Starting phenix.real_space_refine on Wed Mar 4 18:20:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzg_24759/03_2026/7rzg_24759.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzg_24759/03_2026/7rzg_24759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzg_24759/03_2026/7rzg_24759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzg_24759/03_2026/7rzg_24759.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzg_24759/03_2026/7rzg_24759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzg_24759/03_2026/7rzg_24759.cif" } resolution = 4.1 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 9912 2.51 5 N 2588 2.21 5 O 2842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15385 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7718 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 50, 'TRANS': 897} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 7667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7667 Classifications: {'peptide': 940} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 49, 'TRANS': 890} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 3.28, per 1000 atoms: 0.21 Number of scatterers: 15385 At special positions: 0 Unit cell: (109.504, 130.104, 159.377, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 2842 8.00 N 2588 7.00 C 9912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 689.9 milliseconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 14 sheets defined 48.1% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.599A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.585A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.429A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.651A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.998A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.514A pdb=" N TYR A 326 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.794A pdb=" N TYR A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.818A pdb=" N ILE A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.777A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 516 Processing helix chain 'A' and resid 581 through 584 removed outlier: 4.006A pdb=" N TYR A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 604 through 615 removed outlier: 5.029A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.764A pdb=" N THR A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 4.156A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 708 through 722 Proline residue: A 717 - end of helix removed outlier: 4.549A pdb=" N ARG A 722 " --> pdb=" O GLN A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 801 through 815 removed outlier: 3.902A pdb=" N MET A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 855 through 877 removed outlier: 4.042A pdb=" N GLU A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.794A pdb=" N ALA A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.701A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.624A pdb=" N LYS A 929 " --> pdb=" O VAL A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 944 removed outlier: 4.117A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 removed outlier: 4.472A pdb=" N GLY A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.793A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 4.073A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.818A pdb=" N THR B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.668A pdb=" N LEU B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.672A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.862A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.590A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.921A pdb=" N TYR B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER B 435 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.747A pdb=" N TRP B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 4.190A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 586 through 613 removed outlier: 4.872A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 651 removed outlier: 3.627A pdb=" N THR B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 673 through 676 removed outlier: 4.230A pdb=" N GLU B 676 " --> pdb=" O PHE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 677 through 690 Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 704 through 707 removed outlier: 3.822A pdb=" N VAL B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 708 through 722 Proline residue: B 717 - end of helix removed outlier: 4.438A pdb=" N ARG B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 Processing helix chain 'B' and