Starting phenix.real_space_refine on Tue Aug 26 10:32:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g05_50911/08_2025/9g05_50911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g05_50911/08_2025/9g05_50911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g05_50911/08_2025/9g05_50911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g05_50911/08_2025/9g05_50911.map" model { file = "/net/cci-nas-00/data/ceres_data/9g05_50911/08_2025/9g05_50911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g05_50911/08_2025/9g05_50911.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.262 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 S 74 5.16 5 C 11120 2.51 5 N 2832 2.21 5 O 3320 1.98 5 H 17286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34632 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 17124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 17124 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 28, 'TRANS': 998} Chain breaks: 1 Chain: "B" Number of atoms: 17124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 17124 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 28, 'TRANS': 998} Chain breaks: 1 Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "D" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 5.66, per 1000 atoms: 0.16 Number of scatterers: 34632 At special positions: 0 Unit cell: (143.452, 119.963, 114.929, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 O 3320 8.00 N 2832 7.00 C 11120 6.00 H 17286 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 658.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4028 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 20 sheets defined 47.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.884A pdb=" N TYR A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.624A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.651A pdb=" N SER A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.563A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 229 removed outlier: 3.902A pdb=" N ILE A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 removed outlier: 3.629A pdb=" N TYR A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 284 through 297 removed outlier: 3.607A pdb=" N SER A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.650A pdb=" N ASP A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 400 through 417 Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.519A pdb=" N ILE A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 removed outlier: 4.009A pdb=" N ASN A 527 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 removed outlier: 3.692A pdb=" N ARG A 552 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.520A pdb=" N SER A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.651A pdb=" N ASP A 616 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 Processing helix chain 'A' and resid 687 through 701 Processing helix chain 'A' and resid 785 through 801 removed outlier: 4.313A pdb=" N ILE A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 793 " --> pdb=" O TYR A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 847 Proline residue: A 835 - end of helix removed outlier: 3.555A pdb=" N GLU A 839 " --> pdb=" O PRO A 835 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 866 removed outlier: 3.569A pdb=" N TYR A 865 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 866 " --> pdb=" O GLU A 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 862 through 866' Processing helix chain 'A' and resid 870 through 895 removed outlier: 3.996A pdb=" N LYS A 876 " --> pdb=" O ASN A 872 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 Processing helix chain 'A' and resid 919 through 927 removed outlier: 4.065A pdb=" N VAL A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 927 " --> pdb=" O GLN A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 942 removed outlier: 3.942A pdb=" N LYS A 941 " --> pdb=" O ARG A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 951 Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.566A pdb=" N TRP A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 974 Processing helix chain 'A' and resid 976 through 990 removed outlier: 3.763A pdb=" N ILE A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1013 removed outlier: 3.507A pdb=" N ILE A1004 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A1007 " --> pdb=" O ILE A1003 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A1008 " --> pdb=" O ILE A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1033 Processing helix chain 'A' and resid 1034 through 1036 No H-bonds generated for 'chain 'A' and resid 1034 through 1036' Processing helix chain 'B' and resid 20 through 27 Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.592A pdb=" N SER B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.921A pdb=" N ILE B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 removed outlier: 3.625A pdb=" N TYR B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 277 removed outlier: 3.501A pdb=" N ASP B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 299 removed outlier: 3.942A pdb=" N VAL B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.778A pdb=" N ASP B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 400 through 418 removed outlier: 3.583A pdb=" N LYS B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 411 " --> pdb=" O PHE B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 