Starting phenix.real_space_refine on Mon May 4 20:52:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unn_64357/05_2026/9unn_64357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unn_64357/05_2026/9unn_64357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9unn_64357/05_2026/9unn_64357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unn_64357/05_2026/9unn_64357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9unn_64357/05_2026/9unn_64357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unn_64357/05_2026/9unn_64357.map" } resolution = 3.29 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= 0.008 sd= 0.031 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 125 5.16 5 Cl 1 4.86 5 C 15072 2.51 5 N 3901 2.21 5 O 4317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23416 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5756 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 34, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 511 Unresolved non-hydrogen angles: 614 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 27, 'GLN:plan1': 7, 'TRP:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 11, 'PHE:plan': 5, 'HIS:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 334 Chain: "B" Number of atoms: 5603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5603 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 30, 'TRANS': 760} Chain breaks: 1 Unresolved non-hydrogen bonds: 669 Unresolved non-hydrogen angles: 822 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'HIS:plan': 5, 'GLU:plan': 32, 'ARG:plan': 15, 'TRP:plan': 1, 'GLN:plan1': 9, 'ASP:plan': 23, 'PHE:plan': 8, 'TYR:plan': 5, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 446 Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 5866 Classifications: {'peptide': 794} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 34, 'TRANS': 759} Chain breaks: 2 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 22, 'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 9, 'PHE:plan': 4, 'HIS:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 286 Chain: "D" Number of atoms: 5799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5799 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 30, 'TRANS': 764} Chain breaks: 1 Unresolved non-hydrogen bonds: 506 Unresolved non-hydrogen angles: 627 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 37, 'ARG:plan': 12, 'GLN:plan1': 4, 'ASN:plan1': 9, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 354 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {'NAG': 8} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.66, per 1000 atoms: 0.24 Number of scatterers: 23416 At special positions: 0 Unit cell: (113.94, 142.425, 184.625, 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 125 16.00 O 4317 8.00 N 3901 7.00 C 15072 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=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 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=2.03 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 471 " " NAG A 908 " - " ASN A 771 " " NAG B 901 " - " ASN B 340 " " NAG B 902 " - " ASN B 687 " " NAG B 903 " - " ASN B 380 " " NAG B 904 " - " ASN B 444 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 368 " " NAG C 904 " - " ASN C 471 " " NAG C 905 " - " ASN C 771 " " NAG C 906 " - " ASN C 239 " " NAG C 907 " - " ASN C 276 " " NAG C 908 " - " ASN C 350 " " NAG C 909 " - " ASN C 300 " " NAG D 901 " - " ASN D 340 " " NAG D 902 " - " ASN D 380 " " NAG D 903 " - " ASN D 687 " " NAG D 904 " - " ASN D 75 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 33 sheets defined 45.2% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 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 103 through 114 removed outlier: 3.963A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.625A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 170 through 185 removed outlier: 4.209A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.824A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 251 through 254 removed outlier: 3.521A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.901A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.677A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 615 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 709 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.979A pdb=" N LEU A 808 " --> pdb=" O PRO A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 822 Processing helix chain 'A' and resid 822 through 838 removed outlier: 3.919A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 55 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.757A pdb=" N ALA B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.515A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 287 through 310 Processing helix chain 'B' and resid 334 through 340 Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 516 through 522 removed outlier: 3.783A pdb=" N GLU B 520 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 580 Processing helix chain 'B' and resid 600 through 613 Processing helix chain 'B' and resid 624 through 655 Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 707 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 743 through 745 No H-bonds generated for 'chain 'B' and resid 743 through 745' Processing helix chain 'B' and resid 770 through 786 removed outlier: 4.309A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 814 through 816 No H-bonds generated for 'chain 'B' and resid 814 through 816' Processing helix chain 'B' and resid 817 through 840 removed outlier: 3.748A pdb=" N PHE B 821 " --> pdb=" O MET B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.806A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 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 158 removed outlier: 4.094A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.509A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 277 through 296 Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.079A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.584A pdb=" N GLY C 418 " --> pdb=" O MET C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.660A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 615 Processing helix chain 'C' and resid 626 through 657 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 710 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 767 through 782 removed outlier: 4.672A pdb=" N ASN C 771 " --> pdb=" O PRO C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 810 through 822 removed outlier: 3.546A pdb=" N ALA C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 838 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 106 through 121 removed outlier: 4.281A pdb=" N ALA D 110 " --> pdb=" O GLN D 106 " (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 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 287 through 310 Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.743A pdb=" N THR D 333 " --> pdb=" O PRO D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'D' and resid 515 through 520 