Starting phenix.real_space_refine on Sat Jul 4 15:36:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eu7_31308/07_2026/7eu7_31308_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eu7_31308/07_2026/7eu7_31308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eu7_31308/07_2026/7eu7_31308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eu7_31308/07_2026/7eu7_31308.map" model { file = "/net/cci-nas-00/data/ceres_data/7eu7_31308/07_2026/7eu7_31308_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eu7_31308/07_2026/7eu7_31308_neut.cif" } resolution = 3.5 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 93 5.16 5 Cl 1 4.86 5 C 14039 2.51 5 N 3729 2.21 5 O 3911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s 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: 21773 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5530 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 33, 'TRANS': 750} Chain breaks: 3 Unresolved non-hydrogen bonds: 682 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 559 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ARG:plan': 19, 'GLU:plan': 37, 'GLN:plan1': 12, 'ASN:plan1': 12, 'ASP:plan': 17, 'HIS:plan': 3, 'PHE:plan': 6, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 445 Chain: "B" Number of atoms: 5272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5272 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 935 Unresolved non-hydrogen angles: 1172 Unresolved non-hydrogen dihedrals: 770 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'HIS:plan': 5, 'ASP:plan': 35, 'GLU:plan': 41, 'ARG:plan': 13, 'GLN:plan1': 8, 'ASN:plan1': 14, 'PHE:plan': 13, 'TYR:plan': 5, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 573 Chain: "C" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5387 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 33, 'TRANS': 750} Chain breaks: 3 Unresolved non-hydrogen bonds: 826 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 675 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 25, 'GLU:plan': 43, 'GLN:plan1': 16, 'ASN:plan1': 13, 'ASP:plan': 20, 'HIS:plan': 4, 'PHE:plan': 8, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 535 Chain: "D" Number of atoms: 5206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5206 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 296} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 997 Unresolved non-hydrogen angles: 1247 Unresolved non-hydrogen dihedrals: 807 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'HIS:plan': 5, 'ASP:plan': 39, 'GLU:plan': 42, 'ARG:plan': 14, 'GLN:plan1': 8, 'ASN:plan1': 21, 'PHE:plan': 12, 'TYR:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 593 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 130 Unusual residues: {'NAG': 9} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 130 Unusual residues: {'NAG': 9} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.00, per 1000 atoms: 0.23 Number of scatterers: 21773 At special positions: 0 Unit cell: (110.39, 141.93, 181.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 93 16.00 O 3911 8.00 N 3729 7.00 C 14039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.05 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.04 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.02 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 800 " 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 NAG-ASN " NAG A 901 " - " ASN A 61 " " NAG A 902 " - " ASN A 203 " " NAG A 903 " - " ASN A 239 " " NAG A 904 " - " ASN A 276 " " NAG A 905 " - " ASN A 350 " " NAG A 906 " - " ASN A 368 " " NAG A 907 " - " ASN A 440 " " NAG A 908 " - " ASN A 471 " " NAG A 909 " - " ASN A 771 " " NAG B 901 " - " ASN B 340 " " NAG B 902 " - " ASN B 380 " " NAG B 903 " - " ASN B 687 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 239 " " NAG C 904 " - " ASN C 276 " " NAG C 905 " - " ASN C 350 " " NAG C 906 " - " ASN C 368 " " NAG C 907 " - " ASN C 440 " " NAG C 908 " - " ASN C 471 " " NAG C 909 " - " ASN C 771 " " NAG D 901 " - " ASN D 340 " " NAG D 902 " - " ASN D 380 " " NAG D 903 " - " ASN D 687 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 30 sheets defined 44.2% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.935A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.678A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.818A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.717A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.655A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.645A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.594A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.515A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.983A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 665 through 668 removed outlier: 3.794A pdb=" N ASN A 668 " --> pdb=" O THR A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.878A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 4.007A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 810 through 838 removed outlier: 4.184A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.535A pdb=" N ARG B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N THR B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 107 through 121 removed outlier: 4.024A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.017A pdb=" N ALA B 131 " --> pdb=" O HIS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 232 through 245 removed outlier: 3.677A pdb=" N VAL B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.533A pdb=" N VAL B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 4.430A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 555 through 578 Processing helix chain 'B' and resid 600 through 614 Processing helix chain 'B' and resid 624 through 655 removed outlier: 3.725A pdb=" N ILE B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.624A pdb=" N GLN B 671 " --> pdb=" O ASP B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.744A pdb=" N ARG B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 707 removed outlier: 3.518A pdb=" N GLN B 703 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 704 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 771 through 785 removed outlier: 4.127A pdb=" N LEU B 777 " --> pdb=" O ARG B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 797 removed outlier: 3.854A pdb=" N THR B 797 " --> pdb=" O THR B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 817 through 841 removed outlier: 3.694A pdb=" N PHE B 841 " --> pdb=" O TRP B 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 53 removed outlier: 3.606A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.182A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.716A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.875A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.792A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.544A