Starting phenix.real_space_refine on Thu Mar 5 19:43:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eou_31231/03_2026/7eou_31231_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eou_31231/03_2026/7eou_31231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eou_31231/03_2026/7eou_31231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eou_31231/03_2026/7eou_31231.map" model { file = "/net/cci-nas-00/data/ceres_data/7eou_31231/03_2026/7eou_31231_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eou_31231/03_2026/7eou_31231_trim.cif" } resolution = 4.3 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 152 5.16 5 C 15769 2.51 5 N 4118 2.21 5 O 4552 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 24593 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5989 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 730} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6163 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 32, 'TRANS': 750} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 5989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5989 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 730} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6163 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 32, 'TRANS': 750} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' AA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 123 Unusual residues: {'6RM': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'6RM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.44, per 1000 atoms: 0.22 Number of scatterers: 24593 At special positions: 0 Unit cell: (118.8, 145.8, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 F 2 9.00 O 4552 8.00 N 4118 7.00 C 15769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 800 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 800 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 798 " 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 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 203 " " NAG B 903 " - " ASN B 239 " " NAG B 904 " - " ASN B 276 " " NAG B 905 " - " ASN B 368 " " NAG B 906 " - " ASN B 471 " " NAG B 907 " - " ASN B 771 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 203 " " NAG D 903 " - " ASN D 239 " " NAG D 904 " - " ASN D 276 " " NAG D 905 " - " ASN D 368 " " NAG D 906 " - " ASN D 471 " " NAG D 907 " - " ASN D 771 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5768 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 24 sheets defined 44.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 129 through 133 removed outlier: 4.096A pdb=" N MET A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.919A pdb=" N VAL A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.876A pdb=" N VAL A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 removed outlier: 4.460A pdb=" N ASN A 264 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 310 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.592A pdb=" N VAL A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.838A pdb=" N ARG A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.999A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.746A pdb=" N ALA A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 579 removed outlier: 3.824A pdb=" N MET A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 removed outlier: 4.812A pdb=" N ILE A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 653 removed outlier: 3.839A pdb=" N MET A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.775A pdb=" N GLN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 removed outlier: 3.613A pdb=" N TYR A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 676' Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.579A pdb=" N HIS A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 732 through 742 Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 774 through 786 Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 814 through 837 removed outlier: 4.130A pdb=" N MET A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.918A pdb=" N LYS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.715A pdb=" N PHE B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.833A pdb=" N GLN B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 186 removed outlier: 4.136A pdb=" N GLU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 224 through 238 removed outlier: 4.239A pdb=" N ALA B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 276 through 296 removed outlier: 3.721A pdb=" N GLN B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.245A pdb=" N GLU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 3.585A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.783A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.779A pdb=" N HIS B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 Processing helix chain 'B' and resid 627 through 657 removed outlier: 3.585A pdb=" N ILE B 631 " --> pdb=" O PHE B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.538A pdb=" N ASN B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 699 through 701 No H-bonds generated for 'chain 'B' and resid 699 through 701' Processing helix chain 'B' and resid 702 through 707 removed outlier: 3.572A pdb=" N GLU B 707 " --> pdb=" O TYR B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 769 through 782 Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 810 through 843 removed outlier: 4.456A pdb=" N VAL B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 59 Proline residue: C 57 - end of helix Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 129 through 133 removed outlier: 4.094A pdb=" N MET C 133 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 213 through 221 removed outlier: 3.901A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.867A pdb=" N VAL C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 removed outlier: 4.470A pdb=" N ASN C 264 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.594A pdb=" N VAL C 339 " --> pdb=" O PRO C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 removed outlier: 