Starting phenix.real_space_refine on Thu Mar 5 18:00:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unq_64360/03_2026/9unq_64360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unq_64360/03_2026/9unq_64360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9unq_64360/03_2026/9unq_64360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unq_64360/03_2026/9unq_64360.map" model { file = "/net/cci-nas-00/data/ceres_data/9unq_64360/03_2026/9unq_64360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unq_64360/03_2026/9unq_64360.cif" } resolution = 3.2 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= 0.014 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 15142 2.51 5 N 3906 2.21 5 O 4365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23551 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5852 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 34, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 25, 'GLN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 293 Chain: "B" Number of atoms: 5681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5681 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 28, 'TRANS': 750} Chain breaks: 3 Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 628 Unresolved non-hydrogen dihedrals: 442 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 5, 'HIS:plan': 4, 'ASP:plan': 17, 'ARG:plan': 12, 'TRP:plan': 2, 'GLU:plan': 23, 'GLN:plan1': 5, 'PHE:plan': 8, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 352 Chain: "C" Number of atoms: 5944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5944 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 32, 'TRANS': 758} Chain breaks: 3 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 13, 'TRP:plan': 1, 'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 9, 'HIS:plan': 1, 'GLU:plan': 19, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 232 Chain: "D" Number of atoms: 5768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5768 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 29, 'TRANS': 745} Chain breaks: 4 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 9, 'HIS:plan': 5, 'GLU:plan': 25, 'GLN:plan1': 6, 'TYR:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 244 Chain: "A" 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: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {'NAG': 8} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 4.79, per 1000 atoms: 0.20 Number of scatterers: 23551 At special positions: 0 Unit cell: (106.555, 142.425, 181.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 4365 8.00 N 3906 7.00 C 15142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, 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 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 276 " " NAG A 904 " - " ASN A 471 " " NAG A 905 " - " ASN A 771 " " NAG A 906 " - " ASN A 203 " " NAG A 907 " - " ASN A 368 " " NAG B 901 " - " ASN B 75 " " NAG B 902 " - " 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 C 908 " - " ASN C 203 " " NAG D 901 " - " ASN D 341 " " NAG D 902 " - " ASN D 348 " " NAG D 903 " - " ASN D 688 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 767.3 milliseconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5864 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 32 sheets defined 45.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.649A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 126 through 130 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 159 removed outlier: 4.136A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.824A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) 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 255 removed outlier: 3.885A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.738A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.094A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.260A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.694A pdb=" N PHE A 583 " --> pdb=" O LEU A 579 " (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 708 removed outlier: 3.911A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 817 through 841 removed outlier: 4.179A pdb=" N ALA A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.670A pdb=" N LEU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 106 through 120 removed outlier: 4.182A pdb=" N ALA B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 287 through 310 Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.501A pdb=" N GLY B 345 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 555 through 579 removed outlier: 4.286A pdb=" N VAL B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 614 removed outlier: 4.841A pdb=" N ILE B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 653 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 741 Processing helix chain 'B' and resid 770 through 785 removed outlier: 4.540A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 removed outlier: 3.526A pdb=" N GLU B 790 " --> pdb=" O GLY B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 839 removed outlier: 3.894A pdb=" N PHE B 821 " --> pdb=" O MET B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 70 through 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: 4.606A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.658A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 4.283A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.724A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.849A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 256 through 261 removed