Starting phenix.real_space_refine on Mon May 4 20:19:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unp_64359/05_2026/9unp_64359.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unp_64359/05_2026/9unp_64359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9unp_64359/05_2026/9unp_64359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unp_64359/05_2026/9unp_64359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9unp_64359/05_2026/9unp_64359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unp_64359/05_2026/9unp_64359.map" } resolution = 3.27 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= 0.007 sd= 0.028 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 135 5.16 5 Cl 1 4.86 5 C 14860 2.51 5 N 3847 2.21 5 O 4330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 23173 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5694 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 34, 'TRANS': 754} Chain breaks: 2 Unresolved non-hydrogen bonds: 572 Unresolved non-hydrogen angles: 695 Unresolved non-hydrogen dihedrals: 490 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 27, 'GLU:plan': 26, 'ASN:plan1': 9, 'HIS:plan': 5, 'GLN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 7, 'TRP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 412 Chain: "B" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5582 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 28, 'TRANS': 752} Chain breaks: 2 Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 785 Unresolved non-hydrogen dihedrals: 541 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASN:plan1': 7, 'HIS:plan': 7, 'ASP:plan': 17, 'ARG:plan': 14, 'TRP:plan': 2, 'GLU:plan': 22, 'GLN:plan1': 7, 'PHE:plan': 10, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 413 Chain: "C" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 5938 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 33, 'TRANS': 763} Chain breaks: 2 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 15, 'GLN:plan1': 4, 'ASN:plan1': 9, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 17, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 274 Chain: "D" Number of atoms: 5693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5693 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 29, 'TRANS': 745} Chain breaks: 3 Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 358 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 32, 'HIS:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 4, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 301 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.23, per 1000 atoms: 0.23 Number of scatterers: 23173 At special positions: 0 Unit cell: (106.555, 142.425, 185.68, 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 135 16.00 O 4330 8.00 N 3847 7.00 C 14860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, 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 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=2.03 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 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " 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 239 " " NAG A 903 " - " ASN A 273 " " NAG A 904 " - " ASN A 471 " " NAG A 905 " - " ASN A 771 " " NAG B 901 " - " ASN B 687 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 239 " " NAG C 903 " - " ASN C 276 " " NAG C 904 " - " ASN C 350 " " NAG C 905 " - " ASN C 368 " " NAG C 906 " - " ASN C 471 " " NAG C 907 " - " ASN C 771 " " NAG D 901 " - " ASN D 341 " " NAG D 902 " - " ASN D 348 " " NAG D 903 " - " ASN D 688 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 781.8 milliseconds 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5876 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 33 sheets defined 44.9% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 103 through 113 removed outlier: 4.686A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 4.253A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 224 through 238 Processing helix 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: 3.734A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 4.346A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.084A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 550 through 556 removed outlier: 3.668A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 584 removed outlier: 3.683A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 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 792 Processing helix chain 'A' and resid 811 through 844 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 211 through 222 removed outlier: 4.240A pdb=" N THR B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.540A pdb=" N TYR B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 309 removed outlier: 4.026A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.584A pdb=" N VAL B 339 " --> pdb=" O HIS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.905A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 580 removed outlier: 4.085A pdb=" N MET B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 613 removed outlier: 5.307A pdb=" N ILE B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) 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 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' 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 785 removed outlier: 4.392A 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 802 removed outlier: 3.981A pdb=" N ASN B 802 " --> pdb=" O ILE B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 837 removed outlier: 3.596A pdb=" N LEU B 824 " --> pdb=" O VAL B 820 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP B 837 " --> pdb=" O ILE B 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.611A pdb=" N HIS