Starting phenix.real_space_refine on Fri Jul 3 00:27:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m3j_23655/07_2026/7m3j_23655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m3j_23655/07_2026/7m3j_23655.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7m3j_23655/07_2026/7m3j_23655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m3j_23655/07_2026/7m3j_23655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m3j_23655/07_2026/7m3j_23655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m3j_23655/07_2026/7m3j_23655.map" model { file = "/net/cci-nas-00/data/ceres_data/7m3j_23655/07_2026/7m3j_23655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m3j_23655/07_2026/7m3j_23655.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= 0.004 sd= 0.071 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 51 5.16 5 Cl 2 4.86 5 C 7127 2.51 5 N 1888 2.21 5 O 1931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11001 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5438 Classifications: {'peptide': 777} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 29, 'TRANS': 747} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 771 Unresolved non-hydrogen angles: 989 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 36, 'ASN:plan1': 13, 'GLN:plan1': 6, 'ARG:plan': 9, 'TYR:plan': 5, 'TRP:plan': 1, 'PHE:plan': 10} Unresolved non-hydrogen planarities: 407 Chain: "B" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5397 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 265} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 873 Unresolved non-hydrogen angles: 1107 Unresolved non-hydrogen dihedrals: 686 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'ASP:plan': 19, 'GLU:plan': 43, 'GLN:plan1': 9, 'ASN:plan1': 14, 'ARG:plan': 13, 'TYR:plan': 4, 'HIS:plan': 3, 'PHE:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 490 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 76 Unusual residues: {'NAG': 3, 'PO4': 1, 'YP1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'NAG': 2, 'PO4': 1, 'YP1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.31, per 1000 atoms: 0.21 Number of scatterers: 11001 At special positions: 0 Unit cell: (88.8, 98.79, 192.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 51 16.00 P 2 15.00 O 1931 8.00 N 1888 7.00 C 7127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=1.89 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.02 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.02 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 902 " - " ASN A 261 " " NAG A 903 " - " ASN A 468 " " NAG A 904 " - " ASN A 488 " " NAG B 902 " - " ASN B 541 " " NAG B 903 " - " ASN B 488 " " NAG C 1 " - " ASN A 541 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 534.5 milliseconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 16 sheets defined 46.4% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 103 through 120 removed outlier: 3.631A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ASN A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.043A pdb=" N ASN A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 205 removed outlier: 4.262A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.971A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.648A pdb=" N SER A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.732A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.848A pdb=" N PHE A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.595A pdb=" N VAL A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 462 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.750A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.978A pdb=" N ALA A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 3.561A pdb=" N LEU A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 697 removed outlier: 5.740A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.633A pdb=" N ILE A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 746 removed outlier: 3.665A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE A 738 " --> pdb=" O MET A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 4.673A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 790 " --> pdb=" O ILE A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 828 removed outlier: 3.995A pdb=" N ILE A 822 " --> pdb=" O TRP A 818 " (cutoff:3.500A) Proline residue: A 823 - end of helix removed outlier: 3.561A pdb=" N THR A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 852 removed outlier: 3.669A pdb=" N VAL A 838 " --> pdb=" O SER A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 862 removed outlier: 3.751A pdb=" N PHE A 862 " --> pdb=" O TYR A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 869 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.707A pdb=" N PHE B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.930A pdb=" N GLU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.557A pdb=" N ASN B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.732A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 4.191A pdb=" N GLN B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.046A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.955A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 4.654A pdb=" N SER