Starting phenix.real_space_refine on Tue Dec 31 10:44:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzg_24759/12_2024/7rzg_24759.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzg_24759/12_2024/7rzg_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_24759/12_2024/7rzg_24759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzg_24759/12_2024/7rzg_24759.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzg_24759/12_2024/7rzg_24759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzg_24759/12_2024/7rzg_24759.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 8.78, per 1000 atoms: 0.57 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: 3.71 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.87 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: 6.03 Time building geometry restraints manager: 4.31 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: 1.070 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 35.900 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.650 ------------------------------------------------------------------------------- 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= 0.437 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 : 19.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.039 0.004 TRP B 695 HIS 0.014 0.003 HIS B 146 PHE 0.056 0.003 PHE A 168 TYR 0.047 0.003 TYR A 584 ARG 0.006 0.001 ARG A 951 *********************** 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 : 1.764 Fit side-chains revert: symmetry clash REVERT: A 153 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7249 (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: 0.7558 (mptt) REVERT: A 1002 LEU cc_start: 0.8351 (mt) cc_final: 0.8150 (mt) REVERT: B 97 LEU cc_start: 0.1718 (OUTLIER) cc_final: 0.1358 (pt) REVERT: B 248 TYR cc_start: 0.5690 (m-80) cc_final: 0.5418 (m-80) REVERT: B 338 ILE cc_start: 0.8239 (mm) cc_final: 0.7891 (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: 0.6010 (ttm) REVERT: B 799 MET cc_start: 0.4954 (ttt) cc_final: 0.4735 (ttt) REVERT: B 806 MET cc_start: 0.7108 (mmm) cc_final: 0.6714 (mmm) outliers start: 3 outliers final: 0 residues processed: 259 average time/residue: 0.2661 time to fit residues: 103.9808 Evaluate side-chains 171 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 76 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 213 HIS A 357 ASN A 828 GLN A 914 GLN B 146 HIS B 329 ASN B 332 HIS B 528 ASN B 762 GLN B 805 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15769 Z= 0.177 Angle : 0.663 7.443 21328 Z= 0.348 Chirality : 0.045 0.182 2293 Planarity : 0.005 0.078 2760 Dihedral : 5.521 28.410 2050 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.12 % Allowed : 3.19 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.18), residues: 1878 helix: -0.59 (0.17), residues: 830 sheet: -1.33 (0.26), residues: 350 loop : -2.17 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 776 HIS 0.009 0.001 HIS B 681 PHE 0.021 0.002 PHE A 168 TYR 0.017 0.001 TYR A 433 ARG 0.006 0.001 ARG B 472 *********************** 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 287 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8081 (m-30) cc_final: 0.7621 (p0) REVERT: A 217 LYS cc_start: 0.7066 (mmtm) cc_final: 0.6311 (ptpp) REVERT: A 357 ASN cc_start: 0.7685 (m110) cc_final: 0.7314 (m110) REVERT: A 799 MET cc_start: 0.7367 (mtm) cc_final: 0.7144 (mtm) REVERT: B 338 ILE cc_start: 0.8065 (mm) cc_final: 0.7708 (mm) REVERT: B 357 ASN cc_start: 0.6994 (m-40) cc_final: 0.6608 (m-40) REVERT: B 666 TYR cc_start: 0.8023 (t80) cc_final: 0.7803 (t80) REVERT: B 691 THR cc_start: 0.5597 (t) cc_final: 0.5278 (t) REVERT: B 806 MET cc_start: 0.7527 (mmm) cc_final: 0.7136 (mmm) outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 0.2711 time to fit residues: 117.7292 Evaluate side-chains 179 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 142 optimal weight: 0.0040 chunk 116 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- 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 134 HIS A 786 HIS B 93 HIS B 332 HIS B 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15769 Z= 0.203 Angle : 0.643 8.329 21328 Z= 0.335 Chirality : 0.044 0.169 2293 Planarity : 0.005 0.064 2760 Dihedral : 5.196 24.679 2050 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.19), residues: 1878 helix: 0.16 (0.17), residues: 827 sheet: -0.83 (0.26), residues: 352 loop : -1.84 