C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.640A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.587A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 removed outlier: 4.034A 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 205 through 214 Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.715A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.946A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 559 through 581 removed outlier: 3.614A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 Processing helix chain 'C' and resid 629 through 658 removed outlier: 3.837A pdb=" N PHE C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.516A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 709 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 810 through 843 removed outlier: 3.731A pdb=" N ALA C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 46 removed outlier: 3.945A pdb=" N ASP D 46 " --> pdb=" O GLY D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 47 through 57 removed outlier: 4.205A pdb=" N LYS D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.727A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.267A pdb=" N ALA D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 165 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.657A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 288 through 311 removed outlier: 3.533A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.541A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 561 through 581 removed outlier: 3.927A pdb=" N MET D 565 " --> pdb=" O MET D 561 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.613A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 706 removed outlier: 3.541A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 744 through 747 removed outlier: 4.077A pdb=" N LYS D 747 " --> pdb=" O GLU D 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 744 through 747' Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.309A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 814 through 817 Processing helix chain 'D' and resid 818 through 842 removed outlier: 3.771A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 5.748A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.394A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 5.800A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.639A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 477 removed outlier: 7.596A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.508A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.613A pdb=" N THR A 486 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 499 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.871A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 126 removed outlier: 6.271A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 199 through 203 removed outlier: 3.642A pdb=" N PHE B 170 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN B 201 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU B 172 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 203 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 169 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU B 228 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER B 171 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 227 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU B 276 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN B 367 " --> pdb=" O TRP B 372 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP B 372 " --> pdb=" O ASN B 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 479 Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 421 removed outlier: 3.886A pdb=" N VAL B 434 " --> pdb=" O CYS B 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 682 through 684 removed outlier: 6.770A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 682 through 684 removed outlier: 6.770A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 529 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE B 533 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA B 757 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 64 removed outlier: 8.233A pdb=" N TYR C 88 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL C 92 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.462A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.645A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 329 through 330 Processing sheet with id=AC3, first strand: chain 'C' and resid 473 through 478 removed outlier: 8.507A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 473 through 478 removed outlier: 8.507A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE C 753 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N GLN C 536 " --> pdb=" O PHE C 753 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N ARG C 755 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N LYS C 534 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC6, first strand: chain 'C' and resid 486 through 489 removed outlier: 4.060A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN C 499 " --> pdb=" O THR C 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 66 through 71 removed outlier: 6.852A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.588A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE D 228 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 277 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 281 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN D 368 " --> pdb=" O TRP D 373 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TRP D 373 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD1, first strand: chain 'D' and resid 406 through 410 removed outlier: 4.140A pdb=" N ILE D 408 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 418 through 419 Processing sheet with id=AD3, first strand: chain 'D' and resid 438 through 440 removed outlier: 3.567A