outlier: 4.027A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.889A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.879A 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 520 through 527 removed outlier: 3.607A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 556 removed outlier: 3.658A pdb=" N MET C 555 " --> pdb=" O ASP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 582 removed outlier: 3.701A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 580 " --> pdb=" O MET C 576 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.850A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 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 783 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 810 through 842 removed outlier: 3.614A pdb=" N ALA C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 removed outlier: 3.625A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.112A pdb=" N ALA D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.606A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 212 through 221 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: 3.521A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.695A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 496 through 503 removed outlier: 3.544A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.763A pdb=" N ALA D 556 " --> pdb=" O PRO D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 577 Processing helix chain 'D' and resid 601 through 613 Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.643A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET D 631 " --> pdb=" O THR D 627 " (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 771 through 786 removed outlier: 4.389A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 796 Processing helix chain 'D' and resid 818 through 842 removed outlier: 3.633A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 7.600A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.915A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.149A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 5.997A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.436A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.940A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.787A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 40 removed outlier: 5.570A pdb=" N VAL B 38 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 206 removed outlier: 6.790A pdb=" N PHE B 170 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN B 202 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 175 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 227 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TRP B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL B 279 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL B 257 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N TYR B 281 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 376 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 474 through 479 removed outlier: 3.651A pdb=" N MET B 507 " --> pdb=" O SER B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB4, first strand: chain 'B' and resid 437 through 440 removed outlier: 3.712A pdb=" N VAL B 440 " --> pdb=" O MET B 450 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET B 450 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB6, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.455A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.951A 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 683 removed outlier: 6.455A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR B 531 " --> pdb=" O THR B 758 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR B 758 " --> pdb=" O THR B 531 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 64 removed outlier: 7.984A pdb=" N TYR C 88 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL C 92 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.546A 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: 3.881A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.436A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 478 removed outlier: 8.328A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC4, first strand: chain 'C' and resid 486 through 489 removed outlier: 3.650A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.758A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.667A pdb=" N MET D 73 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 198 through 204 removed outlier: 8.392A pdb=" N ILE D 171 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL D 202 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR D 173 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D 204 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 277 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN D 385 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AC9, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD1, first strand: chain 'D' and resid 409 through 410 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 488 through 490 Processing sheet with id=AD4, first strand: chain 'D' and resid 683 through 684 removed outlier: 3.558A pdb=" N ILE D 730 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 683 through 684 removed outlier: 3.558A pdb=" N ILE D 730 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3291 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: 4.44 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7529 1.34 - 1.46: 5570 1.46 - 1.58: 10724 1.58 - 1.70: 0 1.70 - 1.82: 238 Bond restraints: 24061 Sorted by residual: bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 NAG C 906 " pdb=" O5 NAG C 906 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG A 907 " pdb=" O5 NAG A 907 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 24056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 32587 2.52 - 5.04: 215 5.04 - 7.56: 9 7.56 - 10.08: 3 10.08 - 12.60: 1 Bond angle restraints: 32815 Sorted by residual: angle pdb=" C GLY A 485 " pdb=" N THR A 486 " pdb=" CA THR A 486 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" N GLY A 457 " pdb=" CA GLY A 457 " pdb=" C GLY A 457 " ideal model delta sigma weight residual 110.43 115.44 -5.01 1.35e+00 5.49e-01 1.37e+01 angle pdb=" CA LEU B 334 " pdb=" CB LEU B 334 " pdb=" CG LEU B 334 " ideal model delta sigma weight residual 116.30 128.90 -12.60 3.50e+00 8.16e-02 1.30e+01 angle pdb=" CB MET C 209 " pdb=" CG MET C 209 " pdb=" SD MET C 209 " ideal model delta sigma weight residual 112.70 121.19 -8.49 3.00e+00 1.11e-01 8.02e+00 angle pdb=" CA VAL B 257 " pdb=" C VAL B 257 " pdb=" N PRO B 258 " ideal model delta sigma weight residual 116.57 119.14 -2.57 9.80e-01 1.04e+00 6.89e+00 ... (remaining 32810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 13102 17.25 - 34.50: 1029 34.50 - 51.75: 203 51.75 - 68.99: 69 68.99 - 86.24: 12 Dihedral angle restraints: 14415 sinusoidal: 5331 harmonic: 9084 Sorted by residual: dihedral pdb=" CB CYS B 745 " pdb=" SG CYS B 745 " pdb=" SG CYS B 800 " pdb=" CB CYS B 800 " ideal model delta sinusoidal sigma weight residual 93.00 166.94 -73.94 1 1.00e+01 1.00e-02 6.94e+01 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 23.23 69.77 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS C 420 " pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " pdb=" CB CYS C 454 " ideal model delta sinusoidal sigma weight residual 93.00 125.46 -32.46 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 14412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3389 0.060 - 0.119: 511 0.119 - 0.178: 21 0.178 - 0.238: 2 0.238 - 0.297: 3 Chirality restraints: 3926 Sorted by residual: chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 276 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 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 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1 NAG A 907 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG A 907 " pdb=" O5 NAG A 907 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 3923 not shown) Planarity restraints: 4151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 319 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 554 " -0.008 2.00e-02 2.50e+03 1.10e-02 2.12e+00 pdb=" CG PHE C 554 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 554 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 554 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 554 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 554 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 554 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 303 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO C 304 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 304 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 304 " -0.019 5.00e-02 4.00e+02 ... (remaining 4148 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 351 2.68 - 3.23: 23152 3.23 - 3.79: 37781 3.79 - 4.34: 48705 4.34 - 4.90: 81222 Nonbonded interactions: 191211 Sorted by model distance: nonbonded pdb=" OD2 ASP B 731 " pdb=" OH TYR B 761 " model vdw 2.124 3.040 nonbonded pdb=" O ASP A 198 " pdb=" OG1 THR A 201 " model vdw 2.193 3.040 nonbonded pdb=" OH TYR D 287 " pdb=" OD2 ASP D 295 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR A 550 " pdb=" OD1 ASP A 552 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR B 286 " pdb=" OD2 ASP B 294 " model vdw 2.254 3.040 ... (remaining 191206 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 28 through 100 or (resid 101 through 102 and (name N or na \ me CA or name C or name O or name CB )) or resid 103 through 191 or (resid 192 t \ hrough 193 and (name N or name CA or name C or name O or name CB )) or resid 194 \ through 225 or (resid 226 and (name N or name CA or name C or name O or name CB \ )) or resid 227 through 252 or (resid 253 and (name N or name CA or name C or n \ ame O or name CB )) or resid 254 through 389 or (resid 390 and (name N or name C \ A or name C or name O or name CB )) or resid 391 through 416 or (resid 417 and ( \ name N or name CA or name C or name O or name CB )) or resid 418 through 474 or \ (resid 475 and (name N or name CA or name C or name O or name CB )) or resid 476 \ through 492 or (resid 493 through 495 and (name N or name CA or name C or name \ O or name CB )) or resid 496 through 550 or (resid 551 through 552 and (name N o \ r name CA or name C or name O or name CB )) or resid 553 through 554 or (resid 5 \ 55 through 556 and (name N or name CA or name C or name O or name CB )) or resid \ 557 through 558 or (resid 559 and (name N or name CA or name C or name O or nam \ e CB )) or resid 560 through 583 or (resid 601 and (name N or name CA or name C \ or name O or name CB )) or resid 602 through 653 or (resid 654 and (name N or na \ me CA or name C or name O or name CB )) or resid 655 through 657 or (resid 661 t \ hrough 663 and (name N or name CA or name C or name O or name 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 769 or (resid 770 and (name N or name CA or name C or n \ ame O or name CB )) or resid 771 through 908)) selection = (chain 'C' and (resid 28 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 43 