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 776 HIS 0.015 0.001 HIS B 213 PHE 0.016 0.002 PHE B 174 TYR 0.025 0.002 TYR B 594 ARG 0.006 0.001 ARG B 767 *********************** 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 251 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8147 (m-30) cc_final: 0.7538 (p0) REVERT: A 217 LYS cc_start: 0.7251 (mmtm) cc_final: 0.6551 (pttp) REVERT: A 357 ASN cc_start: 0.7818 (m110) cc_final: 0.7599 (m110) REVERT: A 505 ILE cc_start: 0.8321 (mm) cc_final: 0.7920 (mt) REVERT: A 799 MET cc_start: 0.7545 (mtm) cc_final: 0.7336 (mtm) REVERT: A 823 LEU cc_start: 0.8187 (mp) cc_final: 0.7615 (mt) REVERT: A 846 LEU cc_start: 0.7755 (tp) cc_final: 0.7501 (tt) REVERT: A 963 MET cc_start: 0.6687 (pmm) cc_final: 0.6276 (pmm) REVERT: B 113 MET cc_start: -0.1991 (ttt) cc_final: -0.2337 (tmm) REVERT: B 357 ASN cc_start: 0.7130 (m-40) cc_final: 0.6755 (m-40) REVERT: B 466 MET cc_start: 0.6520 (mtp) cc_final: 0.6300 (ttm) REVERT: B 691 THR cc_start: 0.5930 (t) cc_final: 0.5726 (t) REVERT: B 806 MET cc_start: 0.7397 (mmm) cc_final: 0.6652 (mmm) REVERT: B 998 PHE cc_start: 0.8484 (t80) cc_final: 0.8263 (t80) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.2774 time to fit residues: 104.8658 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 : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 40.0000 chunk 171 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 48 optimal weight: 0.0070 overall best weight: 3.2004 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS B 93 HIS B 407 GLN B 762 GLN B 786 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15769 Z= 0.255 Angle : 0.671 7.703 21328 Z= 0.349 Chirality : 0.046 0.238 2293 Planarity : 0.005 0.058 2760 Dihedral : 5.235 23.389 2050 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.19), residues: 1878 helix: 0.30 (0.17), residues: 825 sheet: -0.75 (0.27), residues: 353 loop : -1.61 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 776 HIS 0.008 0.002 HIS A 93 PHE 0.018 0.002 PHE A 169 TYR 0.018 0.002 TYR A 314 ARG 0.005 0.001 ARG A 951 *********************** 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 239 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8645 (pttp) cc_final: 0.8335 (ttpp) REVERT: A 217 LYS cc_start: 0.6886 (mmtm) cc_final: 0.6461 (pttp) REVERT: A 505 ILE cc_start: 0.8460 (mm) cc_final: 0.7987 (mt) REVERT: A 823 LEU cc_start: 0.8267 (mp) cc_final: 0.7854 (mt) REVERT: A 919 ASP cc_start: 0.7265 (m-30) cc_final: 0.6896 (m-30) REVERT: B 113 MET cc_start: -0.1692 (ttt) cc_final: -0.2320 (tmm) REVERT: B 357 ASN cc_start: 0.7141 (m-40) cc_final: 0.6874 (m-40) REVERT: B 466 MET cc_start: 0.6383 (mtp) cc_final: 0.6163 (ttm) REVERT: B 806 MET cc_start: 0.7458 (mmm) cc_final: 0.6628 (mmm) REVERT: B 998 PHE cc_start: 0.8457 (t80) cc_final: 0.8067 (t80) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.2983 time to fit residues: 104.9319 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 : 1.731 ------------------------------------------------------------------------------- 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: 10.0000 chunk 103 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** 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 762 GLN ** B 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 15769 Z= 0.422 Angle : 0.845 8.632 21328 Z= 0.441 Chirality : 0.050 0.178 2293 Planarity : 0.006 0.057 2760 Dihedral : 5.970 28.280 2050 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 1878 helix: -0.15 (0.17), residues: 820 sheet: -0.99 (0.27), residues: 347 loop : -1.85 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 355 HIS 0.011 0.002 HIS B 754 PHE 0.026 0.003 PHE A 659 TYR 0.035 0.003 TYR B 547 ARG 0.012 0.001 ARG B 767 *********************** 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 209 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LYS cc_start: 0.7037 (mmtm) cc_final: 0.6662 (pttp) REVERT: A 226 LEU cc_start: 0.7505 (mm) cc_final: 0.7033 (mm) REVERT: A 823 LEU cc_start: 0.8269 (mp) cc_final: 0.7791 (mt) REVERT: A 917 ASN cc_start: 0.6615 (t0) cc_final: 0.6412 (t0) REVERT: B 466 MET cc_start: 0.6598 (mtp) cc_final: 0.6231 (ttm) REVERT: B 806 MET cc_start: 0.7652 (mmm) cc_final: 0.7062 (mmm) REVERT: B 839 ARG cc_start: 0.7118 (mmt180) cc_final: 0.6911 (mmt180) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.2836 time to fit residues: 90.6607 Evaluate side-chains 