B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 347 through 356 removed outlier: 4.240A pdb=" N GLU B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 356 " --> pdb=" O TRP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 436 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.691A pdb=" N VAL B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 596 Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.847A pdb=" N ILE B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 623 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 637 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.602A pdb=" N SER B 651 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.803A pdb=" N ILE B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 679 through 697 removed outlier: 3.635A pdb=" N ALA B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 746 removed outlier: 3.757A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.513A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 828 removed outlier: 4.013A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 832 through 862 removed outlier: 3.791A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.628A pdb=" N ALA A 26 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 142 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 37 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 6.796A pdb=" N VAL A 209 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 239 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 214 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.586A pdb=" N TYR A 489 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.663A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 495 through 496 Processing sheet with id=AA6, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.858A pdb=" N ARG A 551 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 553 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU A 564 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA8, first strand: chain 'A' and resid 602 through 604 removed outlier: 4.054A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 93 through 100 removed outlier: 6.042A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 100 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE B 38 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AB2, first strand: chain 'B' and resid 237 through 243 removed outlier: 7.684A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE B 267 " --> pdb=" O LEU B 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.074A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 510 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 522 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.758A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.763A pdb=" N VAL B 566 " --> pdb=" O ARG B 551 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB7, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.501A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N CYS B 765 " --> pdb=" O GLU B 604 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1434 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: 1.70 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1746 1.27 - 1.41: 3105 1.41 - 1.55: 6359 1.55 - 1.69: 5 1.69 - 1.83: 60 Bond restraints: 11275 Sorted by residual: bond pdb=" C19 YP1 A 901 " pdb=" C24 YP1 A 901 " ideal model delta sigma weight residual 1.418 1.525 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C19 YP1 B 901 " pdb=" C24 YP1 B 901 " ideal model delta sigma weight residual 1.418 1.524 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N LEU B 88 " pdb=" CA LEU B 88 " ideal model delta sigma weight residual 1.458 1.491 -0.034 7.40e-03 1.83e+04 2.06e+01 bond pdb=" C ILE B 822 " pdb=" N PRO B 823 " ideal model delta sigma weight residual 1.335 1.389 -0.053 1.36e-02 5.41e+03 1.54e+01 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 11270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 14753 2.52 - 5.05: 588 5.05 - 7.57: 71 7.57 - 10.10: 9 10.10 - 12.62: 5 Bond angle restraints: 15426 Sorted by residual: angle pdb=" N THR A 436 " pdb=" CA THR A 436 " pdb=" C THR A 436 " ideal model delta sigma weight residual 110.44 118.67 -8.23 1.20e+00 6.94e-01 4.70e+01 angle pdb=" N LEU A 438 " pdb=" CA LEU A 438 " pdb=" CB LEU A 438 " ideal model delta sigma weight residual 110.05 102.82 7.23 1.44e+00 4.82e-01 2.52e+01 angle pdb=" CA GLU B 354 " pdb=" CB GLU B 354 " pdb=" CG GLU B 354 " ideal model delta sigma weight residual 114.10 123.33 -9.23 2.00e+00 2.50e-01 2.13e+01 angle pdb=" C THR A 436 " pdb=" CA THR A 436 " pdb=" CB THR A 436 " ideal model delta sigma weight residual 111.77 101.53 10.24 2.28e+00 1.92e-01 2.02e+01 angle pdb=" CA GLY A 830 " pdb=" C GLY A 830 " pdb=" O GLY A 830 " ideal model delta sigma weight residual 121.90 117.34 4.56 1.08e+00 8.57e-01 1.78e+01 ... (remaining 15421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 6181 21.09 - 42.17: 238 42.17 - 63.26: 25 63.26 - 84.35: 8 84.35 - 105.43: 9 Dihedral angle restraints: 6461 sinusoidal: 1920 harmonic: 4541 Sorted by residual: dihedral pdb=" CB CYS B 568 " pdb=" SG CYS B 568 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual -86.00 -176.01 90.01 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B 437 " pdb=" SG CYS B 437 " pdb=" SG CYS B 449 " pdb=" CB CYS B 449 " ideal model delta sinusoidal sigma weight residual 93.00 178.89 -85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -170.29 84.29 1 1.00e+01 1.00e-02 8.65e+01 ... (remaining 6458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1593 0.109 - 0.218: 173 0.218 - 0.326: 14 0.326 - 0.435: 4 0.435 - 0.544: 2 Chirality restraints: 1786 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 541 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" CA THR A 445 " pdb=" N THR A 445 " pdb=" C THR A 445 " pdb=" CB THR A 445 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA LEU A 438 " pdb=" N LEU A 438 " pdb=" C LEU A 438 " pdb=" CB LEU A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 1783 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 425 " 0.035 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR B 425 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR B 425 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 425 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 425 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 425 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 425 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 425 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 640 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO A 641 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 84 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO B 85 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3135 2.80 - 3.32: 9907 3.32 - 3.85: 16806 3.85 - 4.37: 17860 4.37 - 4.90: 30914 Nonbonded interactions: 78622 Sorted by model distance: nonbonded pdb=" O LEU A 842 " pdb=" OG SER A 845 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 150 " pdb=" OG SER A 169 " model vdw 2.313 3.040 nonbonded pdb=" O GLY A 43 " pdb=" N ILE A 61 " model vdw 2.341 3.120 nonbonded pdb=" OE1 GLN A 253 " pdb=" NH2 ARG A 286 " model vdw 2.351 3.120 nonbonded pdb=" OE1 GLU B 456 " pdb=" NE1 TRP B 458 " model vdw 2.359 3.120 ... (remaining 78617 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 26 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 116 or (resid 117 thr \ ough 120 and (name N or name CA or name C or name O or name CB )) or resid 136 t \ hrough 171 or (resid 172 and (name N or name CA or name C or name O or name CB ) \ ) or resid 173 through 178 or (resid 179 and (name N or name CA or name C or nam \ e O or name CB )) or resid 180 or (resid 181 and (name N or name CA or name C or \ name O or name CB )) or resid 182 through 190 or (resid 191 and (name N or name \ CA or name C or name O or name CB )) or resid 192 through 210 or (resid 211 and \ (name N or name CA or name C or name O or name CB )) or resid 212 through 231 o \ r (resid 232 through 234 and (name N or name CA or name C or name O or name CB ) \ ) or resid 235 through 242 or (resid 243 through 244 and (name N or name CA or n \ ame C or name O or name CB )) or resid 245 or (resid 246 through 259 and (name N \ or name CA or name C or name O or name CB )) or resid 260 or (resid 261 through \ 264 and (name N or name CA or name C or name O or name CB )) or resid 265 throu \ gh 270 or (resid 271 through 272 and (name N or name CA or name C or name O or n \ ame CB )) or resid 273 through 274 or (resid 275 and (name N or name CA or name \ C or name O or name CB )) or resid 276 or (resid 277 and (name N or name CA or n \ ame C or name O or name CB )) or resid 278 through 280 or (resid 281 and (name N \ or name CA or name C or name O or name CB )) or resid 282 through 284 or (resid \ 285 through 286 and (name N or name CA or name C or name O or name CB )) or res \ id 287 through 288 or (resid 289 and (name N or name CA or name C or name O or n \ ame CB )) or resid 290 through 291 or (resid 292 and (name N or name CA or name \ C or name O or name CB )) or resid 293 through 296 or (resid 297 through 298 and \ (name N or name CA or name C or name O or name CB )) or resid 299 through 300 o \ r (resid 301 through 302 and (name N or name CA or name C or name O or name CB ) \ ) or resid 303 or (resid 304 through 306 and (name N or name CA or name C or nam \ e O or name CB )) or resid 307 through 349 or (resid 350 and (name N or name CA \ or name C or name O or name CB )) or resid 351 through 354 or (resid 355 and (na \ me N or name CA or name C or name O or name CB )) or resid 356 through 357 or (r \ esid 403 through 406 and (name N or name CA or name C or name O or name CB )) or \ resid 407 through 409 or (resid 410 and (name N or name CA or name C or name O \ or name CB )) or resid 411 through 437 or (resid 438 and (name N or name CA or n \ ame C or name O or name CB )) or resid 439 through 458 or (resid 459 and (name N \ or name CA or name C or name O or name CB )) or resid 460 through 472 or (resid \ 473 and (name N or name CA or name C or name O or name CB )) or resid 474 throu \ gh 496 or (resid 497 and (name N or name CA or name C or name O or name CB )) or \ resid 498 through 501 or (resid 502 through 503 and (name N or name CA or name \ C or name O or name CB )) or resid 504 through 506 or (resid 507 and (name N or \ name CA or name C or name O or name CB )) or resid 508 through 518 or (resid 519 \ and (name N or name