pdb=" N GLY D 451 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 490 removed outlier: 3.658A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.754A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 729 through 732 removed outlier: 6.746A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3279 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: 4.70 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5231 1.33 - 1.45: 4981 1.45 - 1.57: 13217 1.57 - 1.69: 0 1.69 - 1.81: 232 Bond restraints: 23661 Sorted by residual: bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.55e+00 bond pdb=" C1 JC9 C 909 " pdb=" N1 JC9 C 909 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" C10 JC9 C 909 " pdb=" N1 JC9 C 909 " ideal model delta sigma weight residual 1.493 1.462 0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 23656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 31762 1.47 - 2.94: 460 2.94 - 4.41: 52 4.41 - 5.88: 28 5.88 - 7.35: 6 Bond angle restraints: 32308 Sorted by residual: angle pdb=" C PHE B 613 " pdb=" N ASN B 614 " pdb=" CA ASN B 614 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 angle pdb=" C LEU A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta sigma weight residual 121.54 126.53 -4.99 1.91e+00 2.74e-01 6.82e+00 angle pdb=" CB MET B 630 " pdb=" CG MET B 630 " pdb=" SD MET B 630 " ideal model delta sigma weight residual 112.70 120.05 -7.35 3.00e+00 1.11e-01 6.00e+00 angle pdb=" CG ARG B 181 " pdb=" CD ARG B 181 " pdb=" NE ARG B 181 " ideal model delta sigma weight residual 112.00 117.05 -5.05 2.20e+00 2.07e-01 5.27e+00 angle pdb=" N GLY A 256 " pdb=" CA GLY A 256 " pdb=" C GLY A 256 " ideal model delta sigma weight residual 113.18 118.50 -5.32 2.37e+00 1.78e-01 5.04e+00 ... (remaining 32303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.46: 13389 22.46 - 44.92: 662 44.92 - 67.38: 96 67.38 - 89.84: 17 89.84 - 112.30: 8 Dihedral angle restraints: 14172 sinusoidal: 5073 harmonic: 9099 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 308 " pdb=" CB CYS C 308 " ideal model delta sinusoidal sigma weight residual 93.00 14.16 78.84 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual 93.00 25.90 67.10 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CB CYS B 87 " pdb=" SG CYS B 87 " pdb=" SG CYS B 320 " pdb=" CB CYS B 320 " ideal model delta sinusoidal sigma weight residual 93.00 149.57 -56.57 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 14169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2715 0.035 - 0.069: 784 0.069 - 0.104: 271 0.104 - 0.139: 109 0.139 - 0.174: 5 Chirality restraints: 3884 Sorted by residual: chirality pdb=" C1 NAG C 905 " pdb=" ND2 ASN C 368 " pdb=" C2 NAG C 905 " pdb=" O5 NAG C 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA THR A 103 " pdb=" N THR A 103 " pdb=" C THR A 103 " pdb=" CB THR A 103 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" C1 NAG A 904 " pdb=" ND2 ASN A 471 " pdb=" C2 NAG A 904 " pdb=" O5 NAG A 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 3881 not shown) Planarity restraints: 4104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 687 " 0.003 2.00e-02 2.50e+03 2.46e-02 7.56e+00 pdb=" CG ASN B 687 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 687 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 687 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG B 901 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 165 " 0.009 2.00e-02 2.50e+03 9.51e-03 1.81e+00 pdb=" CG TYR B 165 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 165 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 165 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 165 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 165 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 165 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 165 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO C 319 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " -0.019 5.00e-02 4.00e+02 ... (remaining 4101 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2103 2.74 - 3.28: 23856 3.28 - 3.82: 39986 3.82 - 4.36: 43923 4.36 - 4.90: 77141 Nonbonded interactions: 187009 Sorted by model distance: nonbonded pdb=" OD2 ASP B 731 " pdb=" OH TYR B 761 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN B 404 " pdb=" OG1 THR B 474 " model vdw 2.241 3.040 nonbonded pdb=" O GLN B 106 " pdb=" OG SER B 132 " model vdw 2.258 3.040 nonbonded pdb=" OE1 GLN B 163 " pdb=" OG1 THR B 428 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR C 539 " pdb=" O THR C 749 " model vdw 2.268 3.040 ... (remaining 187004 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 36 through 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 name CA or name \ C or name O or name CB )) or resid 41 through 57 or (resid 58 through 59 and (n \ ame N or name CA or name C or name O or name CB )) or resid 60 through 130 or (r \ esid 131 and (name N or name CA or name C or name O or name CB )) or resid 132 t \ hrough 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 299 or (resid 300 and (name N or name CA or n \ ame C or name O or name CB )) or resid 301 through 416 or (resid 417 and (name N \ or name CA or name C or name O or name CB )) or resid 418 through 448 or (resid \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 throu \ gh 474 or (resid 475 and (name N or name CA or name C or name O or name CB )) or \ resid 476 through 553 or (resid 554 and (name N or name CA or name C or name O \ or name CB )) or resid 555 through 582 or (resid 601 and (name N or name CA or n \ ame C or name O or name CB )) or resid 602 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 653 or (resid \ 654 and (name N or name CA or name C or name O or name CB )) or resid 655 throu \ gh 661 or (resid 662 through 663 and (name N or name CA or name C or name O or n \ ame CB )) or resid 664 through 703 or (resid 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 7 \ 29 through 768 or (resid 769 through 770 and (name N or name CA or name C or nam \ e O or name CB )) or resid 771 through 800 or resid 809 through 843 or resid 901 \ through 906)) selection = (chain 'C' and (resid 36 through 42 or (resid 43 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 49 or (resid 50 through \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 or (res \ id 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throu \ gh 58 or (resid 59 and (name N or name CA or name C or name O or name CB )) or r \ esid 60 through 67 or (resid 68 and (name N or name CA or name C or name O or na \ me CB )) or resid 69 through 72 or (resid 73 and (name N or name CA or name C or \ name O or name CB )) or resid 74 through 85 or (resid 86 and (name N or name CA \ or name C or name O or name CB )) or resid 87 through 93 or (resid 94 and (name \ N or name CA or name C or name O or name CB )) or resid 95 through 100 or (resi \ d 101 through 102 and (name N or name CA or name C or name O or name CB )) or re \ sid 103 through 123 or (resid 124 and (name N or name CA or name C or name O or \ name CB )) or resid 125 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 155 or (resid 156 and (name N or \ name CA or name C or name O or name CB )) or resid 157 through 171 or (resid 17 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 173 through \ 201 or (resid 202 and (name N or name CA or name C or name O or name CB )) or re \ sid 203 through 236 or (resid 237 and (name N or name CA or name C or name O or \ name CB )) or resid 238 through 251 or (resid 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 through 274 or (resid 275 through 277 an \ d (name N or name CA or name C or name O or name CB )) or resid 278 through 293 \ or (resid 294 and (name N or name CA or name C or name O or name CB )) or resid \ 295 through 296 or (resid 297 through 300 and (name N or name CA or name C or na \ me O or name CB )) or resid 301 through 305 or (resid 306 and (name N or name CA \ or name C or name O or name CB )) or resid 307 through 314 or (resid 315 throug \ h 316 and (name N or name CA or name C or name O or name CB )) or resid 317 thro \ ugh 322 or (resid 323 and (name N or name CA or name C or name O or name CB )) o \ r resid 324 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 (name N or \ name CA or name C or name O or name CB )) or resid 379 through 384 or (resid 38 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 386 through \ 389 or (resid 390 and (name N or name CA or name C or name O or name CB )) or re \ sid 391 through 425 or (resid 426 through 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 or (resid 429 and (name N or name CA or name \ C or name O or name CB )) or resid 430 through 441 or (resid 442 and (name N or \ name CA or name C or name O or name CB )) or resid 443 through 495 or (resid 49 \ 6 through 497 and (name N or name CA or name C or name O or name CB )) or resid \ 498 through 521 or (resid 522 and (name N or name CA or name C or name O or name \ CB )) or resid 523 through 660 or (resid 661 through 663 and (name N or name CA \ or name C or name O or name CB )) or resid 664 through 672 or (resid 673 throug \ h 674 and (name N or name CA or name C or name O or name CB )) or resid 675 thro \ ugh 694 or (resid 695 and (name N or name CA or name C or name O or name CB )) o \ r resid 696 through 698 or (resid 699 and (name N or name CA or name C or name O \ or name CB )) or resid 700 through 701 or (resid 702 and (name N or name CA or \ name C or name O or name CB )) or resid 703 through 705 or (resid 706 and (name \ N or name CA or name C or name O or name CB )) or resid 707 through 736 or (resi \ d 737 and (name N or name CA or name C or name O or name CB )) or resid 738 or ( \ resid 739 through 740 and (name N or name CA or name C or name O or name CB )) o \ r resid 741 through 742 or (resid 743 and (name N or name CA or name C or name O \ or name CB )) or resid 744 through 750 or (resid 751 and (name N or name CA or \ name C or name O or name CB )) or resid 752 through 785 or (resid 786 and (name \ N or name CA or name C or name O or name CB )) or resid 787 through 795 or (resi \ d 796 through 797 and (name N or name CA or name C or name O or name CB )) or re \ sid 798 through 799 or (resid 800 and (name N or name CA or name C or name O or \ name CB )) or resid 809 through 812 or (resid 813 through 814 and (name N or nam \ e CA or name C or name O or name CB )) or resid 815 through 817 or (resid 818 an \ d (name N or name CA or name C or name O or name CB )) or resid 819 through 828 \ or (resid 829 and (name N or name CA or name C or name O or name CB )) or resid \ 830 through 831 or (resid 832 and (name N or name CA or name C or name O or name \ CB )) or resid 833 through 836 or (resid 837 through 843 and (name N or name CA \ or name C or name O or name CB )) or resid 902 through 906 or resid 908)) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.360 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.002 0.043 23690 Z= 0.109 Angle : 0.478 19.981 32382 Z= 0.231 Chirality : 0.040 0.174 3884 Planarity : 0.003 0.033 4088 Dihedral : 13.558 112.296 8257 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 1.02 (0.16), residues: 3116 helix: 2.26 (0.14), residues: 1319 sheet: -0.14 (0.30), residues: 354 loop : -0.62 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.023 0.001 TYR B 165 PHE 0.017 0.001 PHE D 313 TRP 0.017 0.001 TRP C 636 HIS 0.012 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00221 (23661) covalent geometry : angle 0.45262 (32308) SS BOND : bond 0.00174 ( 13) SS BOND : angle 0.56638 ( 26) hydrogen bonds : bond 0.15308 ( 1106) hydrogen bonds : angle 5.63140 ( 3279) link_NAG-ASN : bond 0.00592 ( 16) link_NAG-ASN : angle 3.99963 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.779 Fit side-chains REVERT: C 639 PHE cc_start: 0.7854 (t80) cc_final: 0.7603 (t80) REVERT: C 703 TYR cc_start: 0.6687 (t80) cc_final: 0.6400 (t80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1466 time to fit residues: 55.8304 Evaluate side-chains 207 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 154 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN B 710 GLN C 94 HIS C 101 HIS D 542 ASN D 703 HIS ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.120175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.098746 restraints weight = 77102.836| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.90 r_work: 0.3597 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23690 Z= 0.118 Angle : 0.502 18.808 32382 Z= 0.255 Chirality : 0.042 0.414 3884 Planarity : 0.003 0.038 4088 Dihedral : 5.297 56.031 3656 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.40 % Allowed : 6.02 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.16), residues: 3116 helix: 2.14 (0.14), residues: 1338 sheet: -0.29 (0.28), residues: 375 loop : -0.64 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.020 0.001 TYR D 239 PHE 0.036 0.001 PHE D 671 TRP 0.012 0.001 TRP C 636 HIS 0.005 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00261 (23661) covalent geometry : angle 0.48385 (32308) SS BOND : bond 0.00216 ( 13) SS BOND : angle 1.19240 ( 26) hydrogen bonds : bond 0.03412 ( 1106) hydrogen bonds : angle 4.46187 ( 3279) link_NAG-ASN : bond 0.00631 ( 16) link_NAG-ASN : angle 3.45834 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 220 time to evaluate : 0.912 Fit side-chains REVERT: B 74 MET cc_start: 0.6400 (mpp) cc_final: 0.5791 (mpp) REVERT: B 112 MET cc_start: 0.7607 (mmm) cc_final: 0.7316 (mmm) REVERT: B 161 ILE cc_start: 0.7288 (mm) cc_final: 0.6973 (mm) REVERT: B 200 MET cc_start: 0.7306 (tpt) cc_final: 0.6709 (tpp) REVERT: B 335 HIS cc_start: 0.6598 (m-70) cc_final: 0.6125 (t-90) REVERT: B 653 MET cc_start: 0.7183 (mtt) cc_final: 0.6916 (mtp) REVERT: C 502 MET cc_start: 0.6949 (mtm) cc_final: 0.6661 (mtm) REVERT: C 639 PHE cc_start: 0.8209 (t80) cc_final: 0.7946 (t80) REVERT: C 703 TYR cc_start: 0.6829 (t80) cc_final: 0.6477 (t80) REVERT: D 232 CYS cc_start: 0.7229 (p) cc_final: 0.6691 (p) REVERT: D 616 ASN cc_start: 0.7883 (p0) cc_final: 0.7542 (p0) REVERT: D 814 ASP cc_start: 0.8555 (t70) cc_final: 0.8301 (p0) outliers start: 9 outliers final: 4 residues processed: 222 average time/residue: 0.1569 time to fit residues: 56.3256 Evaluate side-chains 215 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain C residue 705 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 9.9990 chunk 214 optimal weight: 0.0670 chunk 81 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 222 optimal weight: 8.9990 chunk 209 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 67 HIS A 293 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN C 101 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 355 ASN D 127 HIS D 703 HIS D 767 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.109689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.091071 restraints weight = 82818.653| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.68 r_work: 0.3507 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23690 Z= 0.152 Angle : 0.521 18.238 32382 Z= 0.265 Chirality : 0.043 0.441 3884 Planarity : 0.003 0.043 4088 Dihedral : 4.352 49.835 3656 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.89 % Allowed : 8.90 % Favored : 90.21 % 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: 0.72 (0.16), residues: 3116 helix: 2.09 (0.14), residues: 1310 sheet: -0.68 (0.27), residues: 399 loop : -0.72 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.018 0.001 TYR B 165 PHE 0.042 0.002 PHE D 671 TRP 0.012 0.001 TRP C 636 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00357 (23661) covalent geometry : angle 0.50367 (32308) SS BOND : bond 0.00271 ( 13) SS BOND : angle 1.09871 ( 26) hydrogen bonds : bond 0.03339 ( 1106) hydrogen bonds : angle 4.24965 ( 3279) link_NAG-ASN : bond 0.00549 ( 16) link_NAG-ASN : angle 3.37938 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.808 Fit side-chains REVERT: A 74 MET cc_start: 0.8570 (tpp) cc_final: 0.8229 (tpp) REVERT: B 161 ILE cc_start: 0.7269 (mm) cc_final: 0.6904 (mm) REVERT: B 162 MET cc_start: 0.6951 (mtt) cc_final: 0.6673 (mtt) REVERT: B 335 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.5925 (t-90) REVERT: B 653 MET cc_start: 0.7179 (mtt) cc_final: 0.6926 (mtp) REVERT: C 159 ASN cc_start: 0.8427 (t0) cc_final: 0.8032 (t0) REVERT: C 639 PHE cc_start: 0.8242 (t80) cc_final: 0.7937 (t80) REVERT: C 703 TYR cc_start: 0.6944 (t80) cc_final: 0.6652 (t80) REVERT: D 358 MET cc_start: 0.8623 (mmm) cc_final: 0.8361 (mmm) REVERT: D 616 ASN cc_start: 0.7951 (p0) cc_final: 0.7546 (p0) REVERT: D 638 PHE cc_start: 0.9252 (t80) cc_final: 0.9044 (t80) REVERT: D 814 ASP cc_start: 0.8618 (t70) cc_final: 0.8330 (p0) REVERT: D 818 MET cc_start: 0.7816 (mpp) cc_final: 0.7578 (mpp) outliers start: 20 outliers final: 11 residues processed: 225 average time/residue: 0.1480 time to fit residues: 53.7796 Evaluate side-chains 222 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 705 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 103 optimal weight: 0.0980 chunk 184 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 281 optimal weight: 0.0980 chunk 159 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.110146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.088928 restraints weight = 83078.021| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.48 r_work: 0.3547 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23690 Z= 0.104 Angle : 0.488 17.436 32382 Z= 0.247 Chirality : 0.042 