pdb=" N GLU C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 254' Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.578A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.139A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 560 through 580 removed outlier: 4.237A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER C 569 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 614 removed outlier: 4.401A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 658 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.213A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.940A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 809 through 816 removed outlier: 4.034A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 841 removed outlier: 4.470A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 839 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 841 " --> pdb=" O TYR C 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 removed outlier: 4.077A pdb=" N GLU D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.844A pdb=" N GLN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 212 through 220 removed outlier: 3.874A pdb=" N GLN D 216 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.658A pdb=" N VAL D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.746A pdb=" N GLY D 263 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 310 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.885A pdb=" N ASN D 340 " --> pdb=" O PRO D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 472 Processing helix chain 'D' and resid 495 through 502 Processing helix chain 'D' and resid 556 through 578 removed outlier: 3.512A pdb=" N MET D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 614 Processing helix chain 'D' and resid 624 through 652 Processing helix chain 'D' and resid 653 through 655 No H-bonds generated for 'chain 'D' and resid 653 through 655' Processing helix chain 'D' and resid 667 through 672 removed outlier: 3.625A pdb=" N ARG D 672 " --> pdb=" O LYS D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 698 removed outlier: 3.608A pdb=" N ARG D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 706 Processing helix chain 'D' and resid 707 through 709 No H-bonds generated for 'chain 'D' and resid 707 through 709' Processing helix chain 'D' and resid 712 through 723 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 771 through 785 removed outlier: 4.158A pdb=" N LEU D 777 " --> pdb=" O ARG D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 813 through 841 removed outlier: 3.550A pdb=" N MET D 823 " --> pdb=" O GLY D 819 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.493A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.250A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TRP A 247 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU A 269 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 249 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 9.802A pdb=" N LEU A 271 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 266 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.520A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 477 removed outlier: 5.940A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 437 through 439 Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA9, first strand: chain 'A' and resid 729 through 732 removed outlier: 6.090A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 68 through 73 removed outlier: 6.325A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 204 through 206 removed outlier: 3.743A pdb=" N LEU B 228 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 376 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 474 through 479 removed outlier: 3.667A pdb=" N MET B 507 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 523 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.526A pdb=" N VAL B 434 " --> pdb=" O CYS B 456 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB6, first strand: chain 'B' and resid 682 through 683 Processing sheet with id=AB7, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB8, first strand: chain 'C' and resid 61 through 62 removed outlier: 5.695A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.300A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP C 247 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU C 269 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 249 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N LEU C 271 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE C 266 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.499A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 475 through 478 removed outlier: 5.763A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET C 512 " --> pdb=" O LYS C 399 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 412 removed outlier: 3.629A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 729 through 732 removed outlier: 5.790A pdb=" N ILE C 540 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLU C 751 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 542 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C 749 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 68 through 73 removed outlier: 5.987A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 199 through 200 removed outlier: 3.675A pdb=" N PHE D 170 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU D 206 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR D 174 " --> pdb=" O LEU D 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 199 through 200 removed outlier: 3.675A pdb=" N PHE D 170 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL D 169 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU D 228 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER D 171 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N TYR D 230 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 173 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE D 227 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 279 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 363 " --> pdb=" O VAL D 375 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 474 through 479 removed outlier: 3.589A pdb=" N ILE D 408 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET D 507 " --> pdb=" O SER D 407 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD2, first strand: chain 'D' and resid 487 through 489 Processing sheet with id=AD3, first strand: chain 'D' and resid 682 through 683 removed outlier: 6.030A pdb=" N GLY D 683 " --> pdb=" O ILE D 729 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP D 731 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 537 " --> pdb=" O