149 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN A 732 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS B 762 GLN B 796 GLN B 805 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15769 Z= 0.171 Angle : 0.637 7.507 21328 Z= 0.328 Chirality : 0.044 0.183 2293 Planarity : 0.005 0.051 2760 Dihedral : 5.174 23.437 2050 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1878 helix: 0.42 (0.18), residues: 820 sheet: -0.75 (0.27), residues: 355 loop : -1.53 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 513 HIS 0.008 0.001 HIS A 93 PHE 0.019 0.001 PHE B 174 TYR 0.018 0.001 TYR B 547 ARG 0.007 0.000 ARG B 767 *********************** 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 259 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 257 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LYS cc_start: 0.6967 (mmtm) cc_final: 0.6509 (pttm) REVERT: A 505 ILE cc_start: 0.8616 (mm) cc_final: 0.8406 (mm) REVERT: A 823 LEU cc_start: 0.8185 (mp) cc_final: 0.7968 (mt) REVERT: A 963 MET cc_start: 0.6804 (pmm) cc_final: 0.6277 (pmm) REVERT: B 113 MET cc_start: -0.2000 (ttt) cc_final: -0.2312 (tmm) REVERT: B 466 MET cc_start: 0.6438 (mtp) cc_final: 0.6189 (ttm) REVERT: B 556 MET cc_start: 0.5906 (ttm) cc_final: 0.5314 (tpp) REVERT: B 606 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6417 (tp30) REVERT: B 649 MET cc_start: 0.8243 (pmm) cc_final: 0.7983 (pmm) REVERT: B 683 MET cc_start: 0.5417 (mmm) cc_final: 0.5155 (mmm) REVERT: B 806 MET cc_start: 0.7493 (mmm) cc_final: 0.6323 (mmm) REVERT: B 860 GLU cc_start: 0.6765 (pp20) cc_final: 0.6342 (pp20) REVERT: B 872 LYS cc_start: 0.8572 (tttm) cc_final: 0.8339 (tttm) REVERT: B 998 PHE cc_start: 0.8425 (t80) cc_final: 0.8112 (t80) outliers start: 2 outliers final: 1 residues processed: 259 average time/residue: 0.2771 time to fit residues: 108.3906 Evaluate side-chains 171 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 132 optimal weight: 0.0070 chunk 102 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 0.0770 chunk 181 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.2162 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15769 Z= 0.255 Angle : 0.690 10.198 21328 Z= 0.357 Chirality : 0.045 0.158 2293 Planarity : 0.005 0.050 2760 Dihedral : 5.275 24.619 2050 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 1878 helix: 0.46 (0.18), residues: 815 sheet: -0.70 (0.27), residues: 357 loop : -1.54 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 776 HIS 0.010 0.001 HIS B 112 PHE 0.037 0.002 PHE A 866 TYR 0.018 0.002 TYR B 547 ARG 0.005 0.001 ARG B 668 *********************** 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 226 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.5032 (m-80) cc_final: 0.4581 (m-80) REVERT: A 217 LYS cc_start: 0.7362 (mmtm) cc_final: 0.6581 (pttm) REVERT: A 226 LEU cc_start: 0.7379 (mm) cc_final: 0.7025 (mm) REVERT: A 470 LYS cc_start: 0.7953 (mppt) cc_final: 0.7419 (mptt) REVERT: A 919 ASP cc_start: 0.7178 (m-30) cc_final: 0.6966 (m-30) REVERT: B 113 MET cc_start: -0.2190 (ttt) cc_final: -0.2673 (tmm) REVERT: B 466 MET cc_start: 0.6547 (mtp) cc_final: 0.6290 (ttm) REVERT: B 806 MET cc_start: 0.7526 (mmm) cc_final: 0.6771 (mmm) REVERT: B 998 PHE cc_start: 0.8420 (t80) cc_final: 0.8089 (t80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2737 time to fit residues: 93.8649 Evaluate side-chains 161 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.0980 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15769 Z= 0.167 Angle : 0.633 9.192 21328 Z= 0.326 Chirality : 0.044 0.301 2293 Planarity : 0.005 0.059 2760 Dihedral : 4.988 22.329 2050 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1878 helix: 0.62 (0.18), residues: 818 sheet: -0.61 (0.27), residues: 354 loop : -1.43 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 513 HIS 0.017 0.001 HIS B 681 PHE 0.028 0.001 PHE A 866 TYR 0.018 0.001 TYR A 831 ARG 0.007 0.000 ARG B 668 *********************** 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 238 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LYS cc_start: 0.7307 (mmtm) cc_final: 0.6591 (pttm) REVERT: A 226 LEU cc_start: 0.7421 (mm) cc_final: 0.7025 (mm) REVERT: A 505 ILE cc_start: 0.8660 (mm) cc_final: 0.8264 (mm) REVERT: A 744 MET cc_start: 0.8168 (ptm) cc_final: 0.7853 (ppp) REVERT: B 113 MET cc_start: -0.2060 (ttt) cc_final: -0.2493 (tmm) REVERT: B 806 MET cc_start: 0.7434 (mmm) cc_final: 