490 through 505 removed outlier: 4.247A pdb=" N PHE B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.514A pdb=" N ASN B 527 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 528 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.732A pdb=" N ARG B 552 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 587 through 591 Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.730A pdb=" N SER B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 669 removed outlier: 3.756A pdb=" N ASP B 663 " --> pdb=" O ASN B 659 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 664 " --> pdb=" O GLN B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 701 removed outlier: 3.502A pdb=" N CYS B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 781 No H-bonds generated for 'chain 'B' and resid 779 through 781' Processing helix chain 'B' and resid 782 through 801 removed outlier: 4.283A pdb=" N ILE B 791 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER B 792 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 793 " --> pdb=" O TYR B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 847 Proline residue: B 835 - end of helix removed outlier: 3.512A pdb=" N GLU B 839 " --> pdb=" O PRO B 835 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 847 " --> pdb=" O MET B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 866 removed outlier: 3.573A pdb=" N TYR B 865 " --> pdb=" O ILE B 862 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 866 " --> pdb=" O GLU B 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 862 through 866' Processing helix chain 'B' and resid 870 through 895 removed outlier: 4.047A pdb=" N LYS B 876 " --> pdb=" O ASN B 872 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 879 " --> pdb=" O GLU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 917 removed outlier: 3.599A pdb=" N GLY B 917 " --> pdb=" O MET B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 removed outlier: 4.115A pdb=" N VAL B 924 " --> pdb=" O TYR B 920 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 942 Processing helix chain 'B' and resid 943 through 951 Processing helix chain 'B' and resid 963 through 974 Processing helix chain 'B' and resid 976 through 990 removed outlier: 3.766A pdb=" N ILE B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1013 Processing helix chain 'B' and resid 1015 through 1033 Processing helix chain 'B' and resid 1034 through 1037 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.713A pdb=" N PHE A 11 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N ARG A 314 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N PHE A 105 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS A 316 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER A 115 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 316 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 113 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 7 removed outlier: 8.649A pdb=" N VAL A 633 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR A 466 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N MET A 635 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 468 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 627 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 127 Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 158 removed outlier: 4.105A pdb=" N ILE A 179 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 365 removed outlier: 13.529A pdb=" N PHE A 567 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N LEU A 580 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA A 569 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 576 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 512 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N THR A 581 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS A 514 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 624 Processing sheet with id=AA8, first strand: chain 'A' and resid 720 through 722 removed outlier: 4.261A pdb=" N VAL A 720 " --> pdb=" O TYR A 727 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AB1, first strand: chain 'A' and resid 806 through 813 removed outlier: 3.956A pdb=" N LYS A 806 " --> pdb=" O ASN A 824 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 852 " --> pdb=" O TYR A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 5 through 7 removed outlier: 8.698A pdb=" N VAL B 633 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 466 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET B 635 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE B 468 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 627 " --> pdb=" O ILE B 634 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 116 removed outlier: 6.826A pdb=" N VAL B 113 " --> pdb=" O LYS B 316 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 316 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER B 115 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N ARG B 314 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N PHE B 105 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS B 316 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 11 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 127 Processing sheet with id=AB5, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB6, first strand: chain 'B' and resid 156 through 158 removed outlier: 4.107A pdb=" N ILE B 179 