Processing helix chain 'D' and resid 555 through 580 removed outlier: 4.087A pdb=" N VAL D 559 " --> pdb=" O ALA D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 613 Processing helix chain 'D' and resid 624 through 655 Processing helix chain 'D' and resid 667 through 672 Processing helix chain 'D' and resid 673 through 676 removed outlier: 3.767A pdb=" N TYR D 676 " --> pdb=" O PRO D 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 673 through 676' Processing helix chain 'D' and resid 688 through 698 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 722 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 742 through 745 removed outlier: 3.543A pdb=" N CYS D 745 " --> pdb=" O ASP D 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 742 through 745' Processing helix chain 'D' and resid 770 through 785 removed outlier: 4.520A pdb=" N GLN D 774 " --> pdb=" O PRO D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 795 Processing helix chain 'D' and resid 798 through 803 removed outlier: 3.978A pdb=" N ASN D 802 " --> pdb=" O GLY D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 843 removed outlier: 4.157A pdb=" N MET D 823 " --> pdb=" O GLY D 819 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 824 " --> pdb=" O VAL D 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.801A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 197 removed outlier: 7.713A pdb=" N ILE A 163 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 194 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 165 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLN A 196 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 167 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 218 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP A 247 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU A 269 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL A 249 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N LEU A 271 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 478 removed outlier: 5.619A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.681A pdb=" N CYS A 455 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 529 removed outlier: 4.232A pdb=" N GLU A 528 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET A 762 " --> pdb=" O GLU A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.685A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.947A pdb=" N ILE B 36 " --> pdb=" O VAL B 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.309A pdb=" N LEU B 40 " --> pdb=" O MET B 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.064A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 199 through 205 removed outlier: 7.927A pdb=" N LEU B 172 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 203 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR B 174 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR B 205 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 256 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 362 through 367 removed outlier: 4.588A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 406 through 409 removed outlier: 7.201A pdb=" N LEU B 406 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N TYR B 478 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 408 " --> pdb=" O TYR B 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 421 removed outlier: 3.753A pdb=" N VAL B 440 " --> pdb=" O MET B 450 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 434 " --> pdb=" O CYS B 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 487 through 489 Processing sheet with id=AB7, first strand: chain 'B' and resid 507 through 513 removed outlier: 7.963A pdb=" N GLY B 510 " --> pdb=" O ALA B 764 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 764 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU B 512 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA B 757 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 533 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER B 538 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ASP B 726 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG B 681 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 727 " --> pdb=" O ARG B 681 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 507 through 513 removed outlier: 7.963A pdb=" N GLY B 510 " --> pdb=" O ALA B 764 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 764 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU B 512 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA B 757 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 533 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 544 through 545 removed outlier: 4.030A pdb=" N SER B 545 " --> pdb=" O PHE B 658 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N PHE B 658 " --> pdb=" O SER B 545 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 59 through 66 removed outlier: 6.324A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N TYR C 88 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL C 92 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 32 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 195 through 197 removed outlier: 7.977A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.667A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 341 through 342 Processing sheet with id=AC5, first strand: chain 'C' and resid 474 through 476 removed outlier: 6.473A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 410 through 413 removed outlier: 3.807A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 486 through 488 removed outlier: 3.549A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AC9, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.534A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 66 through 73 removed outlier: 6.019A pdb=" N LEU D 34 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL D 70 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE D 36 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU D 72 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D 38 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY D 97 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 199 through 206 removed outlier: 8.263A pdb=" N PHE D 170 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 206 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR D 174 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL D 169 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU D 228 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER D 171 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR D 230 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL D 173 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 256 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 279 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL D 363 " --> pdb=" O VAL D 375 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 475 through 479 removed outlier: 3.721A pdb=" N ILE D 408 " --> pdb=" O ASP D 476 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.503A pdb=" N LYS D 454 " --> pdb=" O CYS D 436 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD6, first strand: chain 'D' and resid 727 through 731 removed outlier: 3.509A pdb=" N VAL D 537 " --> pdb=" O VAL D 748 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 3270 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: 4.49 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7497 1.34 - 1.46: 5624 1.46 - 1.58: 10611 1.58 - 1.70: 0 1.70 - 1.82: 213 Bond restraints: 23945 Sorted by residual: bond pdb=" C5 JC9 B 906 " pdb=" O1 JC9 B 906 " ideal model delta sigma weight residual 1.217 1.418 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" N VAL C 65 " pdb=" CA VAL C 65 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N ASP C 81 " pdb=" CA ASP C 81 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.24e-02 6.50e+03 9.41e+00 bond pdb=" N ILE C 83 " pdb=" CA ILE C 83 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.07e+00 bond pdb=" N ILE C 72 " pdb=" CA ILE C 72 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.78e+00 ... (remaining 23940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 32392 2.28 - 4.55: 333 4.55 - 6.83: 33 6.83 - 9.11: 8 9.11 - 11.38: 2 Bond angle restraints: 32768 Sorted by residual: angle pdb=" CA ASP C 81 " pdb=" CB ASP C 81 " pdb=" CG ASP C 81 " ideal model delta sigma weight residual 112.60 117.56 -4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" C ALA D 548 " pdb=" CA ALA D 548 " pdb=" CB ALA D 548 " ideal model delta sigma weight residual 115.89 110.47 5.42 1.32e+00 5.74e-01 1.69e+01 angle pdb=" C ASN D 541 " pdb=" CA ASN D 541 " pdb=" CB ASN D 541 " ideal model delta sigma weight residual 116.34 110.75 5.59 1.40e+00 5.10e-01 1.60e+01 angle pdb=" C6 JC9 B 906 " pdb=" C5 JC9 B 906 " pdb=" O1 JC9 B 906 " ideal model delta sigma weight residual 121.29 109.91 11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C1 JC9 B 906 " pdb=" C5 JC9 B 906 " pdb=" O1 JC9 B 906 " ideal model delta sigma weight residual 121.39 110.40 10.99 3.00e+00 1.11e-01 1.34e+01 ... (remaining 32763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 13991 32.55 - 65.09: 312 65.09 - 97.64: 19 97.64 - 130.18: 2 130.18 - 162.73: 4 Dihedral angle restraints: 14328 sinusoidal: 5142 harmonic: 9186 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 93.00 178.83 -85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual 93.00 175.74 -82.74 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS D 87 " pdb=" SG CYS D 87 " pdb=" SG CYS D 320 " pdb=" CB CYS D 320 " ideal model delta sinusoidal sigma weight residual 93.00 155.22 -62.22 1 1.00e+01 1.00e-02 5.13e+01 ... (remaining 14325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3586 0.074 - 0.149: 386 0.149 - 0.223: 10 0.223 - 0.297: 1 0.297 - 0.371: 1 Chirality restraints: 3984 Sorted by residual: chirality pdb=" C1 NAG A 908 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG A 908 " pdb=" O5 NAG A 908 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C1 NAG D 902 " pdb=" ND2 ASN D 380 " pdb=" C2 NAG D 902 " pdb=" O5 NAG D 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA VAL C 78 " pdb=" N VAL C 78 " pdb=" C VAL C 78 " pdb=" CB VAL C 78 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3981 not shown) Planarity restraints: 4149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 JC9 B 906 " 0.113 2.00e-02 2.50e+03 1.99e-01 3.95e+02 pdb=" C5 JC9 B 906 " -0.344 2.00e-02 2.50e+03 pdb=" C6 JC9 B 906 " 0.112 2.00e-02 2.50e+03 pdb=" O1 JC9 B 906 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 277 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C GLU C 277 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU C 277 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 278 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 546 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 547 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " -0.028 5.00e-02 4.00e+02 ... (remaining 4146 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3618 2.76 - 3.29: 23826 3.29 - 3.83: 40305 3.83 - 4.36: 44639 4.36 - 4.90: 77841 Nonbonded interactions: 190229 Sorted by model distance: nonbonded pdb=" OE2 GLU A 528 " pdb=" NZ LYS A 769 " model vdw 2.224 3.120 nonbonded pdb=" OE2 GLU D 420 " pdb=" NZ LYS D 457 " model vdw 2.244 3.120 nonbonded pdb=" O ASP C 198 " pdb=" OG1 THR C 201 " model vdw 2.283 3.040 nonbonded pdb=" O VAL D 339 " pdb=" OG SER D 349 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASP D 421 " pdb=" NZ LYS D 454 " model vdw 2.288 3.120 ... (remaining 190224 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 184 or (resid 185 through 188 and (name N or na \ me CA or name C or name O or name CB )) or resid 189 through 336 or (resid 337 a \ nd (name N or name CA or name C or name O or name CB )) or resid 338 through 386 \ or (resid 387 through 388 and (name N or name CA or name C or name O or name CB \ )) or resid 389 or (resid 390 and (name N or name CA or name C or name O or nam \ e CB )) or resid 391 through 411 or (resid 412 and (name N or name CA or name C \ or name O or name CB )) or resid 413 through 543 or (resid 544 through 545 and ( \ name N or name CA or name C or name O or name CB )) or resid 546 through 563 or \ (resid 564 and (name N or name CA or name C or name O or name CB )) or resid 565 \ through 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 580 or (resid 581 through 582 and (name N o \ r name CA or name C or name O or name CB )) or resid 583 through 606 or (resid 6 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 608 through \ 658 or (resid 659 and (name N or name CA or name C or name O or name CB )) or r \ esid 660 through 672 or (resid 673 through 674 and (name N or name CA or name C \ or name O or name CB )) or resid 675 through 702 or (resid 703 through 704 and ( \ name N or name CA or name C or name O or name CB )) or resid 705 through 722 or \ (resid 723 through 725 and (name N or name CA or name C or name O or name CB )) \ or resid 726 or (resid 727 through 728 and (name N or name CA or name C or name \ O or name CB )) or resid 729 through 909)) selection = (chain 'C' and (resid 25 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 55 or (resid 56 throu \ gh 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throu \ gh 69 or (resid 70 through 71 and (name N or name CA or name C or name O or name \ CB )) or resid 72 through 79 or (resid 80 through 81 and (name N or name CA or \ name C or name O or name CB )) or resid 82 through 130 or (resid 131 and (name N \ or name CA or name C or name O or name CB )) or resid 132 through 158 or (resid \ 159 and (name N or name CA or name C or name O or name CB )) or resid 160 throu \ gh 182 or (resid 183 and (name N or name CA or name C or name O or name CB )) or \ resid 184 through 191 or (resid 192 through 193 and (name N or name CA or name \ C or name O or name CB )) or resid 194 through 197 or (resid 198 and (name N or \ name CA or name C or name O or name CB )) or resid 199 through 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 2 \ 25 or (resid 226 and (name N or name CA or name