resid 801 through 815 removed outlier: 4.155A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 855 through 876 removed outlier: 3.682A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.622A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.888A pdb=" N LYS B 929 " --> pdb=" O VAL B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 945 removed outlier: 3.811A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET B 943 " --> pdb=" O PHE B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 4.503A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 69 removed outlier: 6.038A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 88 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 141 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 69 removed outlier: 6.038A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 91 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 141 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.561A pdb=" N MET A 371 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.523A pdb=" N ARG A 491 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.680A pdb=" N LEU A 559 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 633 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.680A pdb=" N LEU A 559 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 776 through 777 removed outlier: 5.936A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 781 " --> pdb=" O LEU A 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 777 removed outlier: 5.936A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLY A 790 " --> pdb=" O SER A 852 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER A 852 " --> pdb=" O GLY A 790 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU A 792 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 850 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR A 794 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N PHE A 848 " --> pdb=" O TYR A 794 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLN A 796 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 846 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP A 798 " --> pdb=" O GLN A 844 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 836 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 69 removed outlier: 3.653A pdb=" N GLU B 63 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 258 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 78 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 260 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 87 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB3, first strand: chain 'B' and resid 549 through 553 removed outlier: 5.878A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 552 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY B 731 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS B 562 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.054A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.054A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 792 " --> pdb=" O VAL B 956 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 836 " --> pdb=" O ARG B 847 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2031 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: 3.11 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4460 1.33 - 1.46: 3022 1.46 - 1.58: 8201 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 15769 Sorted by residual: bond pdb=" N ILE B 94 " pdb=" CA ILE B 94 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.11e-02 8.12e+03 1.41e+01 bond pdb=" N ILE A 843 " pdb=" CA ILE A 843 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N GLY B 95 " pdb=" CA GLY B 95 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.02e-02 9.61e+03 1.00e+01 bond pdb=" CA PRO B 100 " pdb=" C PRO B 100 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.94e+00 bond pdb=" N ILE A 874 " pdb=" CA ILE A 874 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.14e+00 ... (remaining 15764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 19931 2.21 - 4.43: 1195 4.43 - 6.64: 156 6.64 - 8.86: 37 8.86 - 11.07: 9 Bond angle restraints: 21328 Sorted by residual: angle pdb=" N PRO B 100 " pdb=" CA PRO B 100 " pdb=" C PRO B 100 " ideal model delta sigma weight residual 110.70 118.98 -8.28 1.22e+00 6.72e-01 4.60e+01 angle pdb=" CB ARG A 658 " pdb=" CG ARG A 658 " pdb=" CD ARG A 658 " ideal model delta sigma weight residual 111.30 100.23 11.07 2.30e+00 1.89e-01 2.32e+01 angle pdb=" N GLY B1001 " pdb=" CA GLY B1001 " pdb=" C GLY B1001 " ideal model delta sigma weight residual 113.18 123.56 -10.38 