or (resid 44 through \ 45 and (name N or name CA or name C or name O or name CB )) or resid 46 through \ 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name C \ B )) or resid 50 or (resid 51 through 53 and (name N or name CA or name C or nam \ e O or name CB )) or resid 54 through 85 or (resid 86 and (name N or name CA or \ name C or name O or name CB )) or resid 87 through 101 or (resid 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throu \ gh 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) or \ resid 276 through 292 or (resid 293 and (name N or name CA or name C or name O \ or name CB )) or resid 294 through 296 or (resid 297 through 299 and (name N or \ name CA or name C or name O or name CB )) or resid 300 through 302 or (resid 303 \ and (name N or name CA or name C or name O or name CB )) or resid 304 through 3 \ 15 or (resid 316 and (name N or name CA or name C or name O or name CB )) or res \ id 317 through 321 or (resid 322 and (name N or name CA or name C or name O or n \ ame CB )) or resid 323 through 328 or (resid 329 and (name N or name CA or name \ C or name O or name CB )) or resid 330 through 358 or (resid 359 through 360 and \ (name N or name CA or name C or name O or name CB )) or resid 361 through 377 o \ r (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 79 through 405 or (resid 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 521 or (resid 522 and (name N or name CA or name C or \ name O or name CB )) or resid 523 through 656 or (resid 657 through 663 and (na \ me N or name CA or name C or name O or name CB )) or resid 664 through 672 or (r \ esid 673 through 674 and (name N or name CA or name C or name O or name CB )) or \ resid 675 through 694 or (resid 695 and (name N or name CA or name C or name O \ or name CB )) or resid 696 through 698 or (resid 699 and (name N or name CA or n \ ame C or name O or name CB )) or resid 700 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 (resid \ 737 and (name N or name CA or name C or name O or name CB )) or resid 738 or (r \ esid 739 through 740 and (name N or name CA or name C or name O or name CB )) or \ 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 n \ ame 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 796 or (resid \ 797 and (name N or name CA or name C or name O or name CB )) or resid 798 throu \ gh 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 name CA or name \ C or name O or name CB )) or resid 815 through 816 or (resid 817 and (name N or \ name CA or name C or name O or name CB )) or resid 818 through 831 or (resid 832 \ and (name N or name CA or name C or name O or name CB )) or resid 833 through 8 \ 39 or (resid 840 through 841 and (name N or name CA or name C or name O or name \ CB )) or resid 902 through 909)) } 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: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.450 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 0.036 24093 Z= 0.115 Angle : 0.491 12.601 32899 Z= 0.241 Chirality : 0.042 0.297 3926 Planarity : 0.003 0.040 4131 Dihedral : 13.373 86.242 8515 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.86 (0.16), residues: 3105 helix: 2.18 (0.14), residues: 1289 sheet: -0.52 (0.29), residues: 369 loop : -0.62 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.012 0.001 TYR A 367 PHE 0.025 0.001 PHE C 554 TRP 0.012 0.001 TRP B 558 HIS 0.002 0.000 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00232 (24061) covalent geometry : angle 0.48233 (32815) SS BOND : bond 0.00190 ( 12) SS BOND : angle 1.02771 ( 24) hydrogen bonds : bond 0.16430 ( 1126) hydrogen bonds : angle 5.87858 ( 3291) link_NAG-ASN : bond 0.00519 ( 20) link_NAG-ASN : angle 2.12833 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.8407 (ttp) cc_final: 0.8192 (ttp) REVERT: C 415 MET cc_start: 0.6996 (mmm) cc_final: 0.6550 (mtm) REVERT: D 654 MET cc_start: 0.7195 (mpp) cc_final: 0.6886 (mpp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1488 time to fit residues: 54.4565 Evaluate side-chains 205 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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: 0.0470 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 363 GLN A 521 ASN B 153 GLN B 335 HIS B 380 ASN B 615 ASN D 192 ASN D 840 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.108939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.086704 restraints weight = 70442.811| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.16 r_work: 0.3453 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24093 Z= 0.121 Angle : 0.498 10.180 32899 Z= 0.257 Chirality : 0.043 0.342 3926 Planarity : 0.003 0.053 4131 Dihedral : 5.383 55.664 3728 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.43 % Allowed : 6.16 % Favored : 93.41 % 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: 0.79 (0.16), residues: 3105 helix: 2.09 (0.14), residues: 1312 sheet: -0.59 (0.28), residues: 388 loop : -0.65 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 124 TYR 0.017 0.001 TYR A 367 PHE 0.021 0.001 PHE A 554 TRP 0.009 0.001 TRP A 636 HIS 0.005 0.001 HIS D 840 Details of bonding type rmsd covalent geometry : bond 0.00269 (24061) covalent geometry : angle 0.48810 (32815) SS BOND : bond 0.00729 ( 12) SS BOND : angle 1.05618 ( 24) hydrogen bonds : bond 0.03697 ( 1126) hydrogen bonds : angle 4.64013 ( 3291) link_NAG-ASN : bond 0.00541 ( 20) link_NAG-ASN : angle 2.30217 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 230 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7826 (mmp) cc_final: 0.7600 (mmm) REVERT: A 