C or name O or name CB )) or res \ id 227 through 250 or (resid 251 and (name N or name CA or name C or name O or n \ ame CB )) or resid 252 or (resid 253 and (name N or name CA or name C or name O \ or name CB )) or resid 254 through 296 or (resid 297 through 299 and (name N or \ name CA or name C or name O or name CB )) or resid 300 through 321 or (resid 322 \ through 323 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 24 through 328 or (resid 329 and (name N or name CA or name C or name O or name \ CB )) or resid 330 through 370 or (resid 371 and (name N or name CA or name C or \ name O or name CB )) or resid 372 through 376 or (resid 377 through 378 and (na \ me N or name CA or name C or name O or name CB )) or resid 379 through 393 or (r \ esid 394 and (name N or name CA or name C or name O or name CB )) or resid 395 t \ hrough 398 or (resid 399 and (name N or name CA or name C or name O or name CB ) \ ) or resid 400 through 405 or (resid 406 and (name N or name CA or name C or nam \ e O or name CB )) or resid 407 through 487 or (resid 488 through 490 and (name N \ or name CA or name C or name O or name CB )) or resid 491 through 493 or (resid \ 494 through 497 and (name N or name CA or name C or name O or name CB )) or res \ id 498 through 542 or (resid 543 through 545 and (name N or name CA or name C or \ name O or name CB )) or resid 546 through 568 or (resid 569 and (name N or name \ CA or name C or name O or name CB )) or resid 570 through 581 or (resid 582 and \ (name N or name CA or name C or name O or name CB )) or resid 583 through 624 o \ r (resid 625 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 26 through 676 or (resid 677 through 678 and (name N or name CA or name C or nam \ e O or name CB )) or resid 679 through 684 or (resid 685 and (name N or name CA \ or name C or name O or name CB )) or resid 686 through 701 or (resid 702 through \ 704 and (name N or name CA or name C or name O or name CB )) or resid 705 or (r \ esid 706 through 709 and (name N or name CA or name C or name O or name CB )) or \ resid 710 through 718 or (resid 719 through 720 and (name N or name CA or name \ C or name O or name CB )) or resid 721 through 793 or (resid 794 and (name N or \ name CA or name C or name O or name CB )) or resid 795 through 816 or (resid 817 \ through 819 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 20 through 838 or resid 902 through 910)) } ncs_group { reference = (chain 'B' and (resid 33 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB )) or resid 46 or (resid 47 through 52 and (name N or nam \ e CA or name C or name O or name CB )) or resid 53 or (resid 54 through 55 and ( \ name N or name CA or name C or name O or name CB )) or resid 56 through 106 or ( \ resid 107 through 108 and (name N or name CA or name C or name O or name CB )) o \ r resid 109 through 180 or (resid 181 and (name N or name CA or name C or name O \ or name CB )) or resid 182 through 201 or (resid 202 and (name N or name CA or \ name C or name O or name CB )) or resid 203 through 207 or (resid 208 through 21 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 215 through \ 244 or (resid 245 and (name N or name CA or name C or name O or name CB )) or re \ sid 246 through 263 or (resid 264 and (name N or name CA or name C or name O or \ name CB )) or resid 265 through 270 or (resid 271 and (name N or name CA or name \ C or name O or name CB )) or resid 272 through 282 or (resid 283 and (name N or \ name CA or name C or name O or name CB )) or resid 284 or (resid 285 and (name \ N or name CA or name C or name O or name CB )) or resid 286 through 288 or (resi \ d 289 through 291 and (name N or name CA or name C or name O or name CB )) or re \ sid 292 through 310 or (resid 311 through 312 and (name N or name CA or name C o \ r name O or name CB )) or resid 313 through 314 or (resid 315 through 318 and (n \ ame N or name CA or name C or name O or name CB )) or resid 319 through 330 or ( \ resid 331 through 332 and (name N or name CA or name C or name O or name CB )) o \ r resid 333 through 372 or (resid 373 through 374 and (name N or name CA or name \ C or name O or name CB )) or resid 375 through 378 or (resid 379 and (name N or \ name CA or name C or name O or name CB )) or resid 380 through 394 or (resid 39 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 396 through \ 403 or (resid 404 and (name N or name CA or name C or name O or name CB )) or re \ sid 405 through 436 or (resid 437 through 438 and (name N or name CA or name C o \ r name O or name CB )) or resid 439 or (resid 440 through 443 and (name N or nam \ e CA or name C or name O or name CB )) or resid 444 through 468 or (resid 469 an \ d (name N or name CA or name C or name O or name CB )) or resid 470 through 480 \ or (resid 481 and (name N or name CA or name C or name O or name CB )) or resid \ 482 through 519 or (resid 520 and (name N or name CA or name C or name O or name \ CB )) or resid 521 through 539 or (resid 540 and (name N or name CA or name C o \ r name O or name CB )) or resid 541 through 558 or (resid 559 through 560 and (n \ ame N or name CA or name C or name O or name CB )) or resid 561 through 577 or ( \ resid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 \ through 581 or resid 600 through 602 or (resid 603 through 604 and (name N or na \ me CA or name C or name O or name CB )) or resid 605 through 631 or (resid 632 a \ nd (name N or name CA or name C or name O or name CB )) or resid 633 through 657 \ or (resid 658 through 659 and (name N or name CA or name C or name O or name CB \ )) or resid 660 through 662 or (resid 663 and (name N or name CA or name C or n \ ame O or name CB )) or resid 664 through 699 or (resid 700 through 701 and (name \ N or name CA or name C or name O or name CB )) or resid 702 through 789 or (res \ id 790 and (name N or name CA or name C or name O or name CB )) or resid 791 thr \ ough 806 or (resid 807 through 808 and (name N or name CA or name C or name O or \ name CB )) or resid 809 through 816 or (resid 817 through 818 and (name N or na \ me CA or name C or name O or name CB )) or resid 819 through 905)) selection = (chain 'D' and ((resid 33 through 34 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 41 or (resid 42 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 50 or (resid 51 throug \ h 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throug \ h 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or re \ sid 56 through 65 or (resid 66 and (name N or name CA or name C or name O or nam \ e CB )) or resid 67 through 73 or (resid 74 and (name N or name CA or name C or \ name O or name CB )) or resid 75 through 77 or (resid 78 and (name N or name CA \ or name C or name O or name CB )) or resid 79 through 89 or (resid 90 and (name \ N or name CA or name C or name O or name CB )) or resid 91 through 101 or (resid \ 102 through 103 and (name N or name CA or name C or name O or name CB )) or res \ id 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 137 or (resid 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 