CA or name C or name O or name CB )) or resid 520 through 5 \ 24 or (resid 525 through 527 and (name N or name CA or name C or name O or name \ CB )) or resid 528 through 532 or (resid 533 through 534 and (name N or name CA \ or name C or name O or name CB )) or resid 535 through 542 or (resid 543 and (na \ me N or name CA or name C or name O or name CB )) or resid 544 through 546 or (r \ esid 547 through 548 and (name N or name CA or name C or name O or name CB )) or \ resid 549 or (resid 550 and (name N or name CA or name C or name O or name CB ) \ ) or resid 551 through 559 or (resid 560 and (name N or name CA or name C or nam \ e O or name CB )) or resid 561 through 582 or (resid 583 through 584 and (name N \ or name CA or name C or name O or name CB )) or resid 585 through 594 or (resid \ 595 through 597 and (name N or name CA or name C or name O or name CB )) or res \ id 598 through 604 or (resid 605 through 610 and (name N or name CA or name C or \ name O or name CB )) or resid 611 through 635 or (resid 636 through 640 and (na \ me N or name CA or name C or name O or name CB )) or resid 641 through 660 or (r \ esid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 t \ hrough 685 or (resid 686 through 687 and (name N or name CA or name C or name O \ or name CB )) or resid 688 through 691 or (resid 692 through 693 and (name N or \ name CA or name C or name O or name CB )) or resid 694 through 695 or (resid 696 \ through 699 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 00 through 728 or (resid 729 through 737 and (name N or name CA or name C or nam \ e O or name CB )) or resid 738 through 741 or (resid 742 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 through 750 or (resid \ 751 and (name N or name CA or name C or name O or name CB )) or resid 752 throu \ gh 761 or (resid 762 through 764 and (name N or name CA or name C or name O or n \ ame CB )) or resid 765 or (resid 766 through 767 and (name N or name CA or name \ C or name O or name CB )) or (resid 768 through 773 and (name N or name CA or na \ me C or name O or name CB )) or resid 774 through 780 or (resid 781 through 786 \ and (name N or name CA or name C or name O or name CB )) or resid 787 through 78 \ 8 or (resid 789 and (name N or name CA or name C or name O or name CB )) or resi \ d 790 through 792 or (resid 793 through 797 and (name N or name CA or name C or \ name O or name CB )) or resid 798 through 844 or (resid 845 and (name N or name \ CA or name C or name O or name CB )) or resid 846 through 862 or (resid 863 thro \ ugh 874 and (name N or name CA or name C or name O or name CB )) or resid 903 th \ rough 905)) selection = (chain 'B' and (resid 26 through 46 or (resid 47 through 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 51 or (resid 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 60 or (res \ id 61 and (name N or name CA or name C or name O or name CB )) or resid 62 throu \ gh 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or r \ esid 89 through 99 or (resid 100 and (name N or name CA or name C or name O or n \ ame CB )) or resid 101 through 119 or (resid 120 and (name N or name CA or name \ C or name O or name CB )) or resid 136 through 144 or (resid 145 and (name N or \ name CA or name C or name O or name CB )) or resid 146 through 192 or (resid 193 \ through 194 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 95 through 237 or (resid 238 and (name N or name CA or name C or name O or name \ CB )) or resid 239 or (resid 240 through 241 and (name N or name CA or name C or \ name O or name CB )) or resid 242 through 357 or (resid 403 through 406 and (na \ me N or name CA or name C or name O or name CB )) or resid 407 through 411 or (r \ esid 412 and (name N or name CA or name C or name O or name CB )) or resid 413 t \ hrough 435 or (resid 436 and (name N or name CA or name C or name O or name CB ) \ ) or resid 437 through 479 or (resid 480 through 482 and (name N or name CA or n \ ame C or name O or name CB )) or resid 483 through 516 or (resid 517 and (name N \ or name CA or name C or name O or name CB )) or resid 518 through 525 or (resid \ 526 through 527 and (name N or name CA or name C or name O or name CB )) or res \ id 528 through 554 or (resid 555 through 556 and (name N or name CA or name C or \ name O or name CB )) or resid 557 through 565 or (resid 566 through 567 and (na \ me N or name CA or name C or name O or name CB )) or resid 568 through 576 or (r \ esid 577 through 581 and (name N or name CA or name C or name O or name CB )) or \ resid 582 through 593 or (resid 594 through 597 and (name N or name CA or name \ C or name O or name CB )) or resid 598 through 606 or (resid 607 through 610 and \ (name N or name CA or name C or name O or name CB )) or resid 611 through 613 o \ r (resid 614 through 618 and (name N or name CA or name C or name O or name CB ) \ ) or resid 619 through 621 or (resid 622 and (name N or name CA or name C or nam \ e O or name CB )) or resid 623 through 629 or (resid 630 through 631 and (name N \ or name CA or name C or name O or name CB )) or resid 632 or (resid 633 through \ 640 and (name N or name CA or name C or name O or name CB )) or resid 641 or (r \ esid 642 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 649 