0.483 3884 Planarity : 0.003 0.039 4088 Dihedral : 4.108 49.136 3656 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.97 % Allowed : 10.76 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 3116 helix: 2.11 (0.14), residues: 1311 sheet: -0.85 (0.27), residues: 396 loop : -0.67 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 292 TYR 0.013 0.001 TYR A 410 PHE 0.042 0.001 PHE D 671 TRP 0.011 0.001 TRP C 636 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00232 (23661) covalent geometry : angle 0.46930 (32308) SS BOND : bond 0.00246 ( 13) SS BOND : angle 1.83666 ( 26) hydrogen bonds : bond 0.03008 ( 1106) hydrogen bonds : angle 4.13574 ( 3279) link_NAG-ASN : bond 0.00540 ( 16) link_NAG-ASN : angle 3.26388 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.897 Fit side-chains REVERT: A 74 MET cc_start: 0.8583 (tpp) cc_final: 0.8255 (tpp) REVERT: B 161 ILE cc_start: 0.6998 (mm) cc_final: 0.6633 (mm) REVERT: B 162 MET cc_start: 0.6710 (mtt) cc_final: 0.6446 (mtt) REVERT: B 335 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.6072 (t-90) REVERT: B 653 MET cc_start: 0.7216 (mtt) cc_final: 0.6889 (mtp) REVERT: C 159 ASN cc_start: 0.8352 (t0) cc_final: 0.7972 (t0) REVERT: C 639 PHE cc_start: 0.8178 (t80) cc_final: 0.7876 (t80) REVERT: C 671 ARG cc_start: 0.6995 (mtm180) cc_final: 0.6779 (mtm180) REVERT: C 703 TYR cc_start: 0.6815 (t80) cc_final: 0.6502 (t80) REVERT: D 202 VAL cc_start: 0.8070 (t) cc_final: 0.7840 (p) REVERT: D 358 MET cc_start: 0.8521 (mmm) cc_final: 0.8073 (mmm) REVERT: D 616 ASN cc_start: 0.7753 (p0) cc_final: 0.7470 (p0) REVERT: D 814 ASP cc_start: 0.8599 (t70) cc_final: 0.8360 (p0) REVERT: D 818 MET cc_start: 0.7759 (mpp) cc_final: 0.7455 (mpp) outliers start: 22 outliers final: 11 residues processed: 221 average time/residue: 0.1535 time to fit residues: 55.1790 Evaluate side-chains 219 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 705 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 192 optimal weight: 0.0060 chunk 107 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 75 ASN B 111 GLN B 163 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN D 703 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.109034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.090589 restraints weight = 82058.347| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.82 r_work: 0.3504 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23690 Z= 0.144 Angle : 0.509 17.235 32382 Z= 0.259 Chirality : 0.043 0.470 3884 Planarity : 0.003 0.040 4088 Dihedral : 4.054 42.865 3656 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.24 % Allowed : 11.78 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 3116 helix: 2.08 (0.14), residues: 1310 sheet: -0.84 (0.27), residues: 405 loop : -0.73 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 292 TYR 0.013 0.001 TYR A 410 PHE 0.038 0.002 PHE D 671 TRP 0.012 0.001 TRP D 635 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00335 (23661) covalent geometry : angle 0.49278 (32308) SS BOND : bond 0.00885 ( 13) SS BOND : angle 1.09664 ( 26) hydrogen bonds : bond 0.03114 ( 1106) hydrogen bonds : angle 4.10263 ( 3279) link_NAG-ASN : bond 0.00516 ( 16) link_NAG-ASN : angle 3.27729 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 1.007 Fit side-chains REVERT: A 74 MET cc_start: 0.8567 (tpp) cc_final: 0.8148 (tpp) REVERT: B 161 ILE cc_start: 0.7206 (mm) cc_final: 0.6800 (mm) REVERT: B 162 MET cc_start: 0.7053 (mtt) cc_final: 0.6789 (mtt) REVERT: B 200 MET cc_start: 0.7726 (tpt) cc_final: 0.7491 (tpt) REVERT: B 335 HIS cc_start: 0.6561 (OUTLIER) cc_final: 0.5984 (t-90) REVERT: B 653 MET cc_start: 0.7323 (mtt) cc_final: 0.7063 (mtp) REVERT: C 502 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7159 (mtm) REVERT: C 703 TYR cc_start: 0.7000 (t80) cc_final: 0.6744 (t80) REVERT: D 167 TYR cc_start: 0.7951 (m-80) cc_final: 0.7694 (m-80) REVERT: D 202 VAL cc_start: 0.8186 (t) cc_final: 0.7941 (p) REVERT: D 358 MET cc_start: 0.8691 (mmm) cc_final: 0.8464 (mmt) REVERT: D 616 ASN cc_start: 0.7902 (p0) cc_final: 0.7583 (p0) REVERT: D 638 PHE cc_start: 0.9273 (t80) cc_final: 0.8992 (t80) REVERT: D 818 MET cc_start: 0.7656 (mpp) cc_final: 0.7356 (mpp) outliers start: 28 outliers final: 15 residues processed: 238 average time/residue: 0.1604 time to fit residues: 61.6511 Evaluate side-chains 227 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 705 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 134 optimal weight: 8.9990 chunk 238 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 245 optimal weight: 0.4980 chunk 109 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 101 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.108453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.090385 restraints weight = 82427.682| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.77 r_work: 0.3481 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23690 Z= 0.148 Angle : 0.523 16.849 32382 Z= 0.265 Chirality : 0.043 0.474 3884 Planarity : 0.003 0.039 4088 Dihedral : 4.049 43.183 3656 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.20 % Allowed : 12.75 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 3116 helix: 2.01 (0.14), residues: 1308 sheet: -0.83 (0.26), residues: 427 loop : -0.80 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 292 TYR 0.013 0.001 TYR A 410 PHE 0.036 0.002 PHE D 671 TRP 0.012 0.001 TRP D 635 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00347 (23661) covalent geometry : angle 0.50718 (32308) SS BOND : bond 0.00654 ( 13) SS BOND : angle 1.19254 ( 26) hydrogen bonds : bond 0.03141 ( 1106) hydrogen bonds : angle 4.10837 ( 3279) link_NAG-ASN : bond 0.00504 ( 16) link_NAG-ASN : angle 3.28004 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.855 Fit side-chains REVERT: A 74 MET cc_start: 0.8574 (tpp) cc_final: 