3.830A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 515 through 522 removed outlier: 3.957A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.502A pdb=" N SER C 554 " --> pdb=" O GLU C 551 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 551 through 555' Processing helix chain 'C' and resid 556 through 579 removed outlier: 3.822A pdb=" N MET C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 removed outlier: 4.813A pdb=" N ILE C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 653 removed outlier: 3.819A pdb=" N MET C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.777A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 695 Processing helix chain 'C' and resid 698 through 708 removed outlier: 3.584A pdb=" N HIS C 702 " --> pdb=" O TYR C 698 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'C' and resid 732 through 742 Processing helix chain 'C' and resid 743 through 745 No H-bonds generated for 'chain 'C' and resid 743 through 745' Processing helix chain 'C' and resid 774 through 786 Processing helix chain 'C' and resid 788 through 796 Processing helix chain 'C' and resid 814 through 837 removed outlier: 4.061A pdb=" N MET C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 825 " --> pdb=" O PHE C 821 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 50 Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.719A pdb=" N PHE D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.797A pdb=" N GLN D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 186 removed outlier: 4.123A pdb=" N GLU D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 224 through 238 removed outlier: 4.247A pdb=" N ALA D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 276 through 296 removed outlier: 3.724A pdb=" N GLN D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 458 through 471 removed outlier: 3.682A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.769A pdb=" N TYR D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 removed outlier: 3.785A pdb=" N HIS D 571 " --> pdb=" O GLY D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 616 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.587A pdb=" N ILE D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 674 removed outlier: 3.536A pdb=" N ASN D 674 " --> pdb=" O PRO D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 695 Processing helix chain 'D' and resid 699 through 701 No H-bonds generated for 'chain 'D' and resid 699 through 701' Processing helix chain 'D' and resid 702 through 707 removed outlier: 3.574A pdb=" N GLU D 707 " --> pdb=" O TYR D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 769 through 782 removed outlier: 3.616A pdb=" N SER D 775 " --> pdb=" O ASN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 810 through 843 removed outlier: 4.453A pdb=" N VAL D 816 " --> pdb=" O ASN D 812 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 73 removed outlier: 3.662A pdb=" N LEU A 72 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 98 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 206 removed outlier: 6.672A pdb=" N LEU A 172 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU A 206 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 174 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 175 " --> pdb=" O TYR A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 278 through 280 removed outlier: 3.523A pdb=" N GLU A 373 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.444A pdb=" N LEU A 406 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR A 478 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 408 " --> pdb=" O TYR A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 439 through 441 removed outlier: 4.097A pdb=" N VAL A 440 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET A 450 " --> pdb=" O VAL A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 682 through 683 removed outlier: 6.056A pdb=" N GLY A 683 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N ASP A 731 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 748 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 66 removed outlier: 7.672A pdb=" N VAL B 65 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA B 89 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU B 119 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL B 118 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.756A pdb=" N SER B 222 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 267 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 269 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 266 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 333 removed outlier: 3.505A pdb=" N TYR B 330 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 332 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 477 removed outlier: 3.831A pdb=" N VAL B 401 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY B 761 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 528 " --> pdb=" O MET B 762 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 409 through 413 removed outlier: 3.505A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 681 through 683 removed outlier: 7.305A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ASP B 732 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 68 through 73 removed outlier: 3.915A pdb=" N ILE C 36 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 70 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 72 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU C 98 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 124 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.709A pdb=" N LEU C 172 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU C 206 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR C 174 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 175 " --> pdb=" O TYR C 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 278 through 280 removed outlier: 3.537A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 407 through 410 removed outlier: 6.349A pdb=" N ILE C 408 " --> pdb=" O TYR C 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 