583 PHE cc_start: 0.7654 (m-80) cc_final: 0.7433 (m-80) REVERT: B 337 PHE cc_start: 0.6637 (m-80) cc_final: 0.6325 (m-80) REVERT: B 788 MET cc_start: 0.8060 (mmt) cc_final: 0.7776 (mmt) REVERT: C 415 MET cc_start: 0.7098 (mmm) cc_final: 0.6598 (mtm) REVERT: C 607 MET cc_start: 0.8138 (mtp) cc_final: 0.7889 (mmm) REVERT: D 232 CYS cc_start: 0.7542 (p) cc_final: 0.6815 (p) REVERT: D 840 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.6636 (t-170) outliers start: 10 outliers final: 3 residues processed: 234 average time/residue: 0.1544 time to fit residues: 57.7958 Evaluate side-chains 212 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 18 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 284 optimal weight: 0.0060 chunk 97 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 184 optimal weight: 0.0670 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 0.0070 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 ASN C 363 GLN ** D 649 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 = 0.4085 r_free = 0.4085 target = 0.109115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.087486 restraints weight = 73016.411| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.16 r_work: 0.3455 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24093 Z= 0.095 Angle : 0.464 10.453 32899 Z= 0.238 Chirality : 0.042 0.352 3926 Planarity : 0.003 0.040 4131 Dihedral : 4.800 50.937 3728 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.43 % Allowed : 8.35 % Favored : 91.22 % 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: 0.85 (0.16), residues: 3105 helix: 2.16 (0.14), residues: 1303 sheet: -0.63 (0.28), residues: 384 loop : -0.59 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 695 TYR 0.016 0.001 TYR C 681 PHE 0.024 0.001 PHE D 836 TRP 0.009 0.001 TRP B 609 HIS 0.018 0.001 HIS D 840 Details of bonding type rmsd covalent geometry : bond 0.00204 (24061) covalent geometry : angle 0.45414 (32815) SS BOND : bond 0.00238 ( 12) SS BOND : angle 1.14031 ( 24) hydrogen bonds : bond 0.03351 ( 1126) hydrogen bonds : angle 4.40487 ( 3291) link_NAG-ASN : bond 0.00542 ( 20) link_NAG-ASN : angle 2.22993 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 216 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7766 (mmp) cc_final: 0.7526 (mmp) REVERT: A 583 PHE cc_start: 0.7621 (m-80) cc_final: 0.7394 (m-80) REVERT: B 337 PHE cc_start: 0.6475 (m-80) cc_final: 0.6115 (m-80) REVERT: B 502 TYR cc_start: 0.7969 (m-10) cc_final: 0.7729 (m-10) REVERT: B 788 MET cc_start: 0.8056 (mmt) cc_final: 0.7766 (mmt) REVERT: C 415 MET cc_start: 0.7065 (mmm) cc_final: 0.6571 (mtm) REVERT: C 554 PHE cc_start: 0.7632 (p90) cc_final: 0.7154 (p90) REVERT: C 607 MET cc_start: 0.8151 (mtp) cc_final: 0.7950 (mmm) REVERT: C 634 MET cc_start: 0.6655 (ptt) cc_final: 0.6355 (ptm) REVERT: D 232 CYS cc_start: 0.7394 (p) cc_final: 0.6747 (p) REVERT: D 681 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: D 840 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.6516 (t-170) outliers start: 10 outliers final: 6 residues processed: 219 average time/residue: 0.1490 time to fit residues: 52.5514 Evaluate side-chains 217 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 681 PHE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 71 optimal weight: 0.3980 chunk 170 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 168 optimal weight: 0.5980 chunk 64 optimal weight: 0.0020 chunk 252 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 267 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.113403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.091420 restraints weight = 69624.113| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.13 r_work: 0.3452 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24093 Z= 0.098 Angle : 0.463 11.385 32899 Z= 0.236 Chirality : 0.042 0.352 3926 Planarity : 0.003 0.040 4131 Dihedral : 4.300 48.725 3728 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.77 % Allowed : 9.55 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 3105 helix: 2.17 (0.14), residues: 1303 sheet: -0.64 (0.28), residues: 386 loop : -0.59 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.014 0.001 TYR C 681 PHE 0.022 0.001 PHE A 554 TRP 0.007 0.001 TRP B 558 HIS 0.003 0.000 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00217 (24061) covalent geometry : angle 0.45286 (32815) SS BOND : bond 0.00164 ( 12) SS BOND : angle 0.83820 ( 24) hydrogen bonds : bond 0.03130 ( 1126) hydrogen bonds : angle 4.27289 ( 3291) link_NAG-ASN : bond 0.00546 ( 20) link_NAG-ASN : angle 2.24993 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 240 MET cc_start: 0.7689 (mmp) cc_final: 0.7437 (mmp) REVERT: A 583 PHE cc_start: 0.7677 (m-80) cc_final: 0.7436 (m-80) REVERT: B 175 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8256 (p) REVERT: B 502 TYR cc_start: 0.7911 (m-10) cc_final: 0.7700 (m-10) REVERT: B 560 MET cc_start: 0.6921 (ppp) cc_final: 0.6697 (tmm) REVERT: B 788 MET cc_start: 0.8053 (mmt) cc_final: 0.7756 (mmt) REVERT: C 209 MET cc_start: 0.8562 (mmm) cc_final: 0.8348 (mmt) REVERT: C 634 MET cc_start: 0.6604 (ptt) cc_final: 0.6288 (ptm) REVERT: D 232 CYS cc_start: 0.7357 (p) cc_final: 0.6743 (p) REVERT: D 840 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.6773 (t-170) outliers start: 18 outliers final: 10 residues processed: 222 average time/residue: 0.1384 time to fit residues: 50.0428 Evaluate side-chains 218 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 241 optimal weight: 0.3980 chunk 101 optimal weight: 0.0670 chunk 85 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 303 optimal weight: 5.