187 or (resid 188 and (name N or name CA or n \ ame C or name O or name CB )) or resid 189 through 191 or (resid 192 and (name N \ or name CA or name C or name O or name CB )) or resid 193 through 194 or (resid \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throu \ gh 208 or (resid 209 through 214 and (name N or name CA or name C or name O or n \ ame CB )) or resid 215 through 241 or (resid 242 through 243 and (name N or name \ CA or name C or name O or name CB )) or resid 244 through 250 or (resid 251 thr \ ough 252 and (name N or name CA or name C or name O or name CB )) or resid 253 t \ hrough 280 or (resid 281 and (name N or name CA or name C or name O or name CB ) \ ) or resid 282 through 290 or (resid 291 and (name N or name CA or name C or nam \ e O or name CB )) or resid 292 through 305 or (resid 306 and (name N or name CA \ or name C or name O or name CB )) or resid 307 through 308 or (resid 309 through \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throu \ gh 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) or \ resid 361 through 373 or (resid 374 and (name N or name CA or name C or name O \ or name CB )) or resid 375 through 376 or (resid 377 and (name N or name CA or n \ ame C or name O or name CB )) or resid 378 through 380 or (resid 381 through 382 \ and (name N or name CA or name C or name O or name CB )) or resid 383 through 3 \ 88 or (resid 389 and (name N or name CA or name C or name O or name CB )) or res \ id 390 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 397 or (resid 398 and (name N or name \ CA or name C or name O or name CB )) or resid 399 through 401 or (resid 402 thr \ ough 404 and (name N or name CA or name C or name O or name CB )) or resid 405 t \ hrough 419 or (resid 420 through 421 and (name N or name CA or name C or name O \ or name CB )) or resid 422 or (resid 423 and (name N or name CA or name C or nam \ e O or name CB )) or resid 424 through 427 or (resid 428 and (name N or name CA \ or name C or name O or name CB )) or resid 429 through 437 or (resid 438 and (na \ me N or name CA or name C or name O or name CB )) or resid 439 through 449 or (r \ esid 450 through 451 and (name N or name CA or name C or name O or name CB )) or \ resid 452 through 456 or (resid 457 and (name N or name CA or name C or name O \ or name CB )) or resid 458 through 475 or (resid 476 and (name N or name CA or n \ ame C or name O or name CB )) or resid 477 through 487 or (resid 488 through 491 \ and (name N or name CA or name C or name O or name CB )) or resid 492 through 5 \ 02 or (resid 503 and (name N or name CA or name C or name O or name CB )) or res \ id 504 through 516 or (resid 517 and (name N or name CA or name C or name O or n \ ame CB )) or resid 518 through 553 or (resid 554 through 556 and (name N or name \ CA or name C or name O or name CB )) or resid 557 through 559 or (resid 560 and \ (name N or name CA or name C or name O or name CB )) or resid 561 through 575 o \ r (resid 576 through 578 and (name N or name CA or name C or name O or name CB ) \ ) or resid 579 through 581 or resid 600 through 607 or (resid 608 and (name N or \ name CA or name C or name O or name CB )) or resid 609 through 619 or (resid 62 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 621 through \ 658 or (resid 659 and (name N or name CA or name C or name O or name CB )) or re \ sid 660 through 668 or (resid 669 and (name N or name CA or name C or name O or \ name CB )) or resid 670 through 673 or (resid 674 through 677 and (name N or nam \ e CA or name C or name O or name CB )) or resid 678 through 690 or (resid 691 th \ rough 692 and (name N or name CA or name C or name O or name CB )) or resid 693 \ through 694 or (resid 695 and (name N or name CA or name C or name O or name CB \ )) or resid 696 through 700 or (resid 701 and (name N or name CA or name C or na \ me O or name CB )) or resid 702 or (resid 703 and (name N or name CA or name C o \ r name O or name CB )) or resid 704 or (resid 705 and (name N or name CA or name \ C or name O or name CB )) or resid 706 through 714 or (resid 715 through 716 an \ d (name N or name CA or name C or name O or name CB )) or resid 717 through 720 \ or (resid 721 and (name N or name CA or name C or name O or name CB )) or resid \ 722 through 724 or (resid 725 and (name N or name CA or name C or name O or name \ CB )) or resid 726 through 730 or (resid 731 through 733 and (name N or name CA \ or name C or name O or name CB )) or resid 734 through 741 or (resid 742 throug \ h 743 and (name N or name CA or name C or name O or name CB )) or resid 744 thro \ ugh 771 or (resid 772 through 774 and (name N or name CA or name C or name O or \ name CB )) or resid 775 or (resid 776 and (name N or name CA or name C or name O \ or name CB )) or resid 777 through 784 or (resid 785 and (name N or name CA or \ name C or name O or name CB )) or resid 786 through 795 or (resid 796 through 79 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 798 or (resi \ d 799 and (name N or name CA or name C or name O or name CB )) or resid 800 or ( \ resid 801 through 808 and (name N or name CA or name C or name O or name CB )) o \ r resid 809 through 821 or (resid 822 and (name N or name CA or name C or name O \ or name CB )) or resid 823 through 833 or (resid 834 through 835 and (name N or \ name CA or name C or name O or name CB )) or resid 836 through 838 or (resid 83 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 840 or resid \ 901 through 905)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.500 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 0.004 0.201 23986 Z= 0.184 Angle : 0.561 11.383 32875 Z= 0.292 Chirality : 0.043 0.371 3984 Planarity : 0.004 0.199 4124 Dihedral : 13.549 162.730 8344 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 3152 helix: 2.15 (0.14), residues: 1352 sheet: -0.78 (0.27), residues: 424 loop : -1.23 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 386 TYR 0.014 0.001 TYR C 837 PHE 0.017 0.001 PHE D 841 TRP 0.015 0.001 TRP C 731 HIS 0.004 0.001 HIS C 571 Details of bonding type rmsd covalent geometry : bond 0.00351 (23945) covalent geometry : angle 0.55274 (32768) SS BOND : bond 0.00282 ( 16) SS BOND : angle 0.58376 ( 32) hydrogen bonds : bond 0.13046 ( 1120) hydrogen bonds : angle 5.51173 ( 3270) link_NAG-ASN : bond 0.00466 ( 25) link_NAG-ASN : angle 2.03709 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: B 788 MET cc_start: 0.7481 (mmp) cc_final: 0.7245 (mmm) REVERT: B 800 CYS cc_start: 0.4703 (p) cc_final: 0.4481 (p) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1437 time to fit residues: 52.6726 Evaluate side-chains 197 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.0770 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 341 ASN A 449 HIS A 696 GLN B 111 GLN ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS D 146 GLN D 736 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.107650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.084428 restraints weight = 71921.822| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.14 