0.8154 (tpp) REVERT: B 161 ILE cc_start: 0.7211 (mm) cc_final: 0.6814 (mm) REVERT: B 162 MET cc_start: 0.7252 (mtt) cc_final: 0.6993 (mtt) REVERT: B 200 MET cc_start: 0.7830 (tpt) cc_final: 0.7594 (tpt) REVERT: B 653 MET cc_start: 0.7332 (mtt) cc_final: 0.7114 (mtt) REVERT: C 502 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7222 (mtm) REVERT: C 703 TYR cc_start: 0.6944 (t80) cc_final: 0.6732 (t80) REVERT: D 167 TYR cc_start: 0.7955 (m-80) cc_final: 0.7617 (m-80) REVERT: D 202 VAL cc_start: 0.8293 (t) cc_final: 0.8081 (p) REVERT: D 358 MET cc_start: 0.8650 (mmm) cc_final: 0.8408 (mmt) REVERT: D 616 ASN cc_start: 0.7814 (p0) cc_final: 0.7575 (p0) REVERT: D 638 PHE cc_start: 0.9210 (t80) cc_final: 0.8908 (t80) REVERT: D 818 MET cc_start: 0.7947 (mpp) cc_final: 0.7685 (mpp) outliers start: 27 outliers final: 14 residues processed: 233 average time/residue: 0.1461 time to fit residues: 55.3526 Evaluate side-chains 234 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 705 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 254 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.108784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.087354 restraints weight = 82649.834| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.40 r_work: 0.3514 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23690 Z= 0.118 Angle : 0.511 16.243 32382 Z= 0.258 Chirality : 0.042 0.480 3884 Planarity : 0.003 0.039 4088 Dihedral : 3.946 42.960 3656 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.20 % Allowed : 13.37 % Favored : 85.43 % 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: 0.61 (0.16), residues: 3116 helix: 2.05 (0.14), residues: 1309 sheet: -0.89 (0.26), residues: 422 loop : -0.77 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.016 0.001 TYR A 392 PHE 0.034 0.001 PHE D 671 TRP 0.011 0.001 TRP C 636 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00272 (23661) covalent geometry : angle 0.49505 (32308) SS BOND : bond 0.00251 ( 13) SS BOND : angle 1.21459 ( 26) hydrogen bonds : bond 0.03011 ( 1106) hydrogen bonds : angle 4.08208 ( 3279) link_NAG-ASN : bond 0.00505 ( 16) link_NAG-ASN : angle 3.20187 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.865 Fit side-chains REVERT: A 74 MET cc_start: 0.8594 (tpp) cc_final: 0.8193 (tpp) REVERT: A 392 TYR cc_start: 0.6325 (t80) cc_final: 0.5981 (t80) REVERT: B 74 MET cc_start: 0.6104 (mpp) cc_final: 0.5340 (ttm) REVERT: B 161 ILE cc_start: 0.7093 (mm) cc_final: 0.6710 (mm) REVERT: B 162 MET cc_start: 0.6908 (mtt) cc_final: 0.6672 (mtt) REVERT: B 200 MET cc_start: 0.7816 (tpt) cc_final: 0.7592 (tpt) REVERT: B 653 MET cc_start: 0.7227 (mtt) cc_final: 0.7025 (mtt) REVERT: C 159 ASN cc_start: 0.8305 (t0) cc_final: 0.8048 (t0) REVERT: C 498 TRP cc_start: 0.7879 (OUTLIER) cc_final: 0.7405 (m-10) REVERT: C 502 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7205 (mtm) REVERT: D 167 TYR cc_start: 0.7875 (m-80) cc_final: 0.7568 (m-80) REVERT: D 358 MET cc_start: 0.8498 (mmm) cc_final: 0.8244 (mmt) REVERT: D 616 ASN cc_start: 0.7736 (p0) cc_final: 0.7532 (p0) REVERT: D 638 PHE cc_start: 0.9324 (t80) cc_final: 0.9053 (t80) REVERT: D 818 MET cc_start: 0.7978 (mpp) cc_final: 0.7715 (mpp) outliers start: 27 outliers final: 16 residues processed: 233 average time/residue: 0.1643 time to fit residues: 61.2082 Evaluate side-chains 231 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 705 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 228 optimal weight: 4.9990 chunk 296 optimal weight: 0.0470 chunk 87 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN C 86 GLN C 101 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.107005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.088556 restraints weight = 81791.059| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.01 r_work: 0.3427 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 23690 Z= 0.205 Angle : 0.580 16.473 32382 Z= 0.297 Chirality : 0.044 0.448 3884 Planarity : 0.004 0.040 4088 Dihedral : 4.319 45.143 3656 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.24 % Allowed : 13.60 % Favored : 85.16 % 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: 0.32 (0.16), residues: 3116 helix: 1.75 (0.14), residues: 1323 sheet: -1.08 (0.27), residues: 411 loop : -0.89 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 695 TYR 0.031 0.001 TYR C 703 PHE 0.040 0.002 PHE C 639 TRP 0.013 0.001 TRP D 635 HIS 0.008 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00488 (23661) covalent geometry : angle 0.56375 (32308) SS BOND : bond 0.00376 ( 13) SS BOND : angle 1.34477 ( 26) hydrogen bonds : bond 0.03517 ( 1106) hydrogen bonds : angle 4.27285 ( 3279) link_NAG-ASN : bond 0.00505 ( 16) link_NAG-ASN : angle 3.42448 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.900 Fit side-chains REVERT: A 74 MET cc_start: 0.8576 (tpp) cc_final: 0.8162 (tpp) REVERT: A 113 PHE cc_start: 0.7734 (t80) cc_final: 0.7529 (t80) REVERT: B 161 ILE cc_start: 0.7374 (mm) cc_final: 0.6986 (mm) REVERT: B 162 MET cc_start: 0.7225 (mtt) cc_final: 0.6981 (mtt) REVERT: C 159 ASN cc_start: 0.8257 (t0) cc_final: 0.7990 (t0) REVERT: C 498 TRP cc_start: 0.8018 (OUTLIER) cc_final: 0.7706 (m-10) REVERT: C 502 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7447 (mtm) REVERT: C 555 MET cc_start: 0.7968 (mmt) cc_final: 0.7224 (tpp) REVERT: C 607 MET cc_start: 0.8269 (mtm) cc_final: 0.7711 (pmm) REVERT: D 89 MET cc_start: 0.7665 (mtp) cc_final: 0.7378 (mtp) REVERT: D 358 MET cc_start: 0.8630 (mmm) cc_final: 0.8326 (mmt) REVERT: D 616 ASN cc_start: 0.7838 (p0) cc_final: 0.7609 (p0) outliers start: 28 outliers final: 19 residues processed: 239 average time/residue: 0.1470 time to fit residues: 57.1783 Evaluate side-chains 236 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 671 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 207 optimal