2.37e+00 1.78e-01 1.92e+01 angle pdb=" CA GLY A 830 " pdb=" C GLY A 830 " pdb=" N TYR A 831 " ideal model delta sigma weight residual 114.58 118.19 -3.61 8.60e-01 1.35e+00 1.76e+01 angle pdb=" CA GLY A 830 " pdb=" C GLY A 830 " pdb=" O GLY A 830 " ideal model delta sigma weight residual 121.49 117.55 3.94 9.60e-01 1.09e+00 1.68e+01 ... (remaining 21323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8734 17.07 - 34.14: 644 34.14 - 51.21: 129 51.21 - 68.28: 13 68.28 - 85.35: 17 Dihedral angle restraints: 9537 sinusoidal: 3968 harmonic: 5569 Sorted by residual: dihedral pdb=" CA SER B 57 " pdb=" C SER B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual -180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA TYR B 940 " pdb=" C TYR B 940 " pdb=" N LYS B 941 " pdb=" CA LYS B 941 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN B 800 " pdb=" C GLN B 800 " pdb=" N SER B 801 " pdb=" CA SER B 801 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 9534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1541 0.057 - 0.114: 562 0.114 - 0.172: 159 0.172 - 0.229: 24 0.229 - 0.286: 7 Chirality restraints: 2293 Sorted by residual: chirality pdb=" CB ILE B 505 " pdb=" CA ILE B 505 " pdb=" CG1 ILE B 505 " pdb=" CG2 ILE B 505 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA LYS B 884 " pdb=" N LYS B 884 " pdb=" C LYS B 884 " pdb=" CB LYS B 884 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB THR B 380 " pdb=" CA THR B 380 " pdb=" OG1 THR B 380 " pdb=" CG2 THR B 380 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2290 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 224 " 0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C TYR B 224 " -0.084 2.00e-02 2.50e+03 pdb=" O TYR B 224 " 0.031 2.00e-02 2.50e+03 pdb=" N THR B 225 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 472 " 0.078 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO A 473 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 245 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C HIS B 245 " 0.077 2.00e-02 2.50e+03 pdb=" O HIS B 245 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B 246 " -0.026 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 248 2.64 - 3.21: 14576 3.21 - 3.77: 23347 3.77 - 4.34: 31984 4.34 - 4.90: 51089 Nonbonded interactions: 121244 Sorted by model distance: nonbonded pdb=" O HIS A 297 " pdb=" NH1 ARG A 477 " model vdw 2.077 3.120 nonbonded pdb=" OG SER B 348 " pdb=" OE2 GLU B 606 " model vdw 2.156 3.040 nonbonded pdb=" OE1 GLN A 887 " pdb=" NZ LYS A 929 " model vdw 2.168 3.120 nonbonded pdb=" O ARG A 668 " pdb=" ND2 ASN A 672 " model vdw 2.184 3.120 nonbonded pdb=" O VAL B 785 " pdb=" NH1 ARG B 961 " model vdw 2.187 3.120 ... (remaining 121239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 585 or (resid 586 and (name N or name CA or nam \ e C or name O or name CB )) or resid 587 through 656 or (resid 657 and (name N o \ r name CA or name C or name O or name CB )) or resid 658 through 704 or (resid 7 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 706 through \ 763 or (resid 764 through 765 and (name N or name CA or name C or name O or nam \ e CB )) or resid 766 through 769 or (resid 770 and (name N or name CA or name C \ or name O or name CB )) or resid 771 through 962 or resid 989 through 1011)) selection = (chain 'B' and (resid 46 through 57 or resid 59 through 257 or (resid 258 and (n \ ame N or name CA or name C or name O or name CB )) or resid 259 through 349 or ( \ resid 350 and (name N or name CA or name C or name O or name CB )) or resid 351 \ through 439 or (resid 440 and (name N or name CA or name C or name O or name CB \ )) or resid 441 through 541 or (resid 542 through 544 and (name N or name CA or \ name C or name O or name CB )) or resid 545 through 573 or (resid 574 and (name \ N or name CA or name C or name O or name CB )) or resid 575 through 587 or (resi \ d 588 and (name N or name CA or name C or name O or name CB )) or resid 589 thro \ ugh 603 or (resid 604 and (name N or name CA or name C or name O or name CB )) o \ r resid 605 through 757 or (resid 758 and (name N or name CA or name C or name O \ or name CB )) or resid 759 through 1011)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.020 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 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 : 0.007 0.069 15769 Z= 0.352 Angle : 1.165 11.074 21328 Z= 0.670 Chirality : 0.064 0.286 2293 Planarity : 0.009 0.120 2760 Dihedral : 12.777 85.351 5937 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.18 % Allowed : 2.11 