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 ASN B 380 ASN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.111625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.088894 restraints weight = 68996.815| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.18 r_work: 0.3384 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24093 Z= 0.170 Angle : 0.520 11.966 32899 Z= 0.265 Chirality : 0.043 0.346 3926 Planarity : 0.003 0.053 4131 Dihedral : 4.259 47.290 3728 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.94 % Allowed : 10.79 % Favored : 88.27 % 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: 0.62 (0.16), residues: 3105 helix: 1.93 (0.14), residues: 1318 sheet: -0.85 (0.27), residues: 403 loop : -0.67 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 468 TYR 0.020 0.001 TYR B 478 PHE 0.024 0.002 PHE C 627 TRP 0.013 0.001 TRP B 606 HIS 0.027 0.001 HIS D 840 Details of bonding type rmsd covalent geometry : bond 0.00403 (24061) covalent geometry : angle 0.50898 (32815) SS BOND : bond 0.00400 ( 12) SS BOND : angle 1.18986 ( 24) hydrogen bonds : bond 0.03442 ( 1126) hydrogen bonds : angle 4.37592 ( 3291) link_NAG-ASN : bond 0.00528 ( 20) link_NAG-ASN : angle 2.41570 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 218 VAL cc_start: 0.7253 (OUTLIER) cc_final: 0.6924 (m) REVERT: A 240 MET cc_start: 0.7743 (mmp) cc_final: 0.7530 (mmp) REVERT: A 564 LEU cc_start: 0.8435 (mm) cc_final: 0.8164 (mp) REVERT: A 583 PHE cc_start: 0.7709 (m-80) cc_final: 0.7434 (m-80) REVERT: A 632 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7334 (tp) REVERT: B 502 TYR cc_start: 0.8116 (m-10) cc_final: 0.7883 (m-10) REVERT: B 729 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8055 (mp) REVERT: C 501 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7671 (mtp) REVERT: C 641 MET cc_start: 0.8763 (tmm) cc_final: 0.8043 (ttp) REVERT: D 73 MET cc_start: 0.7503 (ttt) cc_final: 0.7151 (ttm) REVERT: D 232 CYS cc_start: 0.7388 (p) cc_final: 0.6774 (p) REVERT: D 621 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8520 (tm-30) outliers start: 22 outliers final: 13 residues processed: 230 average time/residue: 0.1407 time to fit residues: 53.6962 Evaluate side-chains 226 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 566 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 82 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 283 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 HIS ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.108869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.090431 restraints weight = 69438.679| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.96 r_work: 0.3271 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24093 Z= 0.267 Angle : 0.611 13.124 32899 Z= 0.313 Chirality : 0.047 0.345 3926 Planarity : 0.004 0.068 4131 Dihedral : 4.713 47.188 3728 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.46 % Allowed : 11.94 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3105 helix: 1.54 (0.14), residues: 1315 sheet: -0.97 (0.27), residues: 396 loop : -0.85 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 390 TYR 0.025 0.002 TYR B 478 PHE 0.039 0.002 PHE A 484 TRP 0.017 0.002 TRP B 606 HIS 0.011 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00642 (24061) covalent geometry : angle 0.59961 (32815) SS BOND : bond 0.00582 ( 12) SS BOND : angle 1.51747 ( 24) hydrogen bonds : bond 0.03951 ( 1126) hydrogen bonds : angle 4.68792 ( 3291) link_NAG-ASN : bond 0.00558 ( 20) link_NAG-ASN : angle 2.72178 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7180 (m) REVERT: A 354 MET cc_start: 0.7828 (tmm) cc_final: 0.7269 (tmm) REVERT: A 583 PHE cc_start: 0.7771 (m-80) cc_final: 0.7384 (m-80) REVERT: A 632 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7557 (tp) REVERT: B 649 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6121 (mp) REVERT: B 729 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8108 (mp) REVERT: C 169 ASP cc_start: 0.7676 (p0) cc_final: 0.7460 (p0) REVERT: C 394 MET cc_start: 0.7907 (mmm) cc_final: 0.7631 (ttm) REVERT: C 501 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8420 (mtp) REVERT: C 502 MET cc_start: 0.8954 (mmm) cc_final: 0.8722 (mmm) REVERT: C 607 MET cc_start: 0.8422 (tpp) cc_final: 0.8150 (tpp) REVERT: C 641 MET cc_start: 0.8870 (tmm) cc_final: 0.8350 (ttp) REVERT: C 702 MET cc_start: 0.7360 (mmt) cc_final: 0.7101 (mmt) REVERT: D 73 MET cc_start: 0.7801 (ttt) cc_final: 0.7298 (ttm) REVERT: D 232 CYS cc_start: 0.7586 (p) cc_final: 0.6991 (p) REVERT: D 334 MET cc_start: 0.8512 (tpp) cc_final: 0.8167 (mmp) REVERT: D 621 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8637 (tm-30) REVERT: D 654 MET cc_start: 0.7474 (mpp) cc_final: 0.6624 (mpp) REVERT: D 840 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.6725 (t-170) outliers start: 34 outliers final: 18 residues processed: 240 average time/residue: 0.1431 time to fit residues: 55.9621 Evaluate side-chains 230 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 282 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 270 optimal weight: 0.0980 chunk 227 optimal weight: 0.7980 chunk 292 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.110737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087561 restraints weight = 68837.517| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.09 r_work: 0.3383 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24093 Z= 0.122 Angle : 0.556 17.716 32899 Z= 0.275 Chirality : 0.044 0.460 3926 Planarity : 0.003 0.052 4131 