or (resid 650 through 661 and (name N or name CA or name \ C or name O or name CB )) or resid 662 through 668 or (resid 669 and (name N or \ name CA or name C or name O or name CB )) or resid 670 through 678 or (resid 679 \ through 680 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 81 through 700 or (resid 701 through 737 and (name N or name CA or name C or nam \ e O or name CB )) or resid 738 through 743 or (resid 744 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 or (resid 748 through \ 751 and (name N or name CA or name C or name O or name CB )) or resid 752 throu \ gh 760 or (resid 761 through 764 and (name N or name CA or name C or name O or n \ ame CB )) or resid 765 through 791 or (resid 792 through 797 and (name N or name \ CA or name C or name O or name CB )) or resid 798 through 812 or (resid 813 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 819 o \ r (resid 820 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 21 through 828 or (resid 829 and (name N or name CA or name C or name O or name \ CB )) or resid 830 through 837 or (resid 838 through 840 and (name N or name CA \ or name C or name O or name CB )) or resid 841 through 847 or (resid 848 and (na \ me N or name CA or name C or name O or name CB )) or resid 849 through 852 or (r \ esid 853 through 874 and (name N or name CA or name C or name O or name CB )) or \ resid 902 through 904)) } 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: 4.830 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.430 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.010 0.143 11298 Z= 0.472 Angle : 1.166 27.899 15479 Z= 0.643 Chirality : 0.071 0.544 1786 Planarity : 0.008 0.077 1983 Dihedral : 12.371 105.435 3469 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % Cbeta Deviations : 0.20 % 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: -2.70 (0.18), residues: 1546 helix: -1.45 (0.17), residues: 667 sheet: -1.51 (0.37), residues: 166 loop : -2.14 (0.20), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 185 TYR 0.069 0.004 TYR B 425 PHE 0.040 0.004 PHE A 330 TRP 0.036 0.003 TRP A 818 HIS 0.011 0.003 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.01008 / 0.47 (11275) covalent geometry : angle 1.10305 / 0.63 (15426) SS BOND : bond 0.03604 / 1.80 ( 16) SS BOND : angle 5.54914 / 3.23 ( 32) hydrogen bonds : bond 0.16193 / 10.72 ( 485) hydrogen bonds : angle 6.53632 / 4.63 ( 1434) link_BETA1-4 : bond 0.01189 / 0.63 ( 1) link_BETA1-4 : angle 2.41783 / 1.28 ( 3) link_NAG-ASN : bond 0.00895 / 0.50 ( 6) link_NAG-ASN : angle 8.36037 / 4.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.356 Fit side-chains REVERT: B 668 PHE cc_start: 0.8192 (m-80) cc_final: 0.7825 (m-80) REVERT: B 815 PHE cc_start: 0.9121 (m-80) cc_final: 0.8906 (m-80) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.0621 time to fit residues: 10.2111 Evaluate side-chains 73 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 766 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073188 restraints weight = 34391.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073132 restraints weight = 22211.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073488 restraints weight = 16676.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073734 restraints weight = 15684.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073757 restraints weight = 13614.310| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11298 Z= 0.137 Angle : 0.620 11.462 15479 Z= 0.320 Chirality : 0.045 0.329 1786 Planarity : 0.005 0.052 1983 Dihedral : 8.506 91.044 1670 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: -1.55 (0.20), residues: 1546 helix: 0.02 (0.20), residues: 669 sheet: -1.73 (0.35), residues: 178 loop : -1.86 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.019 0.001 TYR A 421 PHE 0.017 0.001 PHE A 114 TRP 0.015 0.001 TRP A 458 HIS 0.003 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (11275) covalent geometry : angle 0.59484 / 0.31 (15426) SS BOND : bond 0.00217 / 0.11 ( 16) SS BOND : angle 1.20214 / 0.88 ( 32) hydrogen bonds : bond 0.05046 / 3.43 ( 485) hydrogen bonds : angle 4.82675 / 3.39 ( 1434) link_BETA1-4 : bond 0.00528 / 0.28 ( 1) link_BETA1-4 : angle 1.30526 / 0.69 ( 3) link_NAG-ASN : bond 0.00774 / 0.41 ( 6) link_NAG-ASN : angle 4.93522 / 2.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.309 Fit side-chains REVERT: A 267 ILE cc_start: 0.9291 (mp) cc_final: 0.9090 (tp) REVERT: B 190 ASP cc_start: 0.8032 (p0) cc_final: 0.7706 (p0) REVERT: B 668 PHE cc_start: 0.8441 (m-80) cc_final: 0.8172 (m-80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0642 time to fit residues: 9.8330 Evaluate side-chains 75 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 136 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 GLN A 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.073583 restraints weight = 34561.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073836 restraints weight = 22752.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073882 restraints weight = 16207.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074103 restraints weight = 16444.