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.16), residues: 1878 helix: -2.57 (0.14), residues: 785 sheet: -1.76 (0.26), residues: 344 loop : -2.62 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 951 TYR 0.047 0.003 TYR A 584 PHE 0.056 0.003 PHE A 168 TRP 0.039 0.004 TRP B 695 HIS 0.014 0.003 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00683 (15769) covalent geometry : angle 1.16504 (21328) hydrogen bonds : bond 0.20004 ( 700) hydrogen bonds : angle 8.57625 ( 2031) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7248 (t) REVERT: A 158 LEU cc_start: 0.8012 (tp) cc_final: 0.7774 (tp) REVERT: A 470 LYS cc_start: 0.7850 (mppt) cc_final: 0.7557 (mptt) REVERT: B 97 LEU cc_start: 0.1718 (OUTLIER) cc_final: 0.1354 (pt) REVERT: B 248 TYR cc_start: 0.5690 (m-80) cc_final: 0.5421 (m-80) REVERT: B 338 ILE cc_start: 0.8239 (mm) cc_final: 0.7890 (mm) REVERT: B 391 ILE cc_start: 0.7995 (mt) cc_final: 0.7774 (mt) REVERT: B 466 MET cc_start: 0.6473 (mtp) cc_final: 0.6011 (ttm) REVERT: B 799 MET cc_start: 0.4955 (ttt) cc_final: 0.4734 (ttt) REVERT: B 806 MET cc_start: 0.7108 (mmm) cc_final: 0.6713 (mmm) outliers start: 3 outliers final: 0 residues processed: 259 average time/residue: 0.1125 time to fit residues: 44.7487 Evaluate side-chains 173 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 329 ASN A 357 ASN A 736 GLN A 786 HIS A 828 GLN A 851 GLN B 146 HIS B 332 HIS B 528 ASN B 762 GLN B 796 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.147335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.123903 restraints weight = 43354.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.125765 restraints weight = 27355.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126473 restraints weight = 19197.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.127810 restraints weight = 14439.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127858 restraints weight = 12095.650| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15769 Z= 0.238 Angle : 0.800 8.855 21328 Z= 0.420 Chirality : 0.048 0.174 2293 Planarity : 0.006 0.089 2760 Dihedral : 5.956 30.816 2050 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.18 % Allowed : 4.22 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.18), residues: 1878 helix: -0.65 (0.17), residues: 822 sheet: -1.42 (0.25), residues: 364 loop : -2.10 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 472 TYR 0.022 0.002 TYR A 314 PHE 0.023 0.002 PHE A 659 TRP 0.019 0.002 TRP A 776 HIS 0.009 0.002 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00540 (15769) covalent geometry : angle 0.79993 (21328) hydrogen bonds : bond 0.05941 ( 700) hydrogen bonds : angle 6.28670 ( 2031) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ASN cc_start: 0.7904 (m110) cc_final: 0.7668 (m110) REVERT: A 505 ILE cc_start: 0.8269 (mm) cc_final: 0.7850 (mt) REVERT: A 592 MET cc_start: 0.6507 (mmp) cc_final: 0.6292 (mmt) REVERT: A 848 PHE cc_start: 0.7574 (m-80) cc_final: 0.7302 (m-80) REVERT: B 338 ILE cc_start: 0.7977 (mm) cc_final: 0.7753 (mm) REVERT: B 466 MET cc_start: 0.6132 (mtp) cc_final: 0.5809 (ttm) REVERT: B 688 LEU cc_start: 0.7315 (tt) cc_final: 0.6653 (tp) REVERT: B 806 MET cc_start: 0.7458 (mmm) cc_final: 0.7069 (mmm) REVERT: B 891 ILE cc_start: 0.7270 (mm) cc_final: 0.6983 (tp) outliers start: 3 outliers final: 0 residues processed: 238 average time/residue: 0.1138 time to fit residues: 41.8569 Evaluate side-chains 163 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 186 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 329 ASN ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS B 332 HIS B 442 HIS B 762 GLN B 786 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.145386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.121899 restraints weight = 43964.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.123413 restraints weight = 28346.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.123830 restraints weight = 20603.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.124768 restraints weight = 17196.