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 178 " --> pdb=" O LYS D 12 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 365 removed outlier: 13.521A pdb=" N PHE B 567 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N LEU B 580 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALA B 569 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 576 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 512 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR B 581 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS B 514 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 623 through 624 Processing sheet with id=AB9, first strand: chain 'B' and resid 720 through 722 removed outlier: 4.234A pdb=" N VAL B 720 " --> pdb=" O TYR B 727 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 764 through 765 Processing sheet with id=AC2, first strand: chain 'B' and resid 806 through 813 removed outlier: 3.966A pdb=" N LYS B 806 " --> pdb=" O ASN B 824 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 852 " --> pdb=" O TYR B 777 " (cutoff:3.500A) 803 hydrogen bonds defined for protein. 2271 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: 8.52 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17266 1.03 - 1.23: 60 1.23 - 1.42: 7420 1.42 - 1.62: 10090 1.62 - 1.81: 128 Bond restraints: 34964 Sorted by residual: bond pdb=" CA PHE A 940 " pdb=" C PHE A 940 " ideal model delta sigma weight residual 1.522 1.432 0.090 1.39e-02 5.18e+03 4.24e+01 bond pdb=" CA LYS A 941 " pdb=" C LYS A 941 " ideal model delta sigma weight residual 1.526 1.578 -0.052 9.20e-03 1.18e+04 3.21e+01 bond pdb=" N ASP A 939 " pdb=" CA ASP A 939 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.33e-02 5.65e+03 8.89e+00 bond pdb=" N PHE A 940 " pdb=" CA PHE A 940 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.33e-02 5.65e+03 8.72e+00 bond pdb=" N LYS A 941 " pdb=" CA LYS A 941 " ideal model delta sigma weight residual 1.468 1.435 0.033 1.24e-02 6.50e+03 7.15e+00 ... (remaining 34959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.98: 63233 6.98 - 13.95: 8 13.95 - 20.93: 0 20.93 - 27.90: 0 27.90 - 34.88: 3 Bond angle restraints: 63244 Sorted by residual: angle pdb=" C GLU B 42 " pdb=" CA GLU B 42 " pdb=" HA GLU B 42 " ideal model delta sigma weight residual 109.00 74.12 34.88 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" HA GLU B 42 " ideal model delta sigma weight residual 110.00 75.52 34.48 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB GLU B 42 " pdb=" CA GLU B 42 " pdb=" HA GLU B 42 " ideal model delta sigma weight residual 109.00 75.84 33.16 3.00e+00 1.11e-01 1.22e+02 angle pdb=" N PHE A 940 " pdb=" CA PHE A 940 " pdb=" CB PHE A 940 " ideal model delta sigma weight residual 110.40 99.51 10.89 1.63e+00 3.76e-01 4.46e+01 angle pdb=" O GLU A 938 " pdb=" C GLU A 938 " pdb=" N ASP A 939 " ideal model delta sigma weight residual 122.46 113.52 8.94 1.38e+00 5.25e-01 4.19e+01 ... (remaining 63239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 15328 16.30 - 32.60: 778 32.60 - 48.89: 152 48.89 - 65.19: 62 65.19 - 81.49: 14 Dihedral angle restraints: 16334 sinusoidal: 8918 harmonic: 7416 Sorted by residual: dihedral pdb=" CA ARG B 384 " pdb=" C ARG B 384 " pdb=" N PRO B 385 " pdb=" CA PRO B 385 " ideal model delta harmonic sigma weight residual -180.00 -141.44 -38.56 0 5.00e+00 4.00e-02 5.95e+01 dihedral pdb=" CA ASP A 814 " pdb=" C ASP A 814 " pdb=" N PRO A 815 " pdb=" CA PRO A 815 " ideal model delta harmonic sigma weight residual -180.00 -150.02 -29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASP B 814 " pdb=" C ASP B 814 " pdb=" N PRO B 815 " pdb=" CA PRO B 815 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 16331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2403 0.077 - 0.155: 172 0.155 - 0.232: 0 0.232 - 0.310: 0 0.310 - 0.387: 1 Chirality restraints: 2576 Sorted by residual: chirality pdb=" CA GLU B 42 " pdb=" N GLU B 42 " pdb=" C GLU B 42 " pdb=" CB GLU B 42 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ILE A 683 " pdb=" N ILE A 683 " pdb=" C ILE A 683 " pdb=" CB ILE A 683 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 2573 not shown) Planarity restraints: 5066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 938 " 0.046 2.00e-02 2.50e+03 8.66e-02 7.50e+01 pdb=" C GLU A 938 " -0.150 2.00e-02 2.50e+03 pdb=" O GLU A 938 " 0.054 2.00e-02 2.50e+03 pdb=" N ASP A 939 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 814 " -0.094 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO B 815 " 0.246 5.00e-02 4.00e+02 pdb=" CA PRO B 815 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO B 815 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 814 " 0.094 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO A 815 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO A 815 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 815 " 0.073 5.00e-02 4.00e+02 ... (remaining 5063 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1042 2.16 - 2.77: 68400 2.77 - 3.38: 91843 3.38 - 3.99: 120780 3.99 - 4.60: 194535 Nonbonded interactions: 476600 Sorted by model distance: nonbonded pdb=" OE1 GLU A 51 " pdb=" H GLY A 282 " model vdw 1.556 2.450 nonbonded pdb=" OE1 GLU B 51 " pdb=" H GLY B 282 " model vdw 1.573 2.450 nonbonded pdb=" OE1 GLU A 991 " pdb=" H GLU A 991 " model vdw 1.580 2.450 nonbonded pdb=" OE1 GLU B 199 " pdb=" H GLU B 199 " model vdw 1.591 2.450 