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.074205 restraints weight = 14326.772| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 11298 Z= 0.128 Angle : 0.560 9.977 15479 Z= 0.287 Chirality : 0.044 0.292 1786 Planarity : 0.004 0.047 1983 Dihedral : 8.108 86.760 1670 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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: -1.02 (0.21), residues: 1546 helix: 0.73 (0.20), residues: 665 sheet: -1.72 (0.36), residues: 175 loop : -1.79 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.030 0.001 TYR A 421 PHE 0.026 0.001 PHE A 846 TRP 0.012 0.001 TRP A 458 HIS 0.003 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (11275) covalent geometry : angle 0.53778 / 0.28 (15426) SS BOND : bond 0.00201 / 0.09 ( 16) SS BOND : angle 0.81939 / 0.57 ( 32) hydrogen bonds : bond 0.04020 / 2.73 ( 485) hydrogen bonds : angle 4.35310 / 3.07 ( 1434) link_BETA1-4 : bond 0.00538 / 0.28 ( 1) link_BETA1-4 : angle 0.96290 / 0.50 ( 3) link_NAG-ASN : bond 0.00661 / 0.37 ( 6) link_NAG-ASN : angle 4.53635 / 2.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.423 Fit side-chains REVERT: A 190 ASP cc_start: 0.7854 (p0) cc_final: 0.7644 (p0) REVERT: A 825 TYR cc_start: 0.9223 (t80) cc_final: 0.8899 (t80) REVERT: B 190 ASP cc_start: 0.8062 (p0) cc_final: 0.7721 (p0) REVERT: B 853 PHE cc_start: 0.8882 (m-80) cc_final: 0.8663 (m-10) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0582 time to fit residues: 9.6884 Evaluate side-chains 75 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.091355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.072896 restraints weight = 34645.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.072710 restraints weight = 23605.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072956 restraints weight = 17926.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.073025 restraints weight = 17353.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073163 restraints weight = 15266.352| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11298 Z= 0.158 Angle : 0.585 9.755 15479 Z= 0.296 Chirality : 0.045 0.288 1786 Planarity : 0.004 0.046 1983 Dihedral : 7.867 92.782 1670 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -0.81 (0.21), residues: 1546 helix: 1.02 (0.20), residues: 665 sheet: -1.85 (0.35), residues: 179 loop : -1.74 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.024 0.001 TYR A 421 PHE 0.048 0.002 PHE A 688 TRP 0.010 0.001 TRP A 458 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (11275) covalent geometry : angle 0.56371 / 0.29 (15426) SS BOND : bond 0.00366 / 0.21 ( 16) SS BOND : angle 0.99203 / 0.73 ( 32) hydrogen bonds : bond 0.04095 / 2.80 ( 485) hydrogen bonds : angle 4.34188 / 3.07 ( 1434) link_BETA1-4 : bond 0.00702 / 0.37 ( 1) link_BETA1-4 : angle 0.95336 / 0.50 ( 3) link_NAG-ASN : bond 0.00570 / 0.32 ( 6) link_NAG-ASN : angle 4.45418 / 2.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.383 Fit side-chains REVERT: A 190 ASP cc_start: 0.7853 (p0) cc_final: 0.7609 (p0) REVERT: A 310 TYR cc_start: 0.8154 (m-10) cc_final: 0.7920 (m-80) REVERT: B 190 ASP cc_start: 0.8107 (p0) cc_final: 0.7778 (p0) REVERT: B 853 PHE cc_start: 0.8751 (m-80) cc_final: 0.8519 (m-10) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0610 time to fit residues: 9.7656 Evaluate side-chains 76 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 0.0010 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 766 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073468 restraints weight = 34465.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073914 restraints weight = 26039.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074255 restraints weight = 17190.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074312 restraints weight = 16891.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.074496 restraints weight = 15001.689| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11298 Z= 0.119 Angle : 0.547 10.656 15479 Z= 0.276 Chirality : 0.044 0.270 1786 Planarity : 0.004 0.051 1983 Dihedral : 7.775 87.614 1670 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.57 (0.21), residues: 1546 helix: 1.27 (0.21), residues: 668 sheet: -1.73 (0.37), residues: 170 loop : -1.67 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.025 0.001 TYR A 421 PHE 0.026 0.001 PHE A 688 TRP 0.012 0.001 TRP A 818 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11275) covalent geometry : angle 0.52757 / 0.27 (15426) SS BOND : bond 0.00140 / 0.06 ( 16) SS BOND : angle 0.78851 / 0.61 ( 32) hydrogen bonds : bond 0.03545 / 2.43 ( 485) hydrogen bonds : angle 4.09065 / 2.90 ( 1434) link_BETA1-4 : bond 0.00555 / 0.29 ( 1) link_BETA1-4 : angle 0.86651 / 0.45 ( 3) link_NAG-ASN : bond 0.00613 / 0.35 ( 6) link_NAG-ASN : angle 4.22120 / 2.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.535 Fit side-chains REVERT: A 190 ASP cc_start: 0.7912 (p0) cc_final: 0.7627 (p0) REVERT: A 275 ASP cc_start: 0.7817 (m-30) cc_final: 0.7535 (m-30) REVERT: B 190 ASP cc_start: 0.8062 (p0) cc_final: 0.7740 (p0) REVERT: B 853 PHE cc_start: 0.8825 (m-80) cc_final: 0.8527 (m-10) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0681 time to fit residues: 10.8621 Evaluate side-chains 72 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072978 restraints weight = 34698.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.073132 restraints weight = 23100.