weight: 0.1980 chunk 263 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 291 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN C 101 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.108380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.089861 restraints weight = 82706.193| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.94 r_work: 0.3481 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23690 Z= 0.105 Angle : 0.530 15.201 32382 Z= 0.267 Chirality : 0.043 0.494 3884 Planarity : 0.003 0.040 4088 Dihedral : 4.050 43.878 3656 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.80 % Allowed : 14.57 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 3116 helix: 1.85 (0.14), residues: 1323 sheet: -1.07 (0.26), residues: 416 loop : -0.78 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 181 TYR 0.022 0.001 TYR C 703 PHE 0.035 0.001 PHE D 671 TRP 0.017 0.001 TRP C 498 HIS 0.004 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00229 (23661) covalent geometry : angle 0.51492 (32308) SS BOND : bond 0.00336 ( 13) SS BOND : angle 1.55283 ( 26) hydrogen bonds : bond 0.03050 ( 1106) hydrogen bonds : angle 4.13236 ( 3279) link_NAG-ASN : bond 0.00522 ( 16) link_NAG-ASN : angle 3.15535 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8545 (tpp) cc_final: 0.8080 (tpp) REVERT: A 240 MET cc_start: 0.5480 (mmm) cc_final: 0.4902 (tpp) REVERT: B 74 MET cc_start: 0.5951 (mpp) cc_final: 0.5026 (ttm) REVERT: B 161 ILE cc_start: 0.7278 (mm) cc_final: 0.6885 (mm) REVERT: B 162 MET cc_start: 0.7271 (mtt) cc_final: 0.7019 (mtt) REVERT: C 159 ASN cc_start: 0.8382 (t0) cc_final: 0.8127 (t0) REVERT: C 237 MET cc_start: 0.8120 (tmm) cc_final: 0.7856 (ppp) REVERT: C 502 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7319 (mtm) REVERT: C 555 MET cc_start: 0.7987 (mmt) cc_final: 0.7226 (tpp) REVERT: D 167 TYR cc_start: 0.8001 (m-80) cc_final: 0.7573 (m-80) REVERT: D 358 MET cc_start: 0.8611 (mmm) cc_final: 0.8311 (mmt) REVERT: D 616 ASN cc_start: 0.7872 (p0) cc_final: 0.7620 (p0) REVERT: D 789 MET cc_start: 0.8732 (tpp) cc_final: 0.8441 (mmm) outliers start: 18 outliers final: 13 residues processed: 227 average time/residue: 0.1550 time to fit residues: 56.7821 Evaluate side-chains 226 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain D residue 671 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 156 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 243 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN C 86 GLN C 101 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.116003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.093065 restraints weight = 74850.577| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.99 r_work: 0.3434 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23690 Z= 0.176 Angle : 0.565 15.510 32382 Z= 0.287 Chirality : 0.044 0.455 3884 Planarity : 0.003 0.039 4088 Dihedral : 4.126 44.636 3656 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.84 % Allowed : 14.75 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 3116 helix: 1.78 (0.14), residues: 1326 sheet: -1.09 (0.27), residues: 412 loop : -0.85 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 181 TYR 0.015 0.001 TYR A 392 PHE 0.039 0.002 PHE C 639 TRP 0.024 0.001 TRP C 56 HIS 0.007 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00414 (23661) covalent geometry : angle 0.54990 (32308) SS BOND : bond 0.00350 ( 13) SS BOND : angle 1.59795 ( 26) hydrogen bonds : bond 0.03264 ( 1106) hydrogen bonds : angle 4.19134 ( 3279) link_NAG-ASN : bond 0.00480 ( 16) link_NAG-ASN : angle 3.22002 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6232 Ramachandran restraints generated. 3116 Oldfield, 0 Emsley, 3116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8614 (tpp) cc_final: 0.8162 (tpp) REVERT: A 240 MET cc_start: 0.5535 (mmm) cc_final: 0.4911 (tpp) REVERT: B 161 ILE cc_start: 0.7207 (mm) cc_final: 0.6865 (mm) REVERT: B 162 MET cc_start: 0.6995 (mtt) cc_final: 0.6786 (mtt) REVERT: C 159 ASN cc_start: 0.8385 (t0) cc_final: 0.8115 (t0) REVERT: C 237 MET cc_start: 0.8096 (tmm) cc_final: 0.7886 (ptm) REVERT: C 502 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7264 (mtm) REVERT: C 555 MET cc_start: 0.7904 (mmt) cc_final: 0.7305 (tpp) REVERT: D 358 MET cc_start: 0.8499 (mmm) cc_final: 0.8194 (mmt) REVERT: D 616 ASN cc_start: 0.7773 (p0) cc_final: 0.7527 (p0) outliers start: 19 outliers final: 16 residues processed: 222 average time/residue: 0.1522 time to fit residues: 54.8133 Evaluate side-chains 227 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 671 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN C 86 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.112599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.090765 restraints weight = 81034.926| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.53 r_work: 0.3466 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23690 Z= 0.162 Angle : 0.560 15.002 32382 Z= 0.283 Chirality : 0.043 0.468 3884 Planarity : 0.003 0.040 4088 Dihedral : 4.168 44.923 3656 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.97 % Allowed : 14.84 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 3116 helix: 1.73 (0.14), residues: 1324 sheet: -1.16 (0.26), residues: 414 loop : -0.86 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 181 TYR 0.014 0.001 TYR C 703 PHE 0.039 0.002 PHE C 639 TRP 0.020 0.001 TRP C 56 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00382 (23661) covalent geometry : angle 0.54543 (32308) SS BOND : bond 0.00298 ( 13) SS BOND : angle 1.48539 ( 26) hydrogen bonds : bond 0.03235 ( 1106) hydrogen bonds : angle 4.21962 ( 3279) link_NAG-ASN : bond 0.00446 ( 16) link_NAG-ASN : angle 3.19332 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6555.67 seconds wall clock time: 112 minutes 46.09 seconds (6766.09 seconds total)