0.7065 (mmm) REVERT: B 874 ILE cc_start: 0.7623 (pt) cc_final: 0.7409 (pt) REVERT: B 998 PHE cc_start: 0.8404 (t80) cc_final: 0.8063 (t80) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2714 time to fit residues: 98.7313 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 : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 851 GLN B 155 HIS ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 HIS B 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15769 Z= 0.278 Angle : 0.721 9.960 21328 Z= 0.374 Chirality : 0.046 0.266 2293 Planarity : 0.005 0.050 2760 Dihedral : 5.246 24.080 2050 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1878 helix: 0.48 (0.18), residues: 817 sheet: -0.65 (0.28), residues: 350 loop : -1.53 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 776 HIS 0.012 0.001 HIS B 681 PHE 0.022 0.002 PHE A 866 TYR 0.025 0.002 TYR A 831 ARG 0.007 0.001 ARG B 668 *********************** 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 211 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7720 (tp) cc_final: 0.7291 (tt) REVERT: A 168 PHE cc_start: 0.5092 (m-80) cc_final: 0.4765 (m-80) REVERT: A 217 LYS cc_start: 0.6950 (mmtm) cc_final: 0.6591 (pttm) REVERT: A 226 LEU cc_start: 0.7283 (mm) cc_final: 0.6765 (mm) REVERT: A 744 MET cc_start: 0.8138 (ptm) cc_final: 0.7936 (ppp) REVERT: B 113 MET cc_start: -0.1826 (ttt) cc_final: -0.2407 (tmm) REVERT: B 556 MET cc_start: 0.5590 (ttp) cc_final: 0.5383 (ttp) REVERT: B 649 MET cc_start: 0.8502 (pmm) cc_final: 0.8053 (pmm) REVERT: B 806 MET cc_start: 0.7577 (mmm) cc_final: 0.7110 (mmm) REVERT: B 998 PHE cc_start: 0.8477 (t80) cc_final: 0.8171 (t80) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2805 time to fit residues: 89.1752 Evaluate side-chains 146 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 118 optimal weight: 0.0020 chunk 158 optimal weight: 6.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 851 GLN B 155 HIS B 407 GLN B 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15769 Z= 0.203 Angle : 0.665 10.526 21328 Z= 0.344 Chirality : 0.045 0.216 2293 Planarity : 0.005 0.049 2760 Dihedral : 5.080 22.628 2050 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1878 helix: 0.56 (0.18), residues: 817 sheet: -0.74 (0.27), residues: 369 loop : -1.47 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 513 HIS 0.008 0.001 HIS A 752 PHE 0.022 0.001 PHE A 866 TYR 0.023 0.001 TYR A 831 ARG 0.007 0.000 ARG B 668 ********************** 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 213 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7670 (tp) cc_final: 0.7195 (tt) REVERT: A 217 LYS cc_start: 0.7303 (mmtm) cc_final: 0.6577 (pttm) REVERT: A 226 LEU cc_start: 0.7252 (mm) cc_final: 0.6765 (mm) REVERT: A 592 MET cc_start: 0.6435 (mmp) cc_final: 0.6178 (mmt) REVERT: B 113 MET cc_start: -0.1935 (ttt) cc_final: -0.2452 (tmm) REVERT: B 254 MET cc_start: 0.4675 (ptp) cc_final: 0.4380 (ptp) REVERT: B 683 MET cc_start: 0.5830 (mmm) cc_final: 0.5448 (mtt) REVERT: B 792 GLU cc_start: 0.6822 (tt0) cc_final: 0.6508 (tt0) REVERT: B 806 MET cc_start: 0.7479 (mmm) cc_final: 0.7102 (mmm) REVERT: B 998 PHE cc_start: 0.8450 (t80) cc_final: 0.8109 (t80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2731 time to fit residues: 88.8133 Evaluate side-chains 159 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 137 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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** B 155 HIS B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.145698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122012 restraints weight = 43377.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.123898 restraints weight = 26630.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.125165 restraints weight = 18313.926| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15769 Z= 0.248 Angle : 0.692 10.402 21328 Z= 0.359 Chirality : 0.045 0.213 2293 Planarity : 0.005 0.049 2760 Dihedral : 5.171 23.854 2050 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1878 helix: 0.50 (0.18), residues: 817 sheet: -0.62 (0.27), residues: 353 loop : -1.59 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 513 HIS 0.010 0.001 HIS A 108 PHE 0.019 0.002 PHE A 866 TYR 0.020 0.002 TYR A 584 ARG 0.006 0.001 ARG B 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2936.69 seconds wall clock time: 55 minutes 25.09 seconds (3325.09 seconds total)