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.125095 restraints weight = 13467.248| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15769 Z= 0.222 Angle : 0.754 8.696 21328 Z= 0.395 Chirality : 0.047 0.163 2293 Planarity : 0.006 0.072 2760 Dihedral : 5.823 28.862 2050 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.18 % Allowed : 6.21 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.18), residues: 1878 helix: -0.20 (0.17), residues: 823 sheet: -1.17 (0.26), residues: 360 loop : -1.88 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 839 TYR 0.020 0.002 TYR A 149 PHE 0.023 0.002 PHE A 169 TRP 0.026 0.002 TRP A 776 HIS 0.015 0.002 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00504 (15769) covalent geometry : angle 0.75412 (21328) hydrogen bonds : bond 0.05319 ( 700) hydrogen bonds : angle 5.86790 ( 2031) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8274 (tp) cc_final: 0.7954 (tt) REVERT: A 217 LYS cc_start: 0.7121 (mmtm) cc_final: 0.6380 (ptpp) REVERT: A 470 LYS cc_start: 0.7950 (mppt) cc_final: 0.7251 (mptt) REVERT: A 505 ILE cc_start: 0.8543 (mm) cc_final: 0.8308 (mm) REVERT: A 592 MET cc_start: 0.6884 (mmp) cc_final: 0.6617 (mmp) REVERT: A 742 MET cc_start: 0.6666 (tpt) cc_final: 0.6371 (mmm) REVERT: A 823 LEU cc_start: 0.8454 (mp) cc_final: 0.8131 (mt) REVERT: A 846 LEU cc_start: 0.7599 (tt) cc_final: 0.7360 (tt) REVERT: B 466 MET cc_start: 0.6224 (mtp) cc_final: 0.5862 (ttm) REVERT: B 584 TYR cc_start: 0.7652 (t80) cc_final: 0.7263 (t80) REVERT: B 606 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6703 (tp30) REVERT: B 792 GLU cc_start: 0.7320 (tt0) cc_final: 0.6750 (tt0) REVERT: B 806 MET cc_start: 0.7584 (mmm) cc_final: 0.7062 (mmm) outliers start: 3 outliers final: 1 residues processed: 213 average time/residue: 0.1176 time to fit residues: 38.0949 Evaluate side-chains 163 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 chunk 167 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 329 ASN ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN B 146 HIS B 442 HIS B 762 GLN B 796 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.145349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.122380 restraints weight = 43902.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.123403 restraints weight = 29293.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.124103 restraints weight = 21839.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.125132 restraints weight = 16916.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.125148 restraints weight = 13414.427| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15769 Z= 0.189 Angle : 0.702 8.885 21328 Z= 0.364 Chirality : 0.046 0.222 2293 Planarity : 0.005 0.061 2760 Dihedral : 5.596 26.920 2050 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.19), residues: 1878 helix: 0.09 (0.17), residues: 811 sheet: -1.05 (0.26), residues: 355 loop : -1.76 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 767 TYR 0.017 0.002 TYR A 149 PHE 0.020 0.002 PHE B 174 TRP 0.014 0.001 TRP A 776 HIS 0.008 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00434 (15769) covalent geometry : angle 0.70217 (21328) hydrogen bonds : bond 0.04778 ( 700) hydrogen bonds : angle 5.64551 ( 2031) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8260 (tp) cc_final: 0.8035 (tt) REVERT: A 217 LYS cc_start: 0.7116 (mmtm) cc_final: 0.6429 (pttm) REVERT: A 505 ILE cc_start: 0.8583 (mm) cc_final: 0.8373 (mm) REVERT: A 592 MET cc_start: 0.6765 (mmp) cc_final: 0.6370 (mmt) REVERT: A 742 MET cc_start: 0.6723 (tpt) cc_final: 0.6482 (mmm) REVERT: A 823 LEU cc_start: 0.8496 (mp) cc_final: 0.8234 (mt) REVERT: A 860 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 963 MET cc_start: 0.6354 (ptm) cc_final: 0.5799 (ptm) REVERT: B 113 MET cc_start: -0.1558 (ttt) cc_final: -0.2037 (tmm) REVERT: B 466 MET cc_start: 0.6435 (mtp) cc_final: 0.6107 (ttm) REVERT: B 584 TYR cc_start: 0.7638 (t80) cc_final: 0.7242 (t80) REVERT: B 592 MET cc_start: 0.7694 (mtm) cc_final: 0.7336 (ttm) REVERT: B 799 MET cc_start: 0.5606 (ttt) cc_final: 0.5332 (ttt) REVERT: B 806 MET cc_start: 0.7440 (mmm) cc_final: 0.7001 (mmm) REVERT: B 998 PHE cc_start: 0.8469 (t80) cc_final: 0.8224 (t80) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.1235 time to fit residues: 41.1525 Evaluate side-chains 169 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN ** A 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN B 93 HIS B 730 HIS B 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.145375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121489 restraints weight = 43628.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.123414 restraints weight = 26949.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.124619 restraints weight = 18327.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.125411 restraints weight = 13927.