VAL D 748 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 3072 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: 4.58 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6998 1.34 - 1.46: 4846 1.46 - 1.58: 10271 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 22265 Sorted by residual: bond pdb=" C10 JC9 D 905 " pdb=" N1 JC9 D 905 " ideal model delta sigma weight residual 1.493 1.454 0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" C ARG D 672 " pdb=" O ARG D 672 " ideal model delta sigma weight residual 1.246 1.230 0.016 9.20e-03 1.18e+04 3.03e+00 bond pdb=" CA THR A 683 " pdb=" C THR A 683 " ideal model delta sigma weight residual 1.530 1.550 -0.019 1.12e-02 7.97e+03 2.95e+00 bond pdb=" CA PRO A 304 " pdb=" C PRO A 304 " ideal model delta sigma weight residual 1.517 1.528 -0.011 6.70e-03 2.23e+04 2.92e+00 bond pdb=" C1 NAG A 907 " pdb=" O5 NAG A 907 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 22260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 29732 1.71 - 3.42: 720 3.42 - 5.14: 108 5.14 - 6.85: 26 6.85 - 8.56: 8 Bond angle restraints: 30594 Sorted by residual: angle pdb=" C SER B 677 " pdb=" N PRO B 678 " pdb=" CA PRO B 678 " ideal model delta sigma weight residual 119.66 125.37 -5.71 7.20e-01 1.93e+00 6.30e+01 angle pdb=" C TRP B 390 " pdb=" N PRO B 391 " pdb=" CA PRO B 391 " ideal model delta sigma weight residual 119.28 127.84 -8.56 1.10e+00 8.26e-01 6.05e+01 angle pdb=" N ILE B 127 " pdb=" CA ILE B 127 " pdb=" C ILE B 127 " ideal model delta sigma weight residual 110.72 117.61 -6.89 1.01e+00 9.80e-01 4.65e+01 angle pdb=" N LEU B 334 " pdb=" CA LEU B 334 " pdb=" C LEU B 334 " ideal model delta sigma weight residual 113.02 120.78 -7.76 1.20e+00 6.94e-01 4.18e+01 angle pdb=" CA ASP D 675 " pdb=" C ASP D 675 " pdb=" N TYR D 676 " ideal model delta sigma weight residual 119.52 115.35 4.17 7.90e-01 1.60e+00 2.78e+01 ... (remaining 30589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 12111 16.72 - 33.44: 773 33.44 - 50.16: 246 50.16 - 66.88: 58 66.88 - 83.59: 12 Dihedral angle restraints: 13200 sinusoidal: 4139 harmonic: 9061 Sorted by residual: dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 175.65 -82.65 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual 93.00 16.23 76.77 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS C 420 " pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " pdb=" CB CYS C 454 " ideal model delta sinusoidal sigma weight residual 93.00 30.61 62.39 1 1.00e+01 1.00e-02 5.15e+01 ... (remaining 13197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3497 0.090 - 0.179: 276 0.179 - 0.269: 12 0.269 - 0.358: 4 0.358 - 0.448: 4 Chirality restraints: 3793 Sorted by residual: chirality pdb=" C1 NAG A 908 " pdb=" ND2 ASN A 471 " pdb=" C2 NAG A 908 " pdb=" O5 NAG A 908 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG A 906 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG A 906 " pdb=" O5 NAG A 906 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" C1 NAG C 906 " pdb=" ND2 ASN C 368 " pdb=" C2 NAG C 906 " pdb=" O5 NAG C 906 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 3790 not shown) Planarity restraints: 3892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 907 " -0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C 907 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 907 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG C 907 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG C 907 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 906 " -0.321 2.00e-02 2.50e+03 2.74e-01 9.35e+02 pdb=" C7 NAG A 906 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 906 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG A 906 " 0.478 2.00e-02 2.50e+03 pdb=" O7 NAG A 906 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " 0.170 2.00e-02 2.50e+03 1.40e-01 2.46e+02 pdb=" C7 NAG A 901 " -0.047 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " -0.226 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " -0.022 2.00e-02 2.50e+03 ... (remaining 3889 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 756 2.72 - 3.26: 22767 3.26 - 3.81: 35350 3.81 - 4.35: 39551 4.35 - 4.90: 69536 Nonbonded interactions: 167960 Sorted by model distance: nonbonded pdb=" CB SER B 677 " pdb=" CD PRO B 678 " model vdw 2.172 3.840 nonbonded pdb=" O PHE D 115 " pdb=" OG SER D 118 " model vdw 2.248 3.040 nonbonded pdb=" O SER A 126 " pdb=" OG SER A 129 " model vdw 2.270 3.040 nonbonded pdb=" O MET B 133 " pdb=" NE2 GLN B 146 " model vdw 2.273 3.120 nonbonded pdb=" CG2 ILE C 83 " pdb=" O ARG C 306 " model vdw 2.274 3.460 ... (remaining 167955 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 25 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 or (resid 43 through 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 or (resid 47 through 49 and ( \ name N or name CA or name C or name O or name CB )) or resid 50 through 73 or (r \ esid 74 through 75 and (name N or name CA or name C or name O or name CB )) or r \ esid 76 through 93 or (resid 94 and (name N or name CA or name C or name O or na \ me CB )) or resid 95 through 152 or (resid 153 and (name N or name CA or name C \ or name O or name CB )) or resid 154 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 through 208 or (resid 209 t \ hrough 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 232 or (resid 233 through 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 through 274 or (resid 275 and (name N or name CA or \ name C or name O or name CB )) or resid 276 through 353 or (resid 354 and (name \ N or name CA or name C or name O or name CB )) or resid 355 through 362 or (res \ id 363 and (name N or name CA or name C or name O or name CB )) or resid 364 thr \ ough 392 or (resid 393 through 394 and (name N or name CA or name C or name O or \ name CB )) or resid 395 through 421 or (resid 422 through 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 488 or (resid 489 a \ nd (name N or name CA or name C or name O or name CB )) or resid 490 through 542 \ or (resid 543 and (name N or name CA or name C or name O or name CB )) or resid \ 544 through 550 or (resid 551 through 556 and (name N or name CA or name C or n \ ame O or name CB )) or resid 557 through 572 or (resid 573 through 577 and (name \ N or name CA or name C or name O or name CB )) or resid 578 or (resid 579 throu \ gh 582 and (name N or name CA or name C or name O or name CB )) or resid 602 or \ (resid 603 through 607 and (name N or name CA or name C or name O or name CB )) \ or resid 608 through 625 or (resid 626 through 632 and (name N or name CA or nam \ e C or name O or name CB )) or resid 633 through 653 or (resid 654 through 659 a \ nd (name N or name CA or name C or name O or name CB )) or resid 660 through 661 \ or (resid 