nonbonded pdb=" OE1 GLU A 199 " pdb=" H GLU A 199 " model vdw 1.592 2.450 ... (remaining 476595 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.860 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 17678 Z= 0.212 Angle : 0.613 11.570 23784 Z= 0.367 Chirality : 0.041 0.387 2576 Planarity : 0.006 0.142 3050 Dihedral : 10.345 59.181 6840 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.18 % Favored : 94.29 % Rotamer: Outliers : 1.07 % Allowed : 4.08 % Favored : 94.85 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.18), residues: 2066 helix: 0.59 (0.18), residues: 942 sheet: -0.29 (0.31), residues: 268 loop : -1.45 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 389 TYR 0.011 0.002 TYR B 982 PHE 0.014 0.002 PHE A 222 TRP 0.010 0.002 TRP B 131 HIS 0.005 0.002 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00478 (17678) covalent geometry : angle 0.61270 (23784) hydrogen bonds : bond 0.20799 ( 795) hydrogen bonds : angle 6.59246 ( 2271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 347 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8435 (ptpp) cc_final: 0.8210 (ptmm) REVERT: A 348 SER cc_start: 0.8729 (t) cc_final: 0.8391 (m) REVERT: A 444 ASP cc_start: 0.7774 (m-30) cc_final: 0.7525 (m-30) REVERT: A 696 LEU cc_start: 0.7926 (tp) cc_final: 0.7516 (mm) REVERT: A 939 ASP cc_start: 0.6482 (OUTLIER) cc_final: 0.6256 (m-30) REVERT: A 986 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7956 (mmmm) REVERT: B 50 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7897 (mtp85) REVERT: B 224 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7639 (tppt) REVERT: B 348 SER cc_start: 0.8780 (t) cc_final: 0.8402 (m) REVERT: B 696 LEU cc_start: 0.7950 (tp) cc_final: 0.7103 (mm) REVERT: B 762 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 833 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8312 (tp) REVERT: B 930 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6043 (pm20) REVERT: B 986 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7929 (mmmm) outliers start: 21 outliers final: 9 residues processed: 367 average time/residue: 0.3583 time to fit residues: 185.5747 Evaluate side-chains 248 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 930 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 954 ASN B 120 ASN B 740 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.122794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.088770 restraints weight = 57208.167| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.09 r_work: 0.2651 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17678 Z= 0.241 Angle : 0.627 22.356 23784 Z= 0.331 Chirality : 0.044 0.354 2576 Planarity : 0.007 0.183 3050 Dihedral : 5.875 58.004 2317 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.32 % Favored : 94.19 % Rotamer: Outliers : 1.33 % Allowed : 7.81 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.18), residues: 2066 helix: 0.79 (0.18), residues: 954 sheet: -0.29 (0.29), residues: 284 loop : -1.70 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 389 TYR 0.014 0.002 TYR B 675 PHE 0.022 0.002 PHE B 27 TRP 0.009 0.002 TRP A 131 HIS 0.007 0.002 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00597 (17678) covalent geometry : angle 0.62737 (23784) hydrogen bonds : bond 0.06546 ( 795) hydrogen bonds : angle 4.78398 ( 2271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8408 (ptpp) cc_final: 0.7960 (ptmm) REVERT: A 110 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7763 (pm20) REVERT: A 224 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7565 (tppt) REVERT: A 251 ASN cc_start: 0.8195 (m-40) cc_final: 0.7772 (m-40) REVERT: A 386 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7576 (mtt-85) REVERT: A 696 LEU cc_start: 0.7850 (tp) cc_final: 0.7399 (mm) REVERT: A 784 ASP cc_start: 0.8493 (m-30) cc_final: 0.8278 (m-30) REVERT: A 829 LYS cc_start: 0.8607 (mttp) cc_final: 0.8407 (mttt) REVERT: A 869 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8264 (pm20) REVERT: A 978 LYS cc_start: 0.8499 (mttt) cc_final: 0.8207 (mmtm) REVERT: A 986 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7974 (mmmm) REVERT: A 1001 ASP cc_start: 0.8622 (t0) cc_final: 0.8407 (t0) REVERT: B 50 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7826 (mtp85) REVERT: B 110 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7797 (pm20) REVERT: B 224 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7771 (tppt) REVERT: B 251 ASN cc_start: 0.8171 (m-40) cc_final: 0.7722 (m-40) REVERT: B 264 ASP cc_start: 0.7436 (m-30) cc_final: 0.7085 (m-30) REVERT: B 321 LYS cc_start: 0.8763 (tttt) cc_final: 0.8497 (ttpt) REVERT: B 386 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.8086 (mtt-85) REVERT: B 696 LEU cc_start: 0.7685 (tp) cc_final: 0.7131 (mm) REVERT: B 833 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8397 (tp) REVERT: B 954 ASN cc_start: 0.8401 (m-40) cc_final: 0.8186 (m-40) REVERT: B 986 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7957 (mmmm) outliers start: 26 outliers final: 18 residues processed: 256 average time/residue: 0.3655 time to fit residues: 132.6430 Evaluate side-chains 242 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 990 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 80 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.095509 restraints weight = 56392.837| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.97 