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.126009 restraints weight = 11459.135| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15769 Z= 0.181 Angle : 0.688 7.965 21328 Z= 0.356 Chirality : 0.045 0.180 2293 Planarity : 0.005 0.057 2760 Dihedral : 5.509 26.253 2050 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 1878 helix: 0.16 (0.17), residues: 815 sheet: -1.00 (0.27), residues: 352 loop : -1.74 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 668 TYR 0.021 0.002 TYR B 609 PHE 0.015 0.002 PHE B 174 TRP 0.011 0.001 TRP A 776 HIS 0.008 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00415 (15769) covalent geometry : angle 0.68844 (21328) hydrogen bonds : bond 0.04631 ( 700) hydrogen bonds : angle 5.54813 ( 2031) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8073 (tp) cc_final: 0.7807 (tt) REVERT: A 217 LYS cc_start: 0.7049 (mmtm) cc_final: 0.6489 (pttm) REVERT: A 592 MET cc_start: 0.6803 (mmp) cc_final: 0.6451 (mmt) REVERT: A 823 LEU cc_start: 0.8620 (mp) cc_final: 0.8242 (mt) REVERT: A 963 MET cc_start: 0.5932 (ptm) cc_final: 0.5534 (ptm) REVERT: B 466 MET cc_start: 0.6475 (mtp) cc_final: 0.6138 (ttm) REVERT: B 584 TYR cc_start: 0.7708 (t80) cc_final: 0.7132 (t80) REVERT: B 691 THR cc_start: 0.5907 (t) cc_final: 0.5695 (t) REVERT: B 806 MET cc_start: 0.7560 (mmm) cc_final: 0.7060 (mmm) REVERT: B 860 GLU cc_start: 0.6674 (pp20) cc_final: 0.6280 (pp20) REVERT: B 998 PHE cc_start: 0.8449 (t80) cc_final: 0.8154 (t80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1246 time to fit residues: 43.3613 Evaluate side-chains 170 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 22 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN B 93 HIS ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN B 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.146373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123486 restraints weight = 43201.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.125247 restraints weight = 27703.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.125853 restraints weight = 17881.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.126461 restraints weight = 15803.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.126752 restraints weight = 12587.449| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15769 Z= 0.143 Angle : 0.647 8.332 21328 Z= 0.333 Chirality : 0.045 0.303 2293 Planarity : 0.005 0.053 2760 Dihedral : 5.276 25.081 2050 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1878 helix: 0.35 (0.18), residues: 817 sheet: -0.83 (0.28), residues: 343 loop : -1.66 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 668 TYR 0.018 0.001 TYR A 831 PHE 0.019 0.002 PHE B 866 TRP 0.008 0.001 TRP A 776 HIS 0.012 0.001 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00327 (15769) covalent geometry : angle 0.64699 (21328) hydrogen bonds : bond 0.04225 ( 700) hydrogen bonds : angle 5.33929 ( 2031) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8123 (tp) cc_final: 0.7835 (tt) REVERT: A 217 LYS cc_start: 0.7323 (mmtm) cc_final: 0.6566 (ptpp) REVERT: A 226 LEU cc_start: 0.7308 (mm) cc_final: 0.6860 (mm) REVERT: A 823 LEU cc_start: 0.8593 (mp) cc_final: 0.8302 (mt) REVERT: A 963 MET cc_start: 0.5585 (ptm) cc_final: 0.5213 (ptm) REVERT: B 113 MET cc_start: -0.1708 (ttt) cc_final: -0.2168 (tmm) REVERT: B 466 MET cc_start: 0.6513 (mtp) cc_final: 0.6252 (ttm) REVERT: B 584 TYR cc_start: 0.7669 (t80) cc_final: 0.7137 (t80) REVERT: B 806 MET cc_start: 0.7493 (mmm) cc_final: 0.7063 (mmm) REVERT: B 860 GLU cc_start: 0.6671 (pp20) cc_final: 0.6299 (pp20) REVERT: B 998 PHE cc_start: 0.8427 (t80) cc_final: 0.8187 (t80) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1207 time to fit residues: 43.6260 Evaluate side-chains 175 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 123 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 chunk 140 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.145061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.121385 restraints weight = 43051.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123255 restraints weight = 26514.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124529 restraints weight = 18280.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.125416 restraints weight = 13822.