662 and (name N or name CA or name C or name O or name CB )) or resid \ 663 through 670 or (resid 671 and (name N or name CA or name C or name O or nam \ e CB )) or resid 672 through 675 or (resid 676 through 678 and (name N or name C \ A or name C or name O or name CB )) or resid 679 through 684 or (resid 685 throu \ gh 686 and (name N or name CA or name C or name O or name CB )) or resid 687 thr \ ough 693 or (resid 694 through 699 and (name N or name CA or name C or name O or \ name CB )) or resid 700 through 726 or (resid 727 through 728 and (name N or na \ me CA or name C or name O or name CB )) or resid 729 through 731 or (resid 732 a \ nd (name N or name CA or name C or name O or name CB )) or resid 733 through 780 \ or (resid 781 and (name N or name CA or name C or name O or name CB )) or resid \ 782 through 786 or (resid 787 and (name N or name CA or name C or name O or nam \ e CB )) or resid 788 through 789 or (resid 790 and (name N or name CA or name C \ or name O or name CB )) or resid 791 through 817 or (resid 818 through 821 and ( \ name N or name CA or name C or name O or name CB )) or (resid 822 through 829 an \ d (name N or name CA or name C or name O or name CB )) or resid 830 or (resid 83 \ 1 through 841 and (name N or name CA or name C or name O or name CB )) or resid \ 901 through 910)) selection = (chain 'C' and (resid 25 through 447 or (resid 448 through 449 and (name N or na \ me CA or name C or name O or name CB )) or resid 450 through 494 or (resid 495 t \ hrough 497 and (name N or name CA or name C or name O or name CB )) or resid 498 \ through 501 or (resid 502 and (name N or name CA or name C or name O or name CB \ )) or resid 503 through 561 or (resid 562 and (name N or name CA or name C or n \ ame O or name CB )) or resid 563 through 565 or (resid 566 and (name N or name C \ A or name C or name O or name CB )) or resid 567 or (resid 568 through 569 and ( \ name N or name CA or name C or name O or name CB )) or resid 570 through 603 or \ (resid 604 through 607 and (name N or name CA or name C or name O or name CB )) \ or resid 608 through 610 or (resid 611 and (name N or name CA or name C or name \ O or name CB )) or resid 612 through 630 or (resid 631 through 632 and (name N o \ r name CA or name C or name O or name CB )) or resid 633 through 638 or (resid 6 \ 39 through 643 and (name N or name CA or name C or name O or name CB )) or resid \ 644 through 812 or (resid 813 through 814 and (name N or name CA or name C or n \ ame O or name CB )) or resid 815 through 910)) } ncs_group { reference = (chain 'B' and (resid 34 through 74 or (resid 75 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 90 or (resid 91 and (na \ me N or name CA or name C or name O or name CB )) or (resid 92 through 95 and (n \ ame N or name CA or name C or name O or name CB )) or resid 96 through 106 or (r \ esid 107 through 108 and (name N or name CA or name C or name O or name CB )) or \ resid 109 through 113 or (resid 114 and (name N or name CA or name C or name O \ or name CB )) or resid 115 through 116 or (resid 117 and (name N or name CA or n \ ame C or name O or name CB )) or resid 118 through 127 or (resid 128 and (name N \ or name CA or name C or name O or name CB )) or resid 129 through 132 or (resid \ 133 and (name N or name CA or name C or name O or name CB )) or resid 134 throu \ gh 201 or (resid 202 and (name N or name CA or name C or name O or name CB )) or \ resid 203 through 287 or (resid 288 through 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 303 or (resid 304 through 306 and \ (name N or name CA or name C or name O or name CB )) or resid 307 through 309 o \ r (resid 310 through 313 and (name N or name CA or name C or name O or name CB ) \ ) or resid 314 through 318 or (resid 319 and (name N or name CA or name C or nam \ e O or name CB )) or resid 320 or (resid 321 and (name N or name CA or name C or \ name O or name CB )) or resid 322 through 332 or (resid 333 through 334 and (na \ me N or name CA or name C or name O or name CB )) or resid 335 through 337 or (r \ esid 338 and (name N or name CA or name C or name O or name CB )) or resid 339 t \ hrough 345 or (resid 346 and (name N or name CA or name C or name O or name CB ) \ ) or resid 347 through 372 or (resid 373 and (name N or name CA or name C or nam \ e O or name CB )) or resid 374 through 393 or (resid 394 through 395 and (name N \ or name CA or name C or name O or name CB )) or resid 396 through 398 or (resid \ 399 through 400 and (name N or name CA or name C or name O or name CB )) or res \ id 401 or (resid 402 through 404 and (name N or name CA or name C or name O or n \ ame CB )) or resid 405 through 468 or (resid 469 through 470 and (name N or name \ CA or name C or name O or name CB )) or resid 471 through 493 or (resid 494 and \ (name N or name CA or name C or name O or name CB )) or resid 495 through 510 o \ r (resid 511 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 12 through 522 or (resid 523 and (name N or name CA or name C or name O or name \ CB )) or resid 524 or (resid 525 and (name N or name CA or name C or name O or n \ ame CB )) or resid 526 through 537 or (resid 538 and (name N or name CA or name \ C or name O or name CB )) or resid 539 through 540 or (resid 541 and (name N or \ name CA or name C or name O or name CB )) or resid 542 through 610 or (resid 611 \ through 613 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 14 through 626 or (resid 627 through 629 and (name N or name CA or name C or nam \ e O or name CB )) or resid 630 through 638 or (resid 639 through 641 and (name N \ or name CA or name C or name O or name CB )) or resid 642 through 647 or (resid \ 648 through 651 and (name N or name CA or name C or name O or name CB )) or res \ id 652 through 660 or (resid 661 and (name N or name CA or name C or name O or n \ ame CB )) or resid 662 or (resid 663 and (name N or name CA or name C or name O \ or name CB )) or resid 664 through 666 or (resid 667 through 669 and (name N or \ name CA or name C or name O or name CB )) or resid 670 through 683 or (resid 684 \ through 685 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 86 through 688 or (resid 689 through 693 and (name N or name CA or name C or nam \ e O or name CB )) or resid 694 through 705 or (resid 706 through 707 and (name N \ or name CA or name C or name O or name CB )) or resid 708 through 724 or (resid \ 725 through 727 and (name N or name CA or name C or name O or name CB )) or res \ id 728 through 753 or (resid 754 through 757 and (name N or name CA or name C or \ name O or name CB )) or resid 758 through 820 or (resid 821 through 841 and (na \ me N or name CA or name C or name O or name CB )) or resid 901 through 904)) selection = (chain 'D' and (resid 34 through 105 or (resid 106 through 108 and (name N or na \ me CA or name C or name O or name CB )) or resid 109 through 209 or (resid 210 t \ hrough 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 220 or (resid 221 and (name N or name CA or name C or name O or name CB \ )) or resid 222 through 311 or (resid 312 through 313 and (name N or name CA or \ name C or name O or name CB )) or resid 314 through 325 or (resid 326 and (name \ N or name CA or name C or name O or name CB )) or resid 327 through 553 or (res \ id 554 through 557 and (name N or name CA or name C or name O or name CB )) or r \ esid 558 through 563 or (resid 564 and (name N or name CA or name C or name O or \ name CB )) or resid 565 through 566 or (resid 567 and (name N or name CA or nam \ e C or name O or name CB )) or resid 568 through 575 or (resid 576 through 599 a \ nd (name N or name CA or name C or name O or name CB )) or resid 600 or (resid 6 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 602 through \ 611 or (resid 612 through 613 and (name N or name CA or name C or name O or nam \ e CB )) or resid 614 through 639 or (resid 640 through 641 and (name N or name C \ A or name C or name O or name CB )) or resid 642 through 675 or (resid 676 throu \ gh 677 and (name N or name CA or name C or name O or name CB )) or resid 678 thr \ ough 821 or (resid 822 through 841 and (name N or name CA or name C or name O or \ name CB )) or resid 901 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: 2.180 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.830 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.003 0.054 22305 Z= 0.169 Angle : 0.683 27.172 30698 Z= 0.396 Chirality : 0.049 0.448 3793 Planarity : 0.008 0.302 3868 Dihedral : 13.081 83.595 7296 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.99 % Allowed : 1.75 % Favored : 95.26 % 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: -0.02 (0.16), residues: 3102 helix: 1.63 (0.15), residues: 1273 sheet: -1.64 (0.23), residues: 467 loop : -0.97 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 523 TYR 0.014 0.001 TYR B 730 PHE 0.020 0.001 PHE C 321 TRP 0.023 0.001 TRP D 198 HIS 0.005 0.000 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (22265) covalent geometry : angle 0.64220 / 0.39 (30594) SS BOND : bond 0.00538 / 0.27 ( 16) SS BOND : angle 2.60483 / 1.53 ( 32) hydrogen bonds : bond 0.15087 / 10.48 ( 1061) hydrogen bonds : angle 6.17242 / 4.60 ( 3072) link_NAG-ASN : bond 0.01505 / 1.18 ( 24) link_NAG-ASN : angle 4.56315 / 3.15 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8216 (ttp-110) REVERT: A 609 PHE cc_start: 0.6384 (t80) cc_final: 0.6013 (t80) REVERT: B 135 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8195 (ptm) REVERT: B 200 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8526 (tmm) REVERT: B 338 MET cc_start: 0.7898 (mmt) cc_final: 0.7590 (mmm) REVERT: C 240 MET cc_start: 0.8629 (mmt) cc_final: 0.8330 (mmp) REVERT: C 780 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.8821 (t-170) REVERT: C 813 MET cc_start: 0.4434 (mmt) cc_final: 0.3209 (mtm) REVERT: D 680 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6074 (t80) outliers start: 53 outliers final: 23 residues processed: 191 average time/residue: 0.1417 time to fit residues: 43.3324 Evaluate side-chains 160 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 198 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 680 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN A 650 ASN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 780 HIS ** D 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.075440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.052458 restraints weight = 83505.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053966 restraints weight = 43833.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054939 restraints weight = 30100.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055423 restraints weight = 24193.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.055840 restraints weight = 21436.027| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 22305 Z= 0.279 Angle : 0.631 8.741 30698 Z= 0.326 Chirality : 0.046 0.305 3793 Planarity : 0.004 0.060 3868 Dihedral : 7.533 66.632 3863 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer: Outliers : 1.69 % Allowed : 8.41 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.12 (0.16), residues: 3102 helix: 1.66 (0.15), residues: 1298 sheet: -1.77 (0.23), residues: 482 loop : -1.17 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 386 TYR 0.017 0.002 TYR B 730 PHE 0.032 0.002 PHE D 524 TRP 0.016 0.001 TRP B 378 HIS 0.011 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.28 (22265) covalent geometry : angle 0.62034 / 0.32 (30594) SS BOND : bond 0.00462 / 0.26 ( 16) SS BOND : angle 1.01934 / 0.77 ( 32) hydrogen bonds : bond 0.03885 / 2.73 ( 1061) hydrogen bonds : angle 4.79154 / 3.56 ( 3072) link_NAG-ASN : bond 0.00415 / 0.30 ( 24) link_NAG-ASN : angle 2.40979 / 1.73 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.776 Fit side-chains REVERT: A 74 MET cc_start: 0.9138 (tmm) cc_final: 0.8462 (tmm) REVERT: A 308 CYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5666 (t) REVERT: A 354 MET cc_start: 0.7636 (mmm) cc_final: 0.7325 (mtm) REVERT: A 397 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8151 (tpt170) REVERT: A 609 PHE cc_start: 0.6366 (t80) cc_final: 0.6016 (t80) REVERT: C 240 MET cc_start: 0.8976 (mmt) cc_final: 0.8586 (mmp) REVERT: C 470 MET cc_start: 0.8976 (ttm) cc_final: 0.8749 (ttm) REVERT: C 813 MET cc_start: 0.3570 (mmt) cc_final: 0.2655 (mtm) outliers start: 30 outliers final: 19 residues processed: 155 average time/residue: 0.1285 time to fit residues: 34.0010 Evaluate side-chains 146 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 136 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 306 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 256 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS A 196 GLN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.077110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054528 restraints weight = 82172.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056113 restraints weight = 42361.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057133 restraints weight = 28707.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057742 restraints weight = 22894.