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.073287 restraints weight = 16517.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.073451 restraints weight = 15617.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.073571 restraints weight = 14426.764| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11298 Z= 0.145 Angle : 0.559 9.706 15479 Z= 0.282 Chirality : 0.044 0.273 1786 Planarity : 0.004 0.044 1983 Dihedral : 7.711 87.428 1670 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: -0.48 (0.21), residues: 1546 helix: 1.36 (0.21), residues: 671 sheet: -1.69 (0.37), residues: 169 loop : -1.66 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.024 0.001 TYR A 421 PHE 0.033 0.001 PHE A 846 TRP 0.009 0.001 TRP A 458 HIS 0.008 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (11275) covalent geometry : angle 0.53929 / 0.28 (15426) SS BOND : bond 0.00166 / 0.09 ( 16) SS BOND : angle 0.95858 / 0.74 ( 32) hydrogen bonds : bond 0.03772 / 2.60 ( 485) hydrogen bonds : angle 4.15115 / 2.94 ( 1434) link_BETA1-4 : bond 0.00405 / 0.21 ( 1) link_BETA1-4 : angle 0.76650 / 0.40 ( 3) link_NAG-ASN : bond 0.00537 / 0.31 ( 6) link_NAG-ASN : angle 4.20791 / 2.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.439 Fit side-chains REVERT: A 190 ASP cc_start: 0.7909 (p0) cc_final: 0.7615 (p0) REVERT: A 275 ASP cc_start: 0.7766 (m-30) cc_final: 0.7486 (m-30) REVERT: B 190 ASP cc_start: 0.8089 (p0) cc_final: 0.7765 (p0) REVERT: B 853 PHE cc_start: 0.8784 (m-80) cc_final: 0.8478 (m-10) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0678 time to fit residues: 10.9819 Evaluate side-chains 79 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS A 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.071778 restraints weight = 34767.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.071865 restraints weight = 23114.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.071875 restraints weight = 17233.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.072059 restraints weight = 16790.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.072173 restraints weight = 15111.467| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11298 Z= 0.185 Angle : 0.593 10.344 15479 Z= 0.303 Chirality : 0.045 0.272 1786 Planarity : 0.004 0.045 1983 Dihedral : 7.836 86.819 1670 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -0.55 (0.21), residues: 1546 helix: 1.32 (0.20), residues: 675 sheet: -1.77 (0.37), residues: 170 loop : -1.72 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.028 0.002 TYR B 425 PHE 0.022 0.002 PHE A 688 TRP 0.014 0.001 TRP A 818 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (11275) covalent geometry : angle 0.57364 / 0.30 (15426) SS BOND : bond 0.00217 / 0.11 ( 16) SS BOND : angle 1.00251 / 0.78 ( 32) hydrogen bonds : bond 0.04140 / 2.86 ( 485) hydrogen bonds : angle 4.26283 / 3.03 ( 1434) link_BETA1-4 : bond 0.00295 / 0.16 ( 1) link_BETA1-4 : angle 0.76523 / 0.40 ( 3) link_NAG-ASN : bond 0.00515 / 0.29 ( 6) link_NAG-ASN : angle 4.34446 / 2.22 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.329 Fit side-chains REVERT: A 190 ASP cc_start: 0.7918 (p0) cc_final: 0.7640 (p0) REVERT: B 190 ASP cc_start: 0.8172 (p0) cc_final: 0.7873 (p0) REVERT: B 853 PHE cc_start: 0.8872 (m-80) cc_final: 0.8478 (m-10) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0676 time to fit residues: 10.5875 Evaluate side-chains 75 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 118 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 0.0670 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 766 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073929 restraints weight = 34503.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074039 restraints weight = 25572.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.074058 restraints weight = 17702.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074230 restraints weight = 16878.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.074448 restraints weight = 15352.192| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11298 Z= 0.111 Angle : 0.536 9.292 15479 Z= 0.269 Chirality : 0.044 0.259 1786 Planarity : 0.004 0.041 1983 Dihedral : 7.605 85.427 1670 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -0.33 (0.21), residues: 1546 helix: 1.50 (0.20), residues: 678 sheet: -1.66 (0.37), residues: 175 loop : -1.62 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.020 0.001 TYR B 425 PHE 0.026 0.001 PHE A 846 TRP 0.011 0.001 TRP A 458 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11275) covalent geometry : angle 0.51709 / 0.26 (15426) SS BOND : bond 0.00140 / 0.07 ( 16) SS BOND : angle 0.67633 / 0.49 ( 32) hydrogen bonds : bond 0.03352 / 2.31 ( 485) hydrogen bonds : angle 3.97175 / 2.83 ( 1434) link_BETA1-4 : bond 0.00535 / 0.28 ( 1) link_BETA1-4 : angle 0.82626 / 0.43 ( 3) link_NAG-ASN : bond 0.00600 / 0.35 ( 6) link_NAG-ASN : angle 4.11482 / 2.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.303 Fit side-chains REVERT: A 190 ASP cc_start: 0.7866 (p0) cc_final: 0.7550 (p0) REVERT: B 190 ASP cc_start: 0.8105 (p0) cc_final: 0.7747 (p0) REVERT: B 846 PHE cc_start: 0.8597 (m-10) cc_final: 0.8259 (m-80) REVERT: B 853 PHE cc_start: 0.8851 (m-80) cc_final: 0.8434 (m-10) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0660 time to fit residues: 10.2918 Evaluate side-chains 76 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.072074 restraints weight = 34576.