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.125891 restraints weight = 11291.121| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15769 Z= 0.168 Angle : 0.676 8.190 21328 Z= 0.349 Chirality : 0.045 0.166 2293 Planarity : 0.005 0.053 2760 Dihedral : 5.336 25.285 2050 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.19), residues: 1878 helix: 0.38 (0.18), residues: 818 sheet: -0.78 (0.28), residues: 338 loop : -1.65 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 668 TYR 0.018 0.002 TYR A 584 PHE 0.022 0.002 PHE A 168 TRP 0.010 0.001 TRP B 776 HIS 0.012 0.001 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00389 (15769) covalent geometry : angle 0.67647 (21328) hydrogen bonds : bond 0.04402 ( 700) hydrogen bonds : angle 5.36477 ( 2031) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8069 (tp) cc_final: 0.7810 (tt) REVERT: A 217 LYS cc_start: 0.7281 (mmtm) cc_final: 0.6566 (pttm) REVERT: A 470 LYS cc_start: 0.7959 (mppt) cc_final: 0.7349 (mptt) REVERT: B 113 MET cc_start: -0.1588 (ttt) cc_final: -0.2251 (tmm) REVERT: B 466 MET cc_start: 0.6595 (mtp) cc_final: 0.6350 (ttm) REVERT: B 584 TYR cc_start: 0.7609 (t80) cc_final: 0.7058 (t80) REVERT: B 806 MET cc_start: 0.7449 (mmm) cc_final: 0.7041 (mmm) REVERT: B 870 MET cc_start: 0.7436 (mmt) cc_final: 0.7081 (mmt) REVERT: B 998 PHE cc_start: 0.8485 (t80) cc_final: 0.8243 (t80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1162 time to fit residues: 39.2063 Evaluate side-chains 165 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 143 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 111 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 917 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 HIS B 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.146285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.122771 restraints weight = 43353.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.124671 restraints weight = 26235.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.125905 restraints weight = 18018.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.126791 restraints weight = 13586.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127279 restraints weight = 11066.634| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15769 Z= 0.136 Angle : 0.649 7.930 21328 Z= 0.333 Chirality : 0.044 0.185 2293 Planarity : 0.005 0.053 2760 Dihedral : 5.200 24.484 2050 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1878 helix: 0.50 (0.18), residues: 819 sheet: -0.59 (0.28), residues: 340 loop : -1.63 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 668 TYR 0.020 0.001 TYR B 666 PHE 0.020 0.001 PHE B 866 TRP 0.022 0.001 TRP B 513 HIS 0.012 0.001 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00310 (15769) covalent geometry : angle 0.64865 (21328) hydrogen bonds : bond 0.04091 ( 700) hydrogen bonds : angle 5.23479 ( 2031) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7902 (tp) cc_final: 0.7616 (tt) REVERT: A 168 PHE cc_start: 0.5226 (m-80) cc_final: 0.4717 (m-80) REVERT: A 217 LYS cc_start: 0.7266 (mmtm) cc_final: 0.6597 (pttm) REVERT: A 226 LEU cc_start: 0.7262 (mm) cc_final: 0.6882 (mm) REVERT: A 592 MET cc_start: 0.7183 (mmp) cc_final: 0.6613 (mmt) REVERT: A 963 MET cc_start: 0.5865 (ptm) cc_final: 0.5596 (ptm) REVERT: B 113 MET cc_start: -0.1415 (ttt) cc_final: -0.2033 (tmm) REVERT: B 584 TYR cc_start: 0.7529 (t80) cc_final: 0.6964 (t80) REVERT: B 592 MET cc_start: 0.7586 (mtm) cc_final: 0.7303 (ttm) REVERT: B 683 MET cc_start: 0.5835 (mmm) cc_final: 0.5501 (mmm) REVERT: B 806 MET cc_start: 0.7411 (mmm) cc_final: 0.7106 (mmm) REVERT: B 872 LYS cc_start: 0.8222 (tttp) cc_final: 0.7974 (tttm) REVERT: B 998 PHE cc_start: 0.8518 (t80) cc_final: 0.8221 (t80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1283 time to fit residues: 43.5604 Evaluate side-chains 164 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 117 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 185 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 ASN A 851 GLN B 112 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 752 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.148380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124702 restraints weight = 42779.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.126616 restraints weight = 26158.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.127974 restraints weight = 18008.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.128906 restraints weight = 13499.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129479 restraints weight = 10915.893| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15769 Z= 0.119 Angle : 0.626 8.337 21328 Z= 0.322 Chirality : 0.044 0.216 2293 Planarity : 0.005 0.052 2760 Dihedral : 4.958 23.010 2050 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.06 % Allowed : 0.48 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1878 helix: 0.71 (0.18), residues: 821 sheet: -0.47 (0.28), residues: 345 loop : -1.55 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 668 TYR 0.019 0.001 TYR B 666 PHE 0.019 0.001 PHE A 715 TRP 0.023 0.001 TRP B 513 HIS 0.012 0.001 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00264 (15769) covalent geometry : angle 0.62595 (21328) hydrogen bonds : bond 0.03826 ( 700) hydrogen bonds : angle 5.04294 ( 2031) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7882 (tp) cc_final: 0.7576 (tt) REVERT: A 168 PHE cc_start: 0.4879 (m-80) cc_final: 0.4441 (m-80) REVERT: A 217 LYS cc_start: 0.7345 (mmtm) cc_final: 0.6663 (pttm) REVERT: A 226 LEU cc_start: 0.7247 (mm) cc_final: 0.6838 (mm) REVERT: A 592 MET cc_start: 0.7176 (mmp) cc_final: 0.6568 (mmt) REVERT: A 963 MET cc_start: 0.5583 (ptm) cc_final: 0.5101 (ptm) REVERT: B 113 MET cc_start: -0.1573 (ttt) cc_final: -0.2116 (tmm) REVERT: B 584 TYR cc_start: 0.7671 (t80) cc_final: 0.7084 (t80) REVERT: B 806 MET cc_start: 0.7459 (mmm) cc_final: 0.7201 (mmm) REVERT: B 998 PHE cc_start: 0.8567 (t80) cc_final: 0.8200 (t80) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.1157 time to fit residues: 42.0390 Evaluate side-chains 168 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 ASN B 155 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 HIS B 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.149322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.126037 restraints weight = 42820.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.127970 restraints weight = 25855.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.129318 restraints weight = 17543.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.130098 restraints weight = 13091.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.130836 restraints weight = 10698.888| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15769 Z= 0.111 Angle : 0.623 7.178 21328 Z= 0.317 Chirality : 0.043 0.193 2293 Planarity : 0.005 0.052 2760 Dihedral : 4.799 22.346 2050 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1878 helix: 0.85 (0.18), residues: 821 sheet: -0.32 (0.28), residues: 344 loop : -1.47 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 668 TYR 0.018 0.001 TYR A 333 PHE 0.022 0.001 PHE B 866 TRP 0.024 0.001 TRP B 513 HIS 0.012 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00245 (15769) covalent geometry : angle 0.62254 (21328) hydrogen bonds : bond 0.03696 ( 700) hydrogen bonds : angle 4.89626 ( 2031) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7848 (tp) cc_final: 0.7536 (tt) REVERT: A 168 PHE cc_start: 0.4670 (m-80) cc_final: 0.4252 (m-80) REVERT: A 217 LYS cc_start: 0.7258 (mmtm) cc_final: 0.6570 (pttm) REVERT: A 226 LEU cc_start: 0.7288 (mm) cc_final: 0.6879 (mm) REVERT: A 428 GLU cc_start: 0.6963 (pt0) cc_final: 0.5661 (pm20) REVERT: A 592 MET cc_start: 0.7217 (mmp) cc_final: 0.6619 (mmt) REVERT: A 963 MET cc_start: 0.5289 (ptm) cc_final: 0.5006 (ptm) REVERT: B 113 MET cc_start: -0.1958 (ttt) cc_final: -0.2363 (tmm) REVERT: B 377 VAL cc_start: 0.7880 (t) cc_final: 0.7364 (p) REVERT: B 466 MET cc_start: 0.6851 (ttm) cc_final: 0.6338 (mtp) REVERT: B 584 TYR cc_start: 0.7641 (t80) cc_final: 0.7042 (t80) REVERT: B 690 MET cc_start: 0.6451 (mmp) cc_final: 0.5461 (mmp) REVERT: B 998 PHE cc_start: 0.8471 (t80) cc_final: 0.8174 (t80) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1153 time to fit residues: 44.2016 Evaluate side-chains 181 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 113 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 672 ASN A 851 GLN B 155 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.145490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.123028 restraints weight = 43310.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124273 restraints weight = 27447.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125390 restraints weight = 19805.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.125882 restraints weight = 14233.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.126047 restraints weight = 12701.905| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15769 Z= 0.176 Angle : 0.695 10.746 21328 Z= 0.357 Chirality : 0.046 0.216 2293 Planarity : 0.005 0.050 2760 Dihedral : 5.066 23.559 2050 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.19), residues: 1878 helix: 0.64 (0.18), residues: 817 sheet: -0.37 (0.28), residues: 341 loop : -1.55 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 668 TYR 0.028 0.002 TYR B 666 PHE 0.023 0.002 PHE B 866 TRP 0.018 0.002 TRP B 513 HIS 0.012 0.001 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00407 (15769) covalent geometry : angle 0.69513 (21328) hydrogen bonds : bond 0.04313 ( 700) hydrogen bonds : angle 5.08276 ( 2031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.18 seconds wall clock time: 42 minutes 36.79 seconds (2556.79 seconds total)