cc_start: 0.8048 (t) cc_final: 0.7649 (m) REVERT: A 749 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7977 (mt) REVERT: A 753 GLU cc_start: 0.8224 (pm20) cc_final: 0.7876 (pm20) REVERT: A 755 GLU cc_start: 0.8453 (tt0) cc_final: 0.8094 (tt0) REVERT: A 758 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8114 (mtt180) REVERT: A 785 TYR cc_start: 0.8402 (m-80) cc_final: 0.7953 (m-10) REVERT: A 849 GLU cc_start: 0.8495 (pt0) cc_final: 0.8278 (pt0) REVERT: A 948 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 38 TYR cc_start: 0.8081 (p90) cc_final: 0.7661 (p90) REVERT: B 73 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7864 (ttt-90) REVERT: B 167 LYS cc_start: 0.7958 (ptpt) cc_final: 0.7526 (ptpt) REVERT: B 168 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7612 (mtpp) REVERT: B 185 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 218 SER cc_start: 0.8554 (m) cc_final: 0.8169 (t) REVERT: B 288 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7373 (mm) REVERT: B 289 GLN cc_start: 0.8331 (mp10) cc_final: 0.8003 (mp10) REVERT: B 297 GLU cc_start: 0.7993 (pt0) cc_final: 0.7424 (pt0) REVERT: B 311 LYS cc_start: 0.8829 (tttm) cc_final: 0.8531 (tttm) REVERT: B 313 LYS cc_start: 0.7908 (ptpp) cc_final: 0.7201 (pttp) REVERT: B 348 ASN cc_start: 0.8522 (m110) cc_final: 0.8075 (m-40) REVERT: B 368 ASP cc_start: 0.7985 (t0) cc_final: 0.7648 (t0) REVERT: B 369 LEU cc_start: 0.8731 (mt) cc_final: 0.8386 (mt) REVERT: B 372 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7863 (ttm170) REVERT: B 393 SER cc_start: 0.8743 (p) cc_final: 0.8394 (p) REVERT: B 417 GLU cc_start: 0.8152 (mp0) cc_final: 0.7697 (mp0) REVERT: B 472 GLU cc_start: 0.7826 (tt0) cc_final: 0.7357 (tt0) REVERT: B 645 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 681 ARG cc_start: 0.8605 (ptp-110) cc_final: 0.8380 (ptm160) REVERT: B 687 ARG cc_start: 0.8357 (mtp-110) cc_final: 0.8062 (mtm-85) REVERT: B 706 TYR cc_start: 0.8817 (t80) cc_final: 0.8392 (t80) REVERT: B 802 MET cc_start: 0.8365 (ttt) cc_final: 0.8119 (ttp) REVERT: B 853 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7236 (t80) REVERT: B 864 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8375 (mtpp) REVERT: B 899 LEU cc_start: 0.8796 (mt) cc_final: 0.8398 (tp) REVERT: B 905 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7653 (p90) REVERT: B 941 GLN cc_start: 0.8862 (mt0) cc_final: 0.8625 (mt0) REVERT: B 944 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7722 (ttm110) REVERT: B 953 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7516 (mtm-85) REVERT: C 30 GLN cc_start: 0.7353 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 81 LYS cc_start: 0.8224 (ptmm) cc_final: 0.7949 (ptmt) REVERT: C 203 ILE cc_start: 0.8518 (mt) cc_final: 0.8211 (pt) REVERT: C 207 LYS cc_start: 0.8903 (pttt) cc_final: 0.8636 (ptmt) REVERT: C 208 THR cc_start: 0.9143 (m) cc_final: 0.8760 (p) REVERT: C 268 SER cc_start: 0.8429 (t) cc_final: 0.8184 (t) REVERT: C 302 GLU cc_start: 0.8221 (pt0) cc_final: 0.8010 (tt0) REVERT: C 316 ASP cc_start: 0.8170 (t0) cc_final: 0.7909 (t0) REVERT: C 403 ASP cc_start: 0.7970 (t0) cc_final: 0.7631 (t0) REVERT: C 453 LYS cc_start: 0.7914 (mtpm) cc_final: 0.7664 (mtpm) REVERT: C 462 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7563 (mm-30) REVERT: C 506 SER cc_start: 0.9098 (m) cc_final: 0.8741 (p) REVERT: C 611 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: C 670 ASN cc_start: 0.8796 (m110) cc_final: 0.8567 (m-40) REVERT: C 730 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8429 (mttm) REVERT: C 818 ASP cc_start: 0.8192 (t0) cc_final: 0.7712 (t0) REVERT: C 821 LYS cc_start: 0.8896 (mttt) cc_final: 0.8283 (mttp) REVERT: C 891 MET cc_start: 0.8824 (mtp) cc_final: 0.8584 (mtp) REVERT: C 935 ASP cc_start: 0.7502 (t0) cc_final: 0.7234 (t0) REVERT: C 939 VAL cc_start: 0.8297 (t) cc_final: 0.7968 (p) REVERT: G 5 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7782 (mp) outliers start: 107 outliers final: 93 residues processed: 650 average time/residue: 0.1750 time to fit residues: 173.4294 Evaluate side-chains 686 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 584 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 821 LYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 883 ARG Chi-restraints excluded: chain B residue 905 TYR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 953 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 593 GLU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain G residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 165 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 264 optimal weight: 0.0270 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN A 582 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 47 ASN C 435 GLN C 940 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092056 restraints weight = 35004.170| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.32 r_work: 0.2946 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23050 Z= 0.147 Angle : 0.560 9.459 31354 Z= 0.293 Chirality : 0.045 0.211 3341 Planarity : 0.004 0.048 4129 Dihedral : 6.463 91.867 3177 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.06 % Favored : 93.90 % Rotamer: Outliers : 4.38 % Allowed : 17.39 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2772 helix: 1.10 (0.29), residues: 352 sheet: 0.07 (0.20), residues: 617 loop : -1.38 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 73 TYR 0.020 0.001 TYR A 12 PHE 0.022 0.001 PHE A 546 TRP 0.011 0.001 TRP C 135 HIS 0.007 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (23050) covalent geometry : angle 0.56028 / 0.29 (31354) hydrogen bonds : bond 0.03723 / 2.52 ( 581) hydrogen bonds : angle 5.37168 / 3.67 ( 1569) =============================================================================== Job complete usr+sys time: 5871.73 seconds wall clock time: 101 minutes 9.31 seconds (6069.31 seconds total)