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071851 restraints weight = 25787.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072144 restraints weight = 18214.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072259 restraints weight = 18233.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072395 restraints weight = 15823.241| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11298 Z= 0.184 Angle : 0.595 10.992 15479 Z= 0.304 Chirality : 0.046 0.273 1786 Planarity : 0.004 0.046 1983 Dihedral : 7.717 87.128 1670 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.45 (0.21), residues: 1546 helix: 1.42 (0.20), residues: 676 sheet: -1.76 (0.37), residues: 174 loop : -1.68 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.040 0.002 TYR B 425 PHE 0.017 0.002 PHE A 809 TRP 0.019 0.001 TRP A 818 HIS 0.004 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (11275) covalent geometry : angle 0.57594 / 0.30 (15426) SS BOND : bond 0.00208 / 0.10 ( 16) SS BOND : angle 1.13158 / 0.90 ( 32) hydrogen bonds : bond 0.04084 / 2.82 ( 485) hydrogen bonds : angle 4.20454 / 2.99 ( 1434) link_BETA1-4 : bond 0.00385 / 0.20 ( 1) link_BETA1-4 : angle 0.72838 / 0.38 ( 3) link_NAG-ASN : bond 0.00495 / 0.29 ( 6) link_NAG-ASN : angle 4.24749 / 2.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.440 Fit side-chains REVERT: A 190 ASP cc_start: 0.7939 (p0) cc_final: 0.7703 (p0) REVERT: B 190 ASP cc_start: 0.8184 (p0) cc_final: 0.7869 (p0) REVERT: B 853 PHE cc_start: 0.8850 (m-80) cc_final: 0.8409 (m-10) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0786 time to fit residues: 11.6716 Evaluate side-chains 74 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 115 optimal weight: 2.9990 chunk 29 optimal weight: 0.0050 chunk 43 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS A 766 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.071849 restraints weight = 34633.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.073182 restraints weight = 20863.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074083 restraints weight = 14573.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074666 restraints weight = 11352.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075083 restraints weight = 9547.801| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11298 Z= 0.130 Angle : 0.568 10.804 15479 Z= 0.284 Chirality : 0.044 0.258 1786 Planarity : 0.004 0.044 1983 Dihedral : 7.592 83.481 1670 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.33 (0.22), residues: 1546 helix: 1.52 (0.20), residues: 676 sheet: -1.72 (0.37), residues: 176 loop : -1.60 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 551 TYR 0.033 0.001 TYR B 425 PHE 0.024 0.001 PHE B 684 TRP 0.010 0.001 TRP B 293 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11275) covalent geometry : angle 0.54956 / 0.28 (15426) SS BOND : bond 0.00144 / 0.07 ( 16) SS BOND : angle 0.99615 / 0.84 ( 32) hydrogen bonds : bond 0.03651 / 2.55 ( 485) hydrogen bonds : angle 4.02958 / 2.87 ( 1434) link_BETA1-4 : bond 0.00480 / 0.25 ( 1) link_BETA1-4 : angle 0.82140 / 0.43 ( 3) link_NAG-ASN : bond 0.00560 / 0.33 ( 6) link_NAG-ASN : angle 4.13533 / 2.11 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.428 Fit side-chains REVERT: A 190 ASP cc_start: 0.7769 (p0) cc_final: 0.7501 (p0) REVERT: B 190 ASP cc_start: 0.7921 (p0) cc_final: 0.7612 (p0) REVERT: B 853 PHE cc_start: 0.8940 (m-80) cc_final: 0.8462 (m-10) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0659 time to fit residues: 9.8411 Evaluate side-chains 73 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 766 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071739 restraints weight = 34733.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.071670 restraints weight = 25784.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072176 restraints weight = 18645.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072227 restraints weight = 17007.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072287 restraints weight = 14890.262| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11298 Z= 0.185 Angle : 0.598 10.118 15479 Z= 0.305 Chirality : 0.045 0.272 1786 Planarity : 0.004 0.049 1983 Dihedral : 7.702 85.545 1670 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.42 (0.22), residues: 1546 helix: 1.44 (0.20), residues: 678 sheet: -1.79 (0.37), residues: 174 loop : -1.65 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.041 0.002 TYR B 425 PHE 0.022 0.001 PHE B 160 TRP 0.019 0.001 TRP B 293 HIS 0.004 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (11275) covalent geometry : angle 0.57875 / 0.30 (15426) SS BOND : bond 0.00190 / 0.09 ( 16) SS BOND : angle 1.14505 / 0.94 ( 32) hydrogen bonds : bond 0.04130 / 2.88 ( 485) hydrogen bonds : angle 4.21046 / 3.00 ( 1434) link_BETA1-4 : bond 0.00411 / 0.22 ( 1) link_BETA1-4 : angle 0.74493 / 0.39 ( 3) link_NAG-ASN : bond 0.00497 / 0.28 ( 6) link_NAG-ASN : angle 4.25211 / 2.17 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1468.83 seconds wall clock time: 26 minutes 0.36 seconds (1560.36 seconds total)