r_work: 0.2733 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 17678 Z= 0.106 Angle : 0.501 13.700 23784 Z= 0.270 Chirality : 0.041 0.358 2576 Planarity : 0.006 0.155 3050 Dihedral : 5.325 58.927 2310 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.94 % Favored : 94.68 % Rotamer: Outliers : 1.02 % Allowed : 9.03 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.18), residues: 2066 helix: 1.26 (0.18), residues: 942 sheet: -0.40 (0.29), residues: 292 loop : -1.56 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 524 TYR 0.013 0.001 TYR B 675 PHE 0.014 0.001 PHE B 27 TRP 0.010 0.001 TRP A 131 HIS 0.009 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00249 (17678) covalent geometry : angle 0.50083 (23784) hydrogen bonds : bond 0.04458 ( 795) hydrogen bonds : angle 4.37387 ( 2271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8911 (mmt) cc_final: 0.8053 (mmt) REVERT: A 107 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7730 (ptmm) REVERT: A 110 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7700 (pm20) REVERT: A 216 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7023 (mm-30) REVERT: A 224 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7490 (tppt) REVERT: A 251 ASN cc_start: 0.8055 (m-40) cc_final: 0.7577 (m110) REVERT: A 386 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7561 (mtt-85) REVERT: A 647 LYS cc_start: 0.7590 (mttp) cc_final: 0.7360 (mptt) REVERT: A 696 LEU cc_start: 0.7515 (tp) cc_final: 0.7080 (mm) REVERT: A 912 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 978 LYS cc_start: 0.8309 (mttt) cc_final: 0.7988 (mmtm) REVERT: A 986 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7770 (mmmm) REVERT: B 50 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7602 (mtp85) REVERT: B 110 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7704 (pm20) REVERT: B 138 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6964 (mt-10) REVERT: B 224 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7605 (tppt) REVERT: B 251 ASN cc_start: 0.8012 (m-40) cc_final: 0.7524 (m110) REVERT: B 264 ASP cc_start: 0.7222 (m-30) cc_final: 0.6869 (m-30) REVERT: B 321 LYS cc_start: 0.8606 (tttt) cc_final: 0.8312 (ttpt) REVERT: B 696 LEU cc_start: 0.7438 (tp) cc_final: 0.6886 (mm) REVERT: B 954 ASN cc_start: 0.8339 (m-40) cc_final: 0.8047 (m-40) REVERT: B 986 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7711 (mmmm) outliers start: 20 outliers final: 12 residues processed: 238 average time/residue: 0.3575 time to fit residues: 122.4063 Evaluate side-chains 227 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 912 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 141 optimal weight: 0.0020 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.091399 restraints weight = 56309.959| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.10 r_work: 0.2727 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17678 Z= 0.132 Angle : 0.515 19.578 23784 Z= 0.270 Chirality : 0.041 0.367 2576 Planarity : 0.006 0.175 3050 Dihedral : 5.132 58.805 2306 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.13 % Favored : 94.48 % Rotamer: Outliers : 1.02 % Allowed : 9.34 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.18), residues: 2066 helix: 1.36 (0.18), residues: 942 sheet: -0.35 (0.30), residues: 292 loop : -1.60 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 524 TYR 0.015 0.001 TYR B 675 PHE 0.015 0.001 PHE B 27 TRP 0.010 0.001 TRP A 131 HIS 0.011 0.002 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00320 (17678) covalent geometry : angle 0.51531 (23784) hydrogen bonds : bond 0.04438 ( 795) hydrogen bonds : angle 4.23968 ( 2271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8246 (ptpp) cc_final: 0.7843 (ptmm) REVERT: A 110 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7687 (pm20) REVERT: A 224 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7569 (tppt) REVERT: A 251 ASN cc_start: 0.8142 (m-40) cc_final: 0.7651 (m110) REVERT: A 314 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7667 (ttp80) REVERT: A 386 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7614 (mtt-85) REVERT: A 647 LYS cc_start: 0.7620 (mttp) cc_final: 0.7398 (mptt) REVERT: A 696 LEU cc_start: 0.7572 (tp) cc_final: 0.7134 (mm) REVERT: A 912 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 948 MET cc_start: 0.7544 (mtp) cc_final: 0.7310 (mmm) REVERT: A 978 LYS cc_start: 0.8461 (mttt) cc_final: 0.8163 (mmtm) REVERT: A 986 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7875 (mmmm) REVERT: B 110 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7698 (pm20) REVERT: B 224 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7701 (tppt) REVERT: B 251 ASN cc_start: 0.8111 (m-40) cc_final: 0.7598 (m110) REVERT: B 264 ASP cc_start: 0.7344 (m-30) cc_final: 0.6979 (m-30) REVERT: B 321 LYS cc_start: 0.8669 (tttt) cc_final: 0.8380 (ttpt) REVERT: B 696 LEU cc_start: 0.7568 (tp) cc_final: 0.7025 (mm) REVERT: B 954 ASN cc_start: 0.8367 (m-40) cc_final: 0.8065 (m-40) REVERT: B 986 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7845 (mmmm) outliers start: 20 outliers final: 12 residues processed: 232 average time/residue: 0.3428 time to fit residues: 116.7204 Evaluate side-chains 225 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 912 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.092139 restraints weight = 