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.057994 restraints weight = 20066.081| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22305 Z= 0.105 Angle : 0.502 8.758 30698 Z= 0.258 Chirality : 0.042 0.222 3793 Planarity : 0.003 0.072 3868 Dihedral : 6.116 63.947 3819 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 1.30 % Allowed : 11.12 % Favored : 87.58 % 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: 0.09 (0.16), residues: 3102 helix: 1.91 (0.15), residues: 1296 sheet: -1.72 (0.22), residues: 502 loop : -1.09 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 386 TYR 0.012 0.001 TYR B 478 PHE 0.020 0.001 PHE D 524 TRP 0.009 0.001 TRP C 151 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (22265) covalent geometry : angle 0.49195 / 0.26 (30594) SS BOND : bond 0.00552 / 0.22 ( 16) SS BOND : angle 1.07934 / 0.87 ( 32) hydrogen bonds : bond 0.02989 / 2.08 ( 1061) hydrogen bonds : angle 4.34498 / 3.23 ( 3072) link_NAG-ASN : bond 0.00385 / 0.25 ( 24) link_NAG-ASN : angle 2.03329 / 1.50 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.9114 (tmm) cc_final: 0.8439 (tmm) REVERT: A 354 MET cc_start: 0.7569 (mmm) cc_final: 0.7314 (mtp) REVERT: A 609 PHE cc_start: 0.6348 (t80) cc_final: 0.6011 (t80) REVERT: C 240 MET cc_start: 0.8801 (mmt) cc_final: 0.8518 (mmp) REVERT: C 470 MET cc_start: 0.8766 (ttm) cc_final: 0.8415 (ttm) REVERT: C 813 MET cc_start: 0.3596 (mmt) cc_final: 0.2850 (mtm) outliers start: 23 outliers final: 15 residues processed: 150 average time/residue: 0.1254 time to fit residues: 32.8943 Evaluate side-chains 140 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 256 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 chunk 185 optimal weight: 0.2980 chunk 248 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN D 614 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.076595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053910 restraints weight = 82746.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055469 restraints weight = 42728.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.056338 restraints weight = 29155.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057028 restraints weight = 23585.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.057285 restraints weight = 20571.033| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22305 Z= 0.140 Angle : 0.502 8.322 30698 Z= 0.256 Chirality : 0.042 0.263 3793 Planarity : 0.003 0.069 3868 Dihedral : 5.443 54.466 3808 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 1.98 % Allowed : 12.03 % Favored : 86.00 % 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: 0.14 (0.16), residues: 3102 helix: 1.97 (0.15), residues: 1296 sheet: -1.65 (0.23), residues: 479 loop : -1.12 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 386 TYR 0.014 0.001 TYR B 478 PHE 0.021 0.001 PHE D 524 TRP 0.010 0.001 TRP B 378 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (22265) covalent geometry : angle 0.49301 / 0.25 (30594) SS BOND : bond 0.00229 / 0.14 ( 16) SS BOND : angle 1.06535 / 0.83 ( 32) hydrogen bonds : bond 0.02895 / 2.02 ( 1061) hydrogen bonds : angle 4.19271 / 3.11 ( 3072) link_NAG-ASN : bond 0.00339 / 0.24 ( 24) link_NAG-ASN : angle 1.95058 / 1.44 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.833 Fit side-chains REVERT: A 74 MET cc_start: 0.9157 (tmm) cc_final: 0.8358 (tmm) REVERT: A 354 MET cc_start: 0.7636 (mmm) cc_final: 0.7347 (mtp) REVERT: A 609 PHE cc_start: 0.6331 (t80) cc_final: 0.5964 (t80) REVERT: B 201 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8172 (mm-40) REVERT: B 518 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8494 (mtt180) REVERT: C 79 CYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6500 (t) REVERT: C 240 MET cc_start: 0.8810 (mmt) cc_final: 0.8600 (mmp) REVERT: C 470 MET cc_start: 0.8833 (ttm) cc_final: 0.8405 (ttm) REVERT: C 813 MET cc_start: 0.3631 (mmt) cc_final: 0.2899 (mtm) outliers start: 35 outliers final: 22 residues processed: 156 average time/residue: 0.1253 time to fit residues: 33.9625 Evaluate side-chains 150 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 257 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 165 optimal weight: 0.0970 chunk 82 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 277 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN D 766 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.077649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.055397 restraints weight = 82067.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057020 restraints weight = 42017.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.058011 restraints weight = 28290.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058523 restraints weight = 22489.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058953 restraints weight = 19883.372| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22305 Z= 0.086 Angle : 0.474 9.296 30698 Z= 0.239 Chirality : 0.042 0.266 3793 Planarity : 0.003 0.064 3868 Dihedral : 4.776 53.974 3804 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 1.64 % Allowed : 13.44 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.16), residues: 3102 helix: 2.07 (0.15), residues: 1298 sheet: -1.49 (0.23), residues: 478 loop : -1.07 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 386 TYR 0.010 0.001 TYR B 478 PHE 0.010 0.001 PHE D 524 TRP 0.010 0.001 TRP C 151 HIS 0.008 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (22265) covalent geometry : angle 0.46490 / 0.24 (30594) SS BOND : bond 0.00214 / 0.13 ( 16) SS BOND : angle 1.02607 / 0.79 ( 32) hydrogen bonds : bond 0.02475 / 1.72 ( 1061) hydrogen bonds : angle 3.96961 / 2.93 ( 3072) link_NAG-ASN : bond 0.00406 / 0.26 ( 24) link_NAG-ASN : angle 1.84313 / 1.35 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.9124 (tmm) cc_final: 0.8345 (tmm) REVERT: A 609 PHE cc_start: 0.6227 (t80) cc_final: 0.5852 (t80) REVERT: C 79 CYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6505 (t) REVERT: C 115 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8726 (mpt180) REVERT: C 470 MET cc_start: 0.8755 (ttm) cc_final: 0.8372 (ttm) REVERT: C 813 MET cc_start: 0.3692 (mmt) cc_final: 0.2816 (mtm) REVERT: D 904 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6075 (tp30) outliers start: 29 outliers final: 18 residues processed: 157 average time/residue: 0.1149 time to fit residues: 31.6931 Evaluate side-chains 149 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 85 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 152 optimal weight: 0.0670 chunk 280 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 52 optimal weight: 50.0000 chunk 39 optimal weight: 0.6980 chunk 264 optimal weight: 8.9990 overall best weight: 2.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.075635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.052549 restraints weight = 84757.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.054123 restraints weight = 43416.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055140 restraints weight = 29367.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055630 restraints weight = 23343.