Dihedral : 4.931 59.546 3728 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.11 % Allowed : 12.93 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3105 helix: 1.73 (0.14), residues: 1314 sheet: -0.79 (0.28), residues: 387 loop : -0.80 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 390 TYR 0.014 0.001 TYR C 410 PHE 0.028 0.001 PHE C 627 TRP 0.013 0.001 TRP C 792 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00278 (24061) covalent geometry : angle 0.52910 (32815) SS BOND : bond 0.00368 ( 12) SS BOND : angle 1.48567 ( 24) hydrogen bonds : bond 0.03440 ( 1126) hydrogen bonds : angle 4.47626 ( 3291) link_NAG-ASN : bond 0.00805 ( 20) link_NAG-ASN : angle 3.94123 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 VAL cc_start: 0.7247 (OUTLIER) cc_final: 0.7006 (m) REVERT: A 354 MET cc_start: 0.7358 (tmm) cc_final: 0.7085 (tmm) REVERT: A 583 PHE cc_start: 0.7782 (m-80) cc_final: 0.7490 (m-80) REVERT: A 632 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7379 (tp) REVERT: B 74 MET cc_start: 0.6541 (ttt) cc_final: 0.6124 (ttt) REVERT: B 649 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5938 (mp) REVERT: C 169 ASP cc_start: 0.7628 (p0) cc_final: 0.7398 (p0) REVERT: C 641 MET cc_start: 0.8810 (tmm) cc_final: 0.7744 (ttp) REVERT: D 73 MET cc_start: 0.7617 (ttt) cc_final: 0.7224 (ttm) REVERT: D 232 CYS cc_start: 0.7497 (p) cc_final: 0.6859 (p) REVERT: D 334 MET cc_start: 0.8388 (tpp) cc_final: 0.8148 (mmp) REVERT: D 654 MET cc_start: 0.7409 (mpp) cc_final: 0.6560 (mpp) REVERT: D 840 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.6670 (t-170) outliers start: 26 outliers final: 16 residues processed: 225 average time/residue: 0.1438 time to fit residues: 52.9091 Evaluate side-chains 222 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 681 PHE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 80 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 277 optimal weight: 4.9990 chunk 311 optimal weight: 8.9990 chunk 278 optimal weight: 0.6980 chunk 28 optimal weight: 0.0470 chunk 25 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 196 optimal weight: 1.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.109156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.090684 restraints weight = 69004.821| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.93 r_work: 0.3283 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24093 Z= 0.216 Angle : 0.606 16.316 32899 Z= 0.302 Chirality : 0.046 0.378 3926 Planarity : 0.004 0.059 4131 Dihedral : 4.754 46.169 3728 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.33 % Allowed : 13.57 % Favored : 85.10 % 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: 0.24 (0.15), residues: 3105 helix: 1.59 (0.14), residues: 1315 sheet: -0.99 (0.27), residues: 402 loop : -0.86 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 124 TYR 0.022 0.001 TYR B 478 PHE 0.029 0.002 PHE A 484 TRP 0.014 0.001 TRP B 606 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00515 (24061) covalent geometry : angle 0.58354 (32815) SS BOND : bond 0.00538 ( 12) SS BOND : angle 1.58807 ( 24) hydrogen bonds : bond 0.03710 ( 1126) hydrogen bonds : angle 4.57911 ( 3291) link_NAG-ASN : bond 0.00715 ( 20) link_NAG-ASN : angle 3.72907 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 VAL cc_start: 0.7587 (OUTLIER) cc_final: 0.7361 (m) REVERT: A 269 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6379 (pp) REVERT: A 330 TYR cc_start: 0.7639 (t80) cc_final: 0.7297 (t80) REVERT: A 354 MET cc_start: 0.7515 (tmm) cc_final: 0.6825 (tmm) REVERT: A 583 PHE cc_start: 0.7821 (m-80) cc_final: 0.7500 (m-80) REVERT: A 632 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7547 (tp) REVERT: B 630 MET cc_start: 0.8646 (tpp) cc_final: 0.8258 (tpp) REVERT: B 649 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6094 (mp) REVERT: C 326 MET cc_start: 0.8645 (mmm) cc_final: 0.8369 (mtt) REVERT: C 641 MET cc_start: 0.8956 (tmm) cc_final: 0.7866 (ttp) REVERT: D 73 MET cc_start: 0.7724 (ttt) cc_final: 0.7291 (ttm) REVERT: D 232 CYS cc_start: 0.7566 (p) cc_final: 0.6951 (p) REVERT: D 334 MET cc_start: 0.8510 (tpp) cc_final: 0.8271 (mmp) REVERT: D 621 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8619 (tm-30) REVERT: D 654 MET cc_start: 0.7481 (mpp) cc_final: 0.6887 (mpp) outliers start: 31 outliers final: 20 residues processed: 232 average time/residue: 0.1421 time to fit residues: 54.4256 Evaluate side-chains 225 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 681 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 45 optimal weight: 0.5980 chunk 227 optimal weight: 0.8980 chunk 274 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 chunk 293 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.110452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087691 restraints weight = 69129.881| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.17 r_work: 0.3373 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24093 Z= 0.131 Angle : 0.565 16.055 32899 Z= 0.278 Chirality : 0.044 0.323 3926 Planarity : 0.003 0.055 4131 Dihedral : 4.471 45.175 3728 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.28 % Allowed : 13.83 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3105 helix: 1.70 (0.14), residues: 1312 sheet: -0.86 (0.28), residues: 383 loop : -0.82 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.014 0.001 TYR C 410 PHE 0.032 0.002 PHE C 627 TRP 0.014 0.001 TRP D 635 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00307 (24061) covalent geometry : angle 0.54451 (32815) SS BOND : bond 0.00515 ( 12) SS