56676.224| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.93 r_work: 0.2759 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17678 Z= 0.159 Angle : 0.517 14.578 23784 Z= 0.277 Chirality : 0.041 0.373 2576 Planarity : 0.006 0.157 3050 Dihedral : 5.182 58.207 2306 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.61 % Favored : 94.00 % Rotamer: Outliers : 1.07 % Allowed : 9.95 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.18), residues: 2066 helix: 1.34 (0.18), residues: 940 sheet: -0.40 (0.29), residues: 292 loop : -1.68 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 524 TYR 0.016 0.001 TYR B 675 PHE 0.016 0.001 PHE A 67 TRP 0.009 0.001 TRP A 131 HIS 0.011 0.002 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00395 (17678) covalent geometry : angle 0.51703 (23784) hydrogen bonds : bond 0.04722 ( 795) hydrogen bonds : angle 4.23771 ( 2271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8356 (ptpp) cc_final: 0.8001 (ptmm) REVERT: A 110 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7732 (pm20) REVERT: A 224 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7703 (tppt) REVERT: A 251 ASN cc_start: 0.8224 (m-40) cc_final: 0.7763 (m110) REVERT: A 314 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7702 (ttp80) REVERT: A 386 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7659 (mtt-85) REVERT: A 696 LEU cc_start: 0.7854 (tp) cc_final: 0.7412 (mm) REVERT: A 978 LYS cc_start: 0.8507 (mttt) cc_final: 0.8256 (mmtm) REVERT: A 986 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7988 (mmmm) REVERT: B 110 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7775 (pm20) REVERT: B 138 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7087 (mt-10) REVERT: B 142 ASN cc_start: 0.7301 (m-40) cc_final: 0.7064 (m-40) REVERT: B 224 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7855 (tppt) REVERT: B 251 ASN cc_start: 0.8181 (m-40) cc_final: 0.7700 (m110) REVERT: B 264 ASP cc_start: 0.7455 (m-30) cc_final: 0.7083 (m-30) REVERT: B 321 LYS cc_start: 0.8738 (tttt) cc_final: 0.8486 (ttpp) REVERT: B 696 LEU cc_start: 0.7734 (tp) cc_final: 0.7174 (mm) REVERT: B 986 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8003 (mmmm) outliers start: 21 outliers final: 15 residues processed: 233 average time/residue: 0.3386 time to fit residues: 114.5226 Evaluate side-chains 226 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 912 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 ASN B 954 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.090770 restraints weight = 56598.059| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.09 r_work: 0.2796 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17678 Z= 0.140 Angle : 0.496 11.880 23784 Z= 0.267 Chirality : 0.041 0.373 2576 Planarity : 0.006 0.147 3050 Dihedral : 5.159 57.987 2306 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.57 % Favored : 94.05 % Rotamer: Outliers : 1.02 % Allowed : 10.15 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.18), residues: 2066 helix: 1.41 (0.18), residues: 940 sheet: -0.33 (0.31), residues: 268 loop : -1.71 (0.18), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 524 TYR 0.015 0.001 TYR B 675 PHE 0.014 0.001 PHE B 27 TRP 0.009 0.001 TRP A 131 HIS 0.010 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00345 (17678) covalent geometry : angle 0.49587 (23784) hydrogen bonds : bond 0.04376 ( 795) hydrogen bonds : angle 4.16431 ( 2271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8365 (ptpp) cc_final: 0.7964 (ptmm) REVERT: A 110 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7709 (pm20) REVERT: A 224 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7603 (tppt) REVERT: A 314 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7716 (ttp80) REVERT: A 386 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7615 (mtt-85) REVERT: A 696 LEU cc_start: 0.7679 (tp) cc_final: 0.7230 (mm) REVERT: A 978 LYS cc_start: 0.8529 (mttt) cc_final: 0.8246 (mmtm) REVERT: A 986 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7880 (mmmm) REVERT: B 138 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7012 (mt-10) REVERT: B 142 ASN cc_start: 0.7221 (m-40) cc_final: 0.6941 (m-40) REVERT: B 224 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7797 (tppt) REVERT: B 251 ASN cc_start: 0.8144 (m-40) cc_final: 0.7658 (m110) REVERT: B 264 ASP cc_start: 0.7452 (m-30) cc_final: 0.7062 (m-30) REVERT: B 321 LYS cc_start: 0.8720 (tttt) cc_final: 0.8437 (ttpp) REVERT: B 696 LEU cc_start: 0.7620 (tp) cc_final: 0.7053 (mm) REVERT: B 986 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7901 (mmmm) outliers start: 20 outliers final: 15 residues processed: 234 average time/residue: 0.3527 time to fit residues: 120.0069 Evaluate side-chains 228 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 912 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 251 ASN A 952 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.089889 restraints weight = 56658.889| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.11 r_work: 0.2701 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17678 Z= 0.160 Angle : 0.527 23.685 23784 Z= 0.277 Chirality : 0.041 0.377 2576 Planarity : 0.006 0.188 3050 Dihedral : 5.147 57.451 2304 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.66 % Favored : 93.95 % Rotamer: Outliers : 0.97 % Allowed : 10.51 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.18), residues: 2066 helix: 