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056051 restraints weight = 20654.356| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22305 Z= 0.137 Angle : 0.494 8.203 30698 Z= 0.249 Chirality : 0.042 0.267 3793 Planarity : 0.003 0.059 3868 Dihedral : 4.761 54.215 3804 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 2.03 % Allowed : 13.78 % Favored : 84.19 % 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: 0.36 (0.16), residues: 3102 helix: 2.15 (0.15), residues: 1299 sheet: -1.48 (0.22), residues: 478 loop : -1.03 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 390 TYR 0.013 0.001 TYR B 478 PHE 0.018 0.001 PHE D 524 TRP 0.009 0.001 TRP B 378 HIS 0.008 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (22265) covalent geometry : angle 0.48578 / 0.25 (30594) SS BOND : bond 0.00196 / 0.13 ( 16) SS BOND : angle 0.99050 / 0.76 ( 32) hydrogen bonds : bond 0.02673 / 1.87 ( 1061) hydrogen bonds : angle 3.96741 / 2.95 ( 3072) link_NAG-ASN : bond 0.00332 / 0.23 ( 24) link_NAG-ASN : angle 1.86230 / 1.36 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.911 Fit side-chains REVERT: A 74 MET cc_start: 0.9191 (tmm) cc_final: 0.8288 (tmm) REVERT: A 354 MET cc_start: 0.7750 (mmm) cc_final: 0.7401 (mtp) REVERT: A 609 PHE cc_start: 0.6193 (t80) cc_final: 0.5842 (t80) REVERT: B 518 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8440 (mtt180) REVERT: C 79 CYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6636 (t) REVERT: C 125 MET cc_start: 0.8189 (mmt) cc_final: 0.7826 (mmm) REVERT: C 813 MET cc_start: 0.3692 (mmt) cc_final: 0.2904 (mtm) outliers start: 36 outliers final: 25 residues processed: 160 average time/residue: 0.1247 time to fit residues: 34.6324 Evaluate side-chains 153 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 188 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 219 optimal weight: 0.6980 chunk 256 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.075373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052441 restraints weight = 84104.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053995 restraints weight = 42901.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.054983 restraints weight = 29026.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055403 restraints weight = 23118.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055868 restraints weight = 20638.952| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22305 Z= 0.145 Angle : 0.501 8.149 30698 Z= 0.252 Chirality : 0.042 0.269 3793 Planarity : 0.003 0.055 3868 Dihedral : 4.776 53.907 3804 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 2.32 % Allowed : 14.06 % Favored : 83.63 % 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: 0.37 (0.16), residues: 3102 helix: 2.18 (0.15), residues: 1300 sheet: -1.57 (0.23), residues: 484 loop : -1.01 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.013 0.001 TYR B 478 PHE 0.021 0.001 PHE D 524 TRP 0.010 0.001 TRP A 768 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (22265) covalent geometry : angle 0.49209 / 0.25 (30594) SS BOND : bond 0.00245 / 0.15 ( 16) SS BOND : angle 0.99491 / 0.74 ( 32) hydrogen bonds : bond 0.02682 / 1.88 ( 1061) hydrogen bonds : angle 3.96855 / 2.95 ( 3072) link_NAG-ASN : bond 0.00337 / 0.23 ( 24) link_NAG-ASN : angle 1.88163 / 1.38 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.861 Fit side-chains REVERT: A 74 MET cc_start: 0.9163 (tmm) cc_final: 0.8341 (tmm) REVERT: A 354 MET cc_start: 0.7773 (mmm) cc_final: 0.7215 (mmm) REVERT: A 609 PHE cc_start: 0.6218 (t80) cc_final: 0.5851 (t80) REVERT: B 134 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 518 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8486 (mtt180) REVERT: B 524 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7819 (p90) REVERT: C 79 CYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6604 (t) REVERT: C 125 MET cc_start: 0.8244 (mmt) cc_final: 0.7901 (mmm) REVERT: C 240 MET cc_start: 0.8609 (mmp) cc_final: 0.8285 (mmt) REVERT: C 470 MET cc_start: 0.8379 (mtp) cc_final: 0.8147 (ttm) REVERT: C 813 MET cc_start: 0.3571 (mmt) cc_final: 0.2833 (mtm) outliers start: 41 outliers final: 30 residues processed: 165 average time/residue: 0.1236 time to fit residues: 35.4222 Evaluate side-chains 159 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 284 optimal weight: 10.0000 chunk 309 optimal weight: 40.0000 chunk 71 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 303 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 232 optimal weight: 50.0000 chunk 227 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.075348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.052404 restraints weight = 83776.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053936 restraints weight = 43025.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054924 restraints weight = 29166.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055511 restraints weight = 23221.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055760 restraints weight = 20385.914| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22305 Z= 0.142 Angle : 0.504 8.097 30698 Z= 0.254 Chirality : 0.043 0.292 3793 Planarity : 0.003 0.050 3868 Dihedral : 4.676 53.910 3802 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 2.20 % Allowed : 14.12 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.16), residues: 3102 helix: 2.20 (0.15), residues: 1301 sheet: -1.56 (0.23), residues: 484 loop : -1.02 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 386 TYR 0.013 0.001 TYR B 478 PHE 0.021 0.001 PHE D 524 TRP 0.009 0.001 TRP D 198 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (22265) covalent geometry : angle 0.49580 / 0.25 (30594) SS BOND : bond 0.00234 / 0.14 ( 16) SS BOND : angle 1.09462 / 0.86 ( 32) hydrogen bonds : bond 0.02673 / 1.88 ( 1061) hydrogen bonds : angle 3.97808 / 2.95 ( 3072) link_NAG-ASN : bond 0.00327 / 0.22 ( 24) link_NAG-ASN : angle 1.86072 / 1.37 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.855 Fit side-chains REVERT: A 74 MET cc_start: 0.9190 (tmm) cc_final: 0.8369 (tmm) REVERT: A 354 MET cc_start: 0.7842 (mmm) cc_final: 0.7208 (mmm) REVERT: A 609 PHE cc_start: 0.6162 (t80) cc_final: 0.5798 (t80) REVERT: B 518 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8495 (mtt180) REVERT: B 524 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7786 (p90) REVERT: C 79 CYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6594 (t) REVERT: C 125 MET cc_start: 0.8236 (mmt) cc_final: 0.7878 (mmm) REVERT: C 240 MET cc_start: 0.8566 (mmp) cc_final: 0.8171 (mmt) REVERT: C 470 MET cc_start: 0.8413 (mtp) cc_final: 0.7993 (ttm) REVERT: C 813 MET cc_start: 0.3545 (mmt) cc_final: 0.2807 (mtm) outliers start: 39 outliers final: 31 residues processed: 162 average time/residue: 0.1231 time to fit residues: 34.8338 Evaluate side-chains 160 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 50.0000 chunk 224 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 133 optimal weight: 50.0000 chunk 156 optimal weight: 20.0000 chunk 56 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.074432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.051176 restraints weight = 85013.