BOND : angle 1.02493 ( 24) hydrogen bonds : bond 0.03354 ( 1126) hydrogen bonds : angle 4.44376 ( 3291) link_NAG-ASN : bond 0.00643 ( 20) link_NAG-ASN : angle 3.57198 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.7133 (m) REVERT: A 237 MET cc_start: 0.8570 (ptp) cc_final: 0.8308 (ppp) REVERT: A 269 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6105 (pp) REVERT: A 354 MET cc_start: 0.7480 (tmm) cc_final: 0.6812 (tmm) REVERT: A 583 PHE cc_start: 0.7830 (m-80) cc_final: 0.7535 (m-80) REVERT: B 630 MET cc_start: 0.8568 (tpp) cc_final: 0.8240 (tpp) REVERT: B 649 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.6111 (mp) REVERT: C 326 MET cc_start: 0.8475 (mmm) cc_final: 0.8181 (mtt) REVERT: C 641 MET cc_start: 0.8873 (tmm) cc_final: 0.7749 (ttp) REVERT: D 73 MET cc_start: 0.7614 (ttt) cc_final: 0.7011 (ttp) REVERT: D 232 CYS cc_start: 0.7498 (p) cc_final: 0.6873 (p) REVERT: D 334 MET cc_start: 0.8384 (tpp) cc_final: 0.8145 (mmp) REVERT: D 508 MET cc_start: 0.7634 (mtp) cc_final: 0.7402 (mtm) REVERT: D 621 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8526 (tm-30) REVERT: D 654 MET cc_start: 0.7345 (mpp) cc_final: 0.6910 (mpp) outliers start: 30 outliers final: 21 residues processed: 223 average time/residue: 0.1393 time to fit residues: 51.6199 Evaluate side-chains 223 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 681 PHE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 60 optimal weight: 0.5980 chunk 301 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 223 optimal weight: 0.5980 chunk 271 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.106545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.083759 restraints weight = 70079.048| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.16 r_work: 0.3375 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24093 Z= 0.124 Angle : 0.566 15.776 32899 Z= 0.279 Chirality : 0.043 0.323 3926 Planarity : 0.003 0.050 4131 Dihedral : 4.371 44.257 3728 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.20 % Allowed : 14.21 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3105 helix: 1.72 (0.14), residues: 1314 sheet: -0.85 (0.28), residues: 383 loop : -0.80 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.013 0.001 TYR C 410 PHE 0.027 0.001 PHE C 554 TRP 0.014 0.001 TRP D 635 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00288 (24061) covalent geometry : angle 0.54520 (32815) SS BOND : bond 0.00518 ( 12) SS BOND : angle 1.87606 ( 24) hydrogen bonds : bond 0.03317 ( 1126) hydrogen bonds : angle 4.39844 ( 3291) link_NAG-ASN : bond 0.00631 ( 20) link_NAG-ASN : angle 3.40527 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 218 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7108 (m) REVERT: A 269 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6235 (pp) REVERT: A 354 MET cc_start: 0.7527 (tmm) cc_final: 0.6881 (tmm) REVERT: A 583 PHE cc_start: 0.7836 (m-80) cc_final: 0.7538 (m-80) REVERT: B 175 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 630 MET cc_start: 0.8527 (tpp) cc_final: 0.8206 (tpp) REVERT: B 649 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6129 (mp) REVERT: C 326 MET cc_start: 0.8477 (mmm) cc_final: 0.8187 (mtt) REVERT: D 73 MET cc_start: 0.7612 (ttt) cc_final: 0.7004 (ttp) REVERT: D 232 CYS cc_start: 0.7533 (p) cc_final: 0.6924 (p) REVERT: D 470 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8359 (tppt) REVERT: D 508 MET cc_start: 0.7641 (mtp) cc_final: 0.7410 (mtm) REVERT: D 621 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8548 (tm-30) REVERT: D 654 MET cc_start: 0.7335 (mpp) cc_final: 0.6930 (mpp) outliers start: 28 outliers final: 20 residues processed: 218 average time/residue: 0.1424 time to fit residues: 51.3256 Evaluate side-chains 223 residues out of total 2729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 574 PHE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 681 PHE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 282 optimal weight: 0.0040 chunk 231 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 166 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 272 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 chunk 192 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 206 optimal weight: 0.1980 chunk 171 optimal weight: 0.9980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 661 GLN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.111451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.092676 restraints weight = 68738.847| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.74 r_work: 0.3371 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24093 Z= 0.098 Angle : 0.536 13.683 32899 Z= 0.266 Chirality : 0.043 0.322 3926 Planarity : 0.003 0.043 4131 Dihedral : 4.179 42.985 3728 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.94 % Allowed : 14.73 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 3105 helix: 1.78 (0.14), residues: 1315 sheet: -0.82 (0.28), residues: 380 loop : -0.73 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.013 0.001 TYR C 410 PHE 0.033 0.001 PHE C 627 TRP 0.018 0.001 TRP D 635 HIS 0.014 0.001 HIS D 840 Details of bonding type rmsd covalent geometry : bond 0.00210 (24061) covalent geometry : angle 0.51872 (32815) SS BOND : bond 0.00266 ( 12) SS BOND : angle 1.40431 ( 24) hydrogen bonds : bond 0.03086 ( 1126) hydrogen bonds : angle 4.28629 ( 3291) link_NAG-ASN : bond 0.00627 ( 20) link_NAG-ASN : angle 3.13896 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5586.02 seconds wall clock time: 96 minutes 14.73 seconds (5774.73 seconds total)