1.38 (0.18), residues: 940 sheet: -0.37 (0.30), residues: 292 loop : -1.71 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 389 TYR 0.015 0.001 TYR B 518 PHE 0.014 0.002 PHE B 27 TRP 0.009 0.001 TRP A 131 HIS 0.010 0.002 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00396 (17678) covalent geometry : angle 0.52662 (23784) hydrogen bonds : bond 0.04635 ( 795) hydrogen bonds : angle 4.18013 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8346 (ptpp) cc_final: 0.7915 (ptmm) REVERT: A 110 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7648 (pm20) REVERT: A 185 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7899 (mtpp) REVERT: A 224 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7537 (tppt) REVERT: A 296 GLU cc_start: 0.8281 (tt0) cc_final: 0.7983 (tt0) REVERT: A 314 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7677 (ttp80) REVERT: A 386 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7620 (mtt-85) REVERT: A 694 LYS cc_start: 0.7828 (tptp) cc_final: 0.7517 (ttmm) REVERT: A 696 LEU cc_start: 0.7630 (tp) cc_final: 0.7159 (mm) REVERT: A 869 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8214 (pm20) REVERT: A 978 LYS cc_start: 0.8490 (mttt) cc_final: 0.8181 (mmtm) REVERT: A 986 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7846 (mmmm) REVERT: B 185 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7893 (mtpp) REVERT: B 224 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7733 (tppt) REVERT: B 251 ASN cc_start: 0.8095 (m-40) cc_final: 0.7591 (m110) REVERT: B 264 ASP cc_start: 0.7522 (m-30) cc_final: 0.7136 (m-30) REVERT: B 321 LYS cc_start: 0.8698 (tttt) cc_final: 0.8385 (ttpp) REVERT: B 696 LEU cc_start: 0.7598 (tp) cc_final: 0.7022 (mm) REVERT: B 986 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7868 (mmmm) outliers start: 19 outliers final: 17 residues processed: 227 average time/residue: 0.3786 time to fit residues: 125.1284 Evaluate side-chains 226 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 912 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 89 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 85 optimal weight: 0.0270 chunk 146 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.091205 restraints weight = 56336.084| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.10 r_work: 0.2719 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17678 Z= 0.126 Angle : 0.504 25.549 23784 Z= 0.265 Chirality : 0.041 0.375 2576 Planarity : 0.005 0.193 3050 Dihedral : 5.140 57.495 2304 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.05 % Rotamer: Outliers : 0.92 % Allowed : 10.71 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.18), residues: 2066 helix: 1.47 (0.18), residues: 940 sheet: -0.29 (0.31), residues: 268 loop : -1.71 (0.18), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 524 TYR 0.014 0.001 TYR B 675 PHE 0.013 0.001 PHE B 27 TRP 0.009 0.001 TRP A 131 HIS 0.010 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00304 (17678) covalent geometry : angle 0.50388 (23784) hydrogen bonds : bond 0.04166 ( 795) hydrogen bonds : angle 4.10255 ( 2271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8329 (ptpp) cc_final: 0.7904 (ptmm) REVERT: A 110 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7662 (pm20) REVERT: A 224 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7543 (tppt) REVERT: A 296 GLU cc_start: 0.8276 (tt0) cc_final: 0.7971 (tt0) REVERT: A 314 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7705 (ttp80) REVERT: A 386 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7592 (mtt-85) REVERT: A 696 LEU cc_start: 0.7574 (tp) cc_final: 0.7155 (mm) REVERT: A 869 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8180 (pm20) REVERT: A 978 LYS cc_start: 0.8475 (mttt) cc_final: 0.8189 (mmtm) REVERT: A 986 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7821 (mmmm) REVERT: B 110 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7689 (pm20) REVERT: B 138 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6907 (mt-10) REVERT: B 142 ASN cc_start: 0.7152 (m-40) cc_final: 0.6853 (m-40) REVERT: B 224 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7738 (tppt) REVERT: B 251 ASN cc_start: 0.8098 (m-40) cc_final: 0.7582 (m110) REVERT: B 264 ASP cc_start: 0.7516 (m-30) cc_final: 0.7123 (m-30) REVERT: B 321 LYS cc_start: 0.8704 (tttt) cc_final: 0.8395 (ttpp) REVERT: B 696 LEU cc_start: 0.7584 (tp) cc_final: 0.7001 (mm) REVERT: B 986 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7772 (mmmm) outliers start: 18 outliers final: 15 residues processed: 224 average time/residue: 0.3291 time to fit residues: 107.4394 Evaluate side-chains 222 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 912 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 148 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.093099 restraints weight = 56174.288| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.99 r_work: 0.2707 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17678 Z= 0.134 Angle : 0.481 7.521 23784 Z= 0.265 Chirality : 0.041 0.377 2576 Planarity : 0.004 0.109 3050 Dihedral : 5.157 57.183 2304 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.71 % Favored : 94.00 % Rotamer: Outliers : 1.02 % Allowed : 10.71 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.36 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.18), residues: 2066 helix: 1.47 (0.18), residues: 940 sheet: -0.28 (0.31), residues: 270 loop : -1.73 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 524 TYR 0.016 0.001 TYR A 518 PHE 0.013 0.001 PHE B 27 TRP 0.009 0.001 TRP A 131 HIS 0.010 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00326 (17678) covalent geometry : angle 0.48136 (23784) hydrogen bonds : bond 0.04244 ( 795) hydrogen bonds : angle 4.09456 ( 2271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8335 (ptpp) cc_final: 0.7925 (ptmm) REVERT: A 110 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7664 (pm20) REVERT: A 224 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7575 (tppt) REVERT: A 296 GLU cc_start: 0.8261 (tt0) cc_final: 0.7967 (tt0) REVERT: A 314 ARG cc_start: 0.8013 (ttp-170) cc_final: 0.7727 (ttp80) REVERT: A 386 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7629 (mtt-85) REVERT: A 696 LEU cc_start: 0.7601 (tp) cc_final: 0.7180 (mm) REVERT: A 869 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8185 (pm20) REVERT: A 978 LYS cc_start: 0.8450 (mttt) cc_final: 0.8193 (mmtm) REVERT: A 986 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7854 (mmmm) REVERT: B 110 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7725 (pm20) REVERT: B 138 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7015 (mt-10) REVERT: B 224 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7781 (tppt) REVERT: B 251 ASN cc_start: 0.8115 (m-40) cc_final: 0.7603 (m110) REVERT: B 264 ASP cc_start: 0.7526 (m-30) cc_final: 0.7136 (m-30) REVERT: B 321 LYS cc_start: 0.8717 (tttt) cc_final: 0.8417 (ttpp) REVERT: B 696 LEU cc_start: 0.7649 (tp) cc_final: 0.7068 (mm) REVERT: B 986 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7816 (mmmm) outliers start: 20 outliers final: 17 residues processed: 222 average time/residue: 0.3576 time to fit residues: 117.0313 Evaluate side-chains 219 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 912 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 158 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 156 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.094470 restraints weight = 56200.961| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.97 r_work: 0.2783 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 17678 Z= 0.095 Angle : 0.452 7.597 23784 Z= 0.249 Chirality : 0.040 0.373 2576 Planarity : 0.004 0.107 3050 Dihedral : 4.945 57.516 2304 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.94 % Favored : 94.77 % Rotamer: Outliers : 0.92 % Allowed : 10.92 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.18), residues: 2066 helix: 1.58 (0.18), residues: 944 sheet: -0.27 (0.31), residues: 278 loop : -1.63 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 524 TYR 0.012 0.001 TYR A 518 PHE 0.011 0.001 PHE A 79 TRP 0.010 0.001 TRP A 131 HIS 0.009 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00221 (17678) covalent geometry : angle 0.45249 (23784) hydrogen bonds : bond 0.03595 ( 795) hydrogen bonds : angle 3.97869 ( 2271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8362 (ptpp) cc_final: 0.8009 (ptmm) REVERT: A 224 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7676 (tppt) REVERT: A 296 GLU cc_start: 0.8291 (tt0) cc_final: 0.8024 (tt0) REVERT: A 314 ARG cc_start: 0.8038 (ttp-170) cc_final: 0.7764 (ttp80) REVERT: A 696 LEU cc_start: 0.7678 (tp) cc_final: 0.7257 (mm) REVERT: A 869 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8224 (pm20) REVERT: A 912 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.7237 (t80) REVERT: A 986 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7935 (mmmm) REVERT: B 138 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7114 (mt-10) REVERT: B 224 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7865 (tppt) REVERT: B 251 ASN cc_start: 0.8194 (m-40) cc_final: 0.7984 (m110) REVERT: B 264 ASP cc_start: 0.7614 (m-30) cc_final: 0.7222 (m-30) REVERT: B 321 LYS cc_start: 0.8731 (tttt) cc_final: 0.8488 (ttpp) REVERT: B 696 LEU cc_start: 0.7773 (tp) cc_final: 0.7210 (mm) REVERT: B 986 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7889 (mmmm) outliers start: 18 outliers final: 14 residues processed: 220 average time/residue: 0.3546 time to fit residues: 115.6228 Evaluate side-chains 212 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 912 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 205 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.093442 restraints weight = 56267.512| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.98 r_work: 0.2755 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17678 Z= 0.128 Angle : 0.471 7.645 23784 Z= 0.259 Chirality : 0.040 0.377 2576 Planarity : 0.004 0.107 3050 Dihedral : 4.958 57.058 2304 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.61 % Favored : 94.09 % Rotamer: Outliers : 0.97 % Allowed : 11.17 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.18), residues: 2066 helix: 1.56 (0.18), residues: 942 sheet: -0.23 (0.30), residues: 278 loop : -1.66 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 524 TYR 0.016 0.001 TYR A 518 PHE 0.013 0.001 PHE B 27 TRP 0.009 0.001 TRP A 131 HIS 0.009 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00311 (17678) covalent geometry : angle 0.47133 (23784) hydrogen bonds : bond 0.04055 ( 795) hydrogen bonds : angle 4.01771 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8186.47 seconds wall clock time: 139 minutes 22.04 seconds (8362.04 seconds total)