r_work: 0.3491 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23986 Z= 0.166 Angle : 0.543 10.785 32875 Z= 0.280 Chirality : 0.044 0.391 3984 Planarity : 0.003 0.053 4124 Dihedral : 6.632 72.736 3874 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.58 % Allowed : 6.82 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 3152 helix: 1.98 (0.14), residues: 1361 sheet: -0.90 (0.26), residues: 448 loop : -1.27 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 244 TYR 0.016 0.001 TYR D 355 PHE 0.019 0.001 PHE D 115 TRP 0.016 0.001 TRP B 390 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00393 (23945) covalent geometry : angle 0.53381 (32768) SS BOND : bond 0.00336 ( 16) SS BOND : angle 0.72238 ( 32) hydrogen bonds : bond 0.03482 ( 1120) hydrogen bonds : angle 4.62810 ( 3270) link_NAG-ASN : bond 0.00500 ( 25) link_NAG-ASN : angle 2.18089 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 813 MET cc_start: 0.6979 (mpp) cc_final: 0.6657 (mtt) REVERT: B 370 ARG cc_start: 0.7447 (mmp-170) cc_final: 0.7208 (mmp-170) REVERT: B 562 PHE cc_start: 0.7832 (t80) cc_final: 0.7586 (t80) REVERT: B 788 MET cc_start: 0.7754 (mmp) cc_final: 0.7288 (mmm) REVERT: D 321 TYR cc_start: 0.5904 (m-10) cc_final: 0.5617 (m-10) REVERT: D 541 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.6365 (m110) REVERT: D 652 PHE cc_start: 0.8465 (t80) cc_final: 0.8256 (t80) outliers start: 13 outliers final: 8 residues processed: 214 average time/residue: 0.1458 time to fit residues: 50.2651 Evaluate side-chains 213 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 617 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 118 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 0.0870 chunk 21 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 296 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS B 615 ASN D 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.107491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084859 restraints weight = 71968.330| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.34 r_work: 0.3498 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23986 Z= 0.109 Angle : 0.484 10.857 32875 Z= 0.249 Chirality : 0.042 0.376 3984 Planarity : 0.003 0.045 4124 Dihedral : 5.527 59.960 3874 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.76 % Allowed : 9.06 % Favored : 90.18 % 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 (0.15), residues: 3152 helix: 2.02 (0.14), residues: 1361 sheet: -0.88 (0.26), residues: 453 loop : -1.23 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 386 TYR 0.014 0.001 TYR C 837 PHE 0.013 0.001 PHE D 562 TRP 0.011 0.001 TRP A 381 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00243 (23945) covalent geometry : angle 0.47342 (32768) SS BOND : bond 0.00248 ( 16) SS BOND : angle 0.54135 ( 32) hydrogen bonds : bond 0.03218 ( 1120) hydrogen bonds : angle 4.38582 ( 3270) link_NAG-ASN : bond 0.00496 ( 25) link_NAG-ASN : angle 2.10753 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7274 (mmm) cc_final: 0.7034 (mmm) REVERT: A 813 MET cc_start: 0.6862 (mpp) cc_final: 0.6594 (mtt) REVERT: B 370 ARG cc_start: 0.7482 (mmp-170) cc_final: 0.7199 (mmp-170) REVERT: B 507 MET cc_start: 0.6644 (tmm) cc_final: 0.6327 (tmm) REVERT: B 562 PHE cc_start: 0.7977 (t80) cc_final: 0.7706 (t80) REVERT: B 788 MET cc_start: 0.7778 (mmp) cc_final: 0.7325 (mmm) REVERT: C 219 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8161 (mt) REVERT: C 470 MET cc_start: 0.7897 (mtt) cc_final: 0.7557 (mtt) REVERT: D 321 TYR cc_start: 0.6116 (m-10) cc_final: 0.5735 (m-10) REVERT: D 649 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6803 (tt) REVERT: D 652 PHE cc_start: 0.8499 (t80) cc_final: 0.8257 (t80) outliers start: 17 outliers final: 10 residues processed: 215 average time/residue: 0.1517 time to fit residues: 52.5177 Evaluate side-chains 211 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 680 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 24 optimal weight: 0.0010 chunk 65 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 165 optimal weight: 0.0020 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.107485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.084785 restraints weight = 72037.342| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.08 r_work: 0.3512 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 23986 Z= 0.108 Angle : 0.480 10.795 32875 Z= 0.246 Chirality : 0.042 0.375 3984 Planarity : 0.003 0.048 4124 Dihedral : 4.858 58.078 3874 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.03 % Allowed : 10.09 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3152 helix: 2.03 (0.14), residues: 1361 sheet: -0.92 (0.26), residues: 455 loop : -1.22 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 386 TYR 0.033 0.001 TYR B 737 PHE 0.012 0.001 PHE D 841 TRP 0.011 0.001 TRP D 55 HIS 0.016 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00244 (23945) covalent geometry : angle 0.47004 (32768) SS BOND : bond 0.00250 ( 16) SS BOND : angle 0.53123 ( 32) hydrogen bonds : bond 0.03063 ( 1120) hydrogen bonds : angle 4.28702 ( 3270) link_NAG-ASN : bond 0.00477 ( 25) link_NAG-ASN : angle 2.10960 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 813 MET cc_start: 0.6804 (mpp) cc_final: 0.6525 (mtt) REVERT: B 370 ARG cc_start: 0.7460 (mmp-170) cc_final: 0.7183 (mmp-170) REVERT: B 507 MET cc_start: 0.6717 (tmm) cc_final: 0.6502 (tmm) REVERT: B 562 PHE cc_start: 0.7861 (t80) cc_final: 0.7617 (t80) REVERT: B 788 MET cc_start: 0.7729 (mmp) cc_final: 0.7275 (mmm) REVERT: C 219 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8137 (mt) REVERT: D 321 TYR cc_start: 0.5962 (m-10) cc_final: 0.5624 (m-10) REVERT: D 649 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6701 (tt) REVERT: D 815 ASP cc_start: 0.7034 (p0) cc_final: 0.6818 (p0) REVERT: D 836 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5778 (tp) outliers start: 23 outliers final: 15 residues processed: 220 average time/residue: 0.1539 time to fit residues: 54.4733 Evaluate side-chains 218 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 836 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 181 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 215 optimal weight: 0.0470 chunk 177 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.108322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085196 restraints weight = 71333.825| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.53 r_work: 0.3474 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23986 Z= 0.115 Angle : 0.486 10.866 32875 Z= 0.248 Chirality : 0.042 0.373 3984 Planarity : 0.003 0.051 4124 Dihedral : 4.471 57.122 3874 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.48 % Allowed : 11.35 % Favored : 87.17 % 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 (0.15), residues: 3152 helix: 2.02 (0.14), residues: 1360 sheet: -0.91 (0.25), residues: 460 loop : -1.20 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 630 TYR 0.014 0.001 TYR D 286 PHE 0.014 0.001 PHE D 115 TRP 0.018 0.001 TRP D 55 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00265 (23945) covalent geometry : angle 0.47612 (32768) SS BOND : bond 0.00242 ( 16) SS BOND : angle 0.48890 ( 32) hydrogen bonds : bond 0.03017 ( 1120) hydrogen bonds : angle 4.20751 ( 3270) link_NAG-ASN : bond 0.00479 ( 25) link_NAG-ASN : angle 2.12014 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7449 (mmm) cc_final: 0.7106 (mmm) REVERT: B 370 ARG cc_start: 0.7491 (mmp-170) cc_final: 0.7227 (mmp-170) REVERT: B 507 MET cc_start: 0.6764 (tmm) cc_final: 0.6452 (tmm) REVERT: B 561 MET cc_start: 0.7274 (tmm) cc_final: 0.6826 (tmm) REVERT: B 562 PHE cc_start: 0.8080 (t80) cc_final: 0.7815 (t80) REVERT: B 788 MET cc_start: 0.7729 (mmp) cc_final: 0.7283 (mmm) REVERT: B 808 MET cc_start: 0.8002 (mmm) cc_final: 0.6971 (mtt) REVERT: C 219 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8212 (mt) REVERT: C 470 MET cc_start: 0.7766 (mtt) cc_final: 0.7459 (mtt) REVERT: C 576 MET cc_start: 0.8427 (mtp) cc_final: 0.8215 (mtt) REVERT: D 321 TYR cc_start: 0.6054 (m-10) cc_final: 0.5712 (m-10) REVERT: D 649 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6819 (tt) REVERT: D 815 ASP cc_start: 0.7446 (p0) cc_final: 0.7219 (p0) REVERT: D 836 ILE cc_start: 0.6002 (OUTLIER) cc_final: 0.5751 (tp) outliers start: 33 outliers final: 19 residues processed: 229 average time/residue: 0.1451 time to fit residues: 54.1645 Evaluate side-chains 223 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 836 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 227 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 648 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.107978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.084838 restraints weight = 71590.577| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.53 r_work: 0.3467 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23986 Z= 0.119 Angle : 0.493 10.884 32875 Z= 0.251 Chirality : 0.042 0.375 3984 Planarity : 0.003 0.052 4124 Dihedral : 4.312 57.127 3874 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.30 % Allowed : 12.83 % Favored : 85.87 % 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 (0.15), residues: 3152 helix: 1.98 (0.14), residues: 1360 sheet: -0.94 (0.25), residues: 453 loop : -1.18 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 386 TYR 0.013 0.001 TYR D 286 PHE 0.027 0.001 PHE A 832 TRP 0.018 0.001 TRP D 55 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00275 (23945) covalent geometry : angle 0.48238 (32768) SS BOND : bond 0.00243 ( 16) SS BOND : angle 0.54683 ( 32) hydrogen bonds : bond 0.03018 ( 1120) hydrogen bonds : angle 4.17890 ( 3270) link_NAG-ASN : bond 0.00471 ( 25) link_NAG-ASN : angle 2.14936 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 829 PHE cc_start: 0.4796 (t80) cc_final: 0.4251 (m-10) REVERT: B 370 ARG cc_start: 0.7493 (mmp-170) cc_final: 0.7244 (mmp-170) REVERT: B 507 MET cc_start: 0.6782 (tmm) cc_final: 0.6436 (tmm) REVERT: B 562 PHE cc_start: 0.8085 (t80) cc_final: 0.7839 (t80) REVERT: B 788 MET cc_start: 0.7724 (mmp) cc_final: 0.7284 (mmm) REVERT: C 219 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8180 (mt) REVERT: C 576 MET cc_start: 0.8406 (mtp) cc_final: 0.8136 (mtt) REVERT: D 73 LEU cc_start: 0.8006 (mm) cc_final: 0.7761 (mt) REVERT: D 321 TYR cc_start: 0.6060 (m-10) cc_final: 0.5821 (m-10) REVERT: D 649 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6913 (tt) REVERT: D 815 ASP cc_start: 0.7510 (p0) cc_final: 0.7276 (p0) REVERT: D 836 ILE cc_start: 0.5998 (OUTLIER) cc_final: 0.5744 (tp) outliers start: 29 outliers final: 20 residues processed: 224 average time/residue: 0.1471 time to fit residues: 53.1461 Evaluate side-chains 222 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 836 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 650 ASN C 477 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.104591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.082725 restraints weight = 71916.092| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.45 r_work: 0.3398 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23986 Z= 0.217 Angle : 0.589 11.702 32875 Z= 0.302 Chirality : 0.045 0.393 3984 Planarity : 0.004 0.057 4124 Dihedral : 4.658 54.608 3874 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.57 % Allowed : 13.18 % Favored : 85.25 % 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: -0.01 (0.15), residues: 3152 helix: 1.63 (0.14), residues: 1356 sheet: -1.15 (0.24), residues: 471 loop : -1.31 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 468 TYR 0.023 0.002 TYR D 286 PHE 0.032 0.002 PHE A 832 TRP 0.034 0.002 TRP B 390 HIS 0.007 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00518 (23945) covalent geometry : angle 0.57885 (32768) SS BOND : bond 0.00400 ( 16) SS BOND : angle 0.71756 ( 32) hydrogen bonds : bond 0.03643 ( 1120) hydrogen bonds : angle 4.45194 ( 3270) link_NAG-ASN : bond 0.00471 ( 25) link_NAG-ASN : angle 2.38913 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7677 (mmm) cc_final: 0.7254 (mmm) REVERT: B 392 ARG cc_start: 0.4862 (tmt-80) cc_final: 0.4563 (tmt-80) REVERT: B 507 MET cc_start: 0.6755 (tmm) cc_final: 0.6349 (tmm) REVERT: B 562 PHE cc_start: 0.8091 (t80) cc_final: 0.7891 (t80) REVERT: B 788 MET cc_start: 0.7789 (mmp) cc_final: 0.7362 (mmm) REVERT: B 808 MET cc_start: 0.7969 (mmm) cc_final: 0.7336 (mpp) REVERT: B 815 ASP cc_start: 0.7431 (m-30) cc_final: 0.7133 (m-30) REVERT: C 681 TYR cc_start: 0.7338 (p90) cc_final: 0.6913 (p90) REVERT: D 227 ILE cc_start: 0.8811 (mt) cc_final: 0.8488 (mp) REVERT: D 649 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7080 (tt) REVERT: D 653 MET cc_start: 0.7879 (mtp) cc_final: 0.7674 (mtm) REVERT: D 747 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6512 (pp) outliers start: 35 outliers final: 26 residues processed: 231 average time/residue: 0.1509 time to fit residues: 56.3537 Evaluate side-chains 226 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 680 PHE Chi-restraints excluded: chain D residue 747 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 185 optimal weight: 0.1980 chunk 127 optimal weight: 0.6980 chunk 313 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 280 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN D 648 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.106087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.084463 restraints weight = 71502.240| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.25 r_work: 0.3461 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23986 Z= 0.116 Angle : 0.512 11.184 32875 Z= 0.261 Chirality : 0.042 0.391 3984 Planarity : 0.003 0.059 4124 Dihedral : 4.372 54.887 3874 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.30 % Allowed : 13.95 % Favored : 84.75 % 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 (0.15), residues: 3152 helix: 1.77 (0.14), residues: 1360 sheet: -1.09 (0.25), residues: 460 loop : -1.25 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 52 TYR 0.010 0.001 TYR C 837 PHE 0.045 0.001 PHE A 832 TRP 0.024 0.001 TRP B 390 HIS 0.004 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00265 (23945) covalent geometry : angle 0.50086 (32768) SS BOND : bond 0.00239 ( 16) SS BOND : angle 0.74090 ( 32) hydrogen bonds : bond 0.03115 ( 1120) hydrogen bonds : angle 4.26478 ( 3270) link_NAG-ASN : bond 0.00479 ( 25) link_NAG-ASN : angle 2.22940 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.6544 (t0) REVERT: A 555 MET cc_start: 0.7588 (mmm) cc_final: 0.7193 (mmm) REVERT: A 621 GLU cc_start: 0.7803 (pm20) cc_final: 0.7567 (mp0) REVERT: B 338 MET cc_start: 0.7338 (mmm) cc_final: 0.6702 (mmm) REVERT: B 507 MET cc_start: 0.6842 (tmm) cc_final: 0.6463 (tmm) REVERT: B 520 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: B 562 PHE cc_start: 0.8039 (t80) cc_final: 0.7827 (t80) REVERT: B 788 MET cc_start: 0.7700 (mmp) cc_final: 0.7271 (mmm) REVERT: B 808 MET cc_start: 0.7994 (mmm) cc_final: 0.7346 (mpp) REVERT: B 815 ASP cc_start: 0.7287 (m-30) cc_final: 0.6953 (m-30) REVERT: C 163 ILE cc_start: 0.8080 (pt) cc_final: 0.7856 (pt) REVERT: C 681 TYR cc_start: 0.7300 (p90) cc_final: 0.6948 (p90) REVERT: D 227 ILE cc_start: 0.8776 (mt) cc_final: 0.8449 (mp) REVERT: D 649 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6962 (tt) outliers start: 29 outliers final: 19 residues processed: 226 average time/residue: 0.1473 time to fit residues: 53.9315 Evaluate side-chains 220 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 680 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 72 optimal weight: 0.0040 chunk 227 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 308 optimal weight: 3.9990 chunk 303 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN D 648 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.105678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.082831 restraints weight = 71843.557| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.08 r_work: 0.3464 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23986 Z= 0.118 Angle : 0.519 11.161 32875 Z= 0.263 Chirality : 0.042 0.384 3984 Planarity : 0.003 0.060 4124 Dihedral : 4.294 54.863 3874 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.12 % Allowed : 14.22 % Favored : 84.66 % 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: 0.17 (0.15), residues: 3152 helix: 1.81 (0.14), residues: 1359 sheet: -1.07 (0.25), residues: 460 loop : -1.24 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 52 TYR 0.013 0.001 TYR D 286 PHE 0.050 0.001 PHE A 832 TRP 0.025 0.001 TRP D 55 HIS 0.003 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00273 (23945) covalent geometry : angle 0.50801 (32768) SS BOND : bond 0.00258 ( 16) SS BOND : angle 1.02421 ( 32) hydrogen bonds : bond 0.03096 ( 1120) hydrogen bonds : angle 4.22823 ( 3270) link_NAG-ASN : bond 0.00474 ( 25) link_NAG-ASN : angle 2.21541 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7546 (mmm) cc_final: 0.7213 (mmm) REVERT: B 338 MET cc_start: 0.7379 (mmm) cc_final: 0.6693 (mmm) REVERT: B 507 MET cc_start: 0.6987 (tmm) cc_final: 0.6603 (tmm) REVERT: B 788 MET cc_start: 0.7746 (mmp) cc_final: 0.7323 (mmm) REVERT: B 808 MET cc_start: 0.8027 (mmm) cc_final: 0.7392 (mpp) REVERT: B 815 ASP cc_start: 0.7240 (m-30) cc_final: 0.6905 (m-30) REVERT: C 74 MET cc_start: 0.8380 (tpp) cc_final: 0.8137 (tpp) REVERT: C 681 TYR cc_start: 0.7308 (p90) cc_final: 0.6973 (p90) REVERT: D 227 ILE cc_start: 0.8775 (mt) cc_final: 0.8472 (mp) REVERT: D 649 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6880 (tt) outliers start: 25 outliers final: 20 residues processed: 221 average time/residue: 0.1461 time to fit residues: 52.1528 Evaluate side-chains 219 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 680 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 171 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 270 optimal weight: 0.0870 chunk 242 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 782 ASN D 648 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.104394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081277 restraints weight = 72059.710| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.05 r_work: 0.3428 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23986 Z= 0.194 Angle : 0.573 11.638 32875 Z= 0.291 Chirality : 0.044 0.392 3984 Planarity : 0.004 0.061 4124 Dihedral : 4.478 49.396 3874 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.17 % Allowed : 13.99 % Favored : 84.84 % 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: -0.03 (0.15), residues: 3152 helix: 1.62 (0.14), residues: 1358 sheet: -1.21 (0.24), residues: 468 loop : -1.31 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 52 TYR 0.018 0.002 TYR D 286 PHE 0.054 0.002 PHE A 832 TRP 0.031 0.002 TRP D 55 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00463 (23945) covalent geometry : angle 0.56191 (32768) SS BOND : bond 0.00420 ( 16) SS BOND : angle 0.84565 ( 32) hydrogen bonds : bond 0.03432 ( 1120) hydrogen bonds : angle 4.37566 ( 3270) link_NAG-ASN : bond 0.00461 ( 25) link_NAG-ASN : angle 2.34623 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 MET cc_start: 0.7348 (mmm) cc_final: 0.6688 (mmm) REVERT: B 507 MET cc_start: 0.6902 (tmm) cc_final: 0.6507 (tmm) REVERT: B 788 MET cc_start: 0.7728 (mmp) cc_final: 0.7306 (mmm) REVERT: B 815 ASP cc_start: 0.7258 (m-30) cc_final: 0.6915 (m-30) REVERT: C 681 TYR cc_start: 0.7331 (p90) cc_final: 0.7072 (p90) REVERT: D 227 ILE cc_start: 0.8853 (mt) cc_final: 0.8551 (mp) REVERT: D 649 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.6976 (tt) outliers start: 26 outliers final: 23 residues processed: 220 average time/residue: 0.1454 time to fit residues: 51.7257 Evaluate side-chains 224 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 813 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 680 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 60 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 648 ASN D 703 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.109279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.085780 restraints weight = 70866.878| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.74 r_work: 0.3425 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23986 Z= 0.130 Angle : 0.537 11.675 32875 Z= 0.271 Chirality : 0.043 0.395 3984 Planarity : 0.003 0.060 4124 Dihedral : 4.349 47.928 3874 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.12 % Allowed : 14.39 % Favored : 84.48 % 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: 0.03 (0.15), residues: 3152 helix: 1.68 (0.14), residues: 1359 sheet: -1.20 (0.24), residues: 464 loop : -1.29 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 52 TYR 0.013 0.001 TYR D 286 PHE 0.053 0.001 PHE A 832 TRP 0.033 0.001 TRP D 55 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00304 (23945) covalent geometry : angle 0.52659 (32768) SS BOND : bond 0.00301 ( 16) SS BOND : angle 0.70339 ( 32) hydrogen bonds : bond 0.03196 ( 1120) hydrogen bonds : angle 4.29720 ( 3270) link_NAG-ASN : bond 0.00472 ( 25) link_NAG-ASN : angle 2.27096 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5651.70 seconds wall clock time: 97 minutes 26.51 seconds (5846.51 seconds total)