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.052715 restraints weight = 43979.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.053667 restraints weight = 29942.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054094 restraints weight = 24004.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054550 restraints weight = 21418.219| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22305 Z= 0.199 Angle : 0.546 7.931 30698 Z= 0.277 Chirality : 0.043 0.291 3793 Planarity : 0.003 0.047 3868 Dihedral : 4.952 53.907 3802 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 2.15 % Allowed : 14.40 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 3102 helix: 2.13 (0.15), residues: 1311 sheet: -1.68 (0.22), residues: 503 loop : -1.04 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 518 TYR 0.015 0.001 TYR B 478 PHE 0.031 0.001 PHE D 524 TRP 0.011 0.001 TRP B 558 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (22265) covalent geometry : angle 0.53709 / 0.28 (30594) SS BOND : bond 0.00241 / 0.16 ( 16) SS BOND : angle 1.19621 / 0.93 ( 32) hydrogen bonds : bond 0.02957 / 2.07 ( 1061) hydrogen bonds : angle 4.08405 / 3.03 ( 3072) link_NAG-ASN : bond 0.00316 / 0.23 ( 24) link_NAG-ASN : angle 1.97386 / 1.45 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.875 Fit side-chains REVERT: A 74 MET cc_start: 0.9208 (tmm) cc_final: 0.8304 (tmm) REVERT: A 354 MET cc_start: 0.7883 (mmm) cc_final: 0.7448 (mtp) REVERT: A 609 PHE cc_start: 0.6104 (t80) cc_final: 0.5754 (t80) REVERT: B 135 MET cc_start: 0.7971 (ptt) cc_final: 0.7757 (ptt) REVERT: B 518 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8383 (mtt180) REVERT: C 79 CYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6598 (t) REVERT: C 125 MET cc_start: 0.8255 (mmt) cc_final: 0.7926 (mmm) REVERT: C 240 MET cc_start: 0.8571 (mmp) cc_final: 0.8209 (mmt) REVERT: C 470 MET cc_start: 0.8477 (mtp) cc_final: 0.7942 (ttm) REVERT: C 813 MET cc_start: 0.3565 (mmt) cc_final: 0.2831 (mtm) outliers start: 38 outliers final: 31 residues processed: 162 average time/residue: 0.1224 time to fit residues: 34.4792 Evaluate side-chains 158 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 59 optimal weight: 50.0000 chunk 116 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.0060 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.075402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052478 restraints weight = 84222.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054041 restraints weight = 42870.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.055036 restraints weight = 28982.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055557 restraints weight = 23110.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055945 restraints weight = 20439.903| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22305 Z= 0.115 Angle : 0.500 8.010 30698 Z= 0.252 Chirality : 0.042 0.320 3793 Planarity : 0.003 0.045 3868 Dihedral : 4.705 53.832 3802 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 1.69 % Allowed : 15.02 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 3102 helix: 2.22 (0.15), residues: 1309 sheet: -1.58 (0.23), residues: 486 loop : -1.06 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 386 TYR 0.013 0.001 TYR B 478 PHE 0.019 0.001 PHE D 170 TRP 0.017 0.001 TRP B 558 HIS 0.008 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (22265) covalent geometry : angle 0.49195 / 0.25 (30594) SS BOND : bond 0.00211 / 0.13 ( 16) SS BOND : angle 1.09407 / 0.87 ( 32) hydrogen bonds : bond 0.02597 / 1.83 ( 1061) hydrogen bonds : angle 3.96637 / 2.94 ( 3072) link_NAG-ASN : bond 0.00350 / 0.23 ( 24) link_NAG-ASN : angle 1.84647 / 1.35 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.896 Fit side-chains REVERT: A 74 MET cc_start: 0.9205 (tmm) cc_final: 0.8363 (tmm) REVERT: A 354 MET cc_start: 0.7821 (mmm) cc_final: 0.7430 (mtp) REVERT: A 609 PHE cc_start: 0.6090 (t80) cc_final: 0.5746 (t80) REVERT: B 518 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8444 (mtt180) REVERT: B 524 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7920 (p90) REVERT: B 637 PHE cc_start: 0.8006 (t80) cc_final: 0.7602 (t80) REVERT: C 79 CYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6580 (t) REVERT: C 125 MET cc_start: 0.8219 (mmt) cc_final: 0.7878 (mmm) REVERT: C 155 MET cc_start: 0.8541 (mmp) cc_final: 0.8296 (mmm) REVERT: C 240 MET cc_start: 0.8558 (mmp) cc_final: 0.8148 (mmt) REVERT: C 470 MET cc_start: 0.8395 (mtp) cc_final: 0.7923 (ttm) REVERT: C 813 MET cc_start: 0.3591 (mmt) cc_final: 0.2831 (mtm) outliers start: 30 outliers final: 26 residues processed: 155 average time/residue: 0.1215 time to fit residues: 32.5699 Evaluate side-chains 155 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 1 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 153 optimal weight: 0.0470 chunk 243 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.075297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.052366 restraints weight = 84510.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053918 restraints weight = 43136.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054889 restraints weight = 29194.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055465 restraints weight = 23396.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055739 restraints weight = 20535.077| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22305 Z= 0.129 Angle : 0.504 7.816 30698 Z= 0.254 Chirality : 0.042 0.275 3793 Planarity : 0.003 0.044 3868 Dihedral : 4.652 53.972 3802 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 1.69 % Allowed : 14.91 % Favored : 83.40 % 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: 0.41 (0.16), residues: 3102 helix: 2.25 (0.15), residues: 1308 sheet: -1.63 (0.22), residues: 504 loop : -1.00 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 386 TYR 0.013 0.001 TYR B 478 PHE 0.020 0.001 PHE D 524 TRP 0.015 0.001 TRP B 558 HIS 0.008 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (22265) covalent geometry : angle 0.49552 / 0.25 (30594) SS BOND : bond 0.00199 / 0.13 ( 16) SS BOND : angle 1.21857 / 0.92 ( 32) hydrogen bonds : bond 0.02600 / 1.83 ( 1061) hydrogen bonds : angle 3.93142 / 2.92 ( 3072) link_NAG-ASN : bond 0.00335 / 0.23 ( 24) link_NAG-ASN : angle 1.84514 / 1.35 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.11 seconds wall clock time: 67 minutes 13.39 seconds (4033.39 seconds total)