439 through 441 removed outlier: 4.107A pdb=" N VAL C 440 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET C 450 " --> pdb=" O VAL C 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 682 through 683 removed outlier: 6.159A pdb=" N GLY C 683 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N ASP C 731 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 748 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 65 through 66 removed outlier: 7.692A pdb=" N VAL D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASN D 28 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA D 89 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU D 119 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL D 118 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 194 through 197 removed outlier: 3.757A pdb=" N SER D 222 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 267 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 269 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE D 266 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 330 through 333 removed outlier: 4.485A pdb=" N ASP D 332 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY D 336 " --> pdb=" O ASP D 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 473 through 477 removed outlier: 3.749A pdb=" N LEU D 398 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 475 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 401 " --> pdb=" O MET D 512 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY D 761 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 528 " --> pdb=" O MET D 762 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 409 through 413 removed outlier: 3.535A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 681 through 683 removed outlier: 7.241A pdb=" N ALA D 682 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N ASP D 732 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 540 " --> pdb=" O THR D 749 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2889 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: 4.59 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3982 1.32 - 1.44: 6899 1.44 - 1.57: 14016 1.57 - 1.69: 0 1.69 - 1.81: 260 Bond restraints: 25157 Sorted by residual: bond pdb=" C9 AA A 902 " pdb=" N9 AA A 902 " ideal model delta sigma weight residual 1.314 1.422 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" N 6RM B 908 " pdb=" C2 6RM B 908 " ideal model delta sigma weight residual 1.412 1.370 0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" N 6RM C 902 " pdb=" C2 6RM C 902 " ideal model delta sigma weight residual 1.412 1.371 0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C13 AA A 902 " pdb=" C9 AA A 902 " ideal model delta sigma weight residual 1.435 1.399 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C12 AA A 902 " pdb=" C9 AA A 902 " ideal model delta sigma weight residual 1.434 1.399 0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 25152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 33421 1.35 - 2.69: 535 2.69 - 4.04: 119 4.04 - 5.38: 29 5.38 - 6.73: 8 Bond angle restraints: 34112 Sorted by residual: angle pdb=" N VAL A 662 " pdb=" CA VAL A 662 " pdb=" C VAL A 662 " ideal model delta sigma weight residual 111.90 109.20 2.70 8.10e-01 1.52e+00 1.11e+01 angle pdb=" N ILE D 254 " pdb=" CA ILE D 254 " pdb=" C ILE D 254 " ideal model delta sigma weight residual 113.42 109.61 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" N ILE B 254 " pdb=" CA ILE B 254 " pdb=" C ILE B 254 " ideal model delta sigma weight residual 113.42 109.61 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" N GLY B 457 " pdb=" CA GLY B 457 " pdb=" C GLY B 457 " ideal model delta sigma weight residual 110.58 114.84 -4.26 1.35e+00 5.49e-01 9.97e+00 angle pdb=" N VAL C 662 " pdb=" CA VAL C 662 " pdb=" C VAL C 662 " ideal model delta sigma weight residual 111.56 109.22 2.34 8.60e-01 1.35e+00 7.39e+00 ... (remaining 34107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 14484 17.44 - 34.87: 564 34.87 - 52.31: 107 52.31 - 69.75: 3 69.75 - 87.19: 2 Dihedral angle restraints: 15160 sinusoidal: 6230 harmonic: 8930 Sorted by residual: dihedral pdb=" N LEU B 752 " pdb=" CA LEU B 752 " pdb=" CB LEU B 752 " pdb=" CG LEU B 752 " ideal model delta sinusoidal sigma weight residual -60.00 -117.61 57.61 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N LEU D 752 " pdb=" CA LEU D 752 " pdb=" CB LEU D 752 " pdb=" CG LEU D 752 " ideal model delta sinusoidal sigma weight residual -60.00 -111.78 51.78 3 1.50e+01 4.44e-03 9.05e+00 dihedral pdb=" N MET C 162 " pdb=" CA MET C 162 " pdb=" CB MET C 162 " pdb=" CG MET C 162 " ideal model delta sinusoidal sigma weight residual -180.00 -129.29 -50.71 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 15157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2519 0.031 - 0.063: 904 0.063 - 0.094: 249 0.094 - 0.126: 199 0.126 - 0.157: 9 Chirality restraints: 3880 Sorted by residual: chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 239 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" C1 NAG B 903 " pdb=" ND2 ASN B 239 " pdb=" C2 NAG B 903 " pdb=" O5 NAG B 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" C1 NAG D 906 " pdb=" ND2 ASN D 471 " pdb=" C2 NAG D 906 " pdb=" O5 NAG D 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 3877 not shown) Planarity restraints: 4303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 6RM C 902 " 0.021 2.00e-02 2.50e+03 5.52e-02 9.89e+01 pdb=" C 6RM C 902 " -0.107 2.00e-02 2.50e+03 pdb=" O 6RM C 902 " -0.065 2.00e-02 2.50e+03 pdb=" C1 6RM C 902 " -0.014 2.00e-02 2.50e+03 pdb=" C14 6RM C 902 " 0.084 2.00e-02 2.50e+03 pdb=" C2 6RM C 902 " 0.011 2.00e-02 2.50e+03 pdb=" C3 6RM C 902 " -0.007 2.00e-02 2.50e+03 pdb=" C4 6RM C 902 " 0.005 2.00e-02 2.50e+03 pdb=" C5 6RM C 902 " 0.029 2.00e-02 2.50e+03 pdb=" C6 6RM C 902 " 0.046 2.00e-02 2.50e+03 pdb=" C7 6RM C 902 " -0.091 2.00e-02 2.50e+03 pdb=" N1 6RM C 902 " 0.065 2.00e-02 2.50e+03 pdb=" S 6RM C 902 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 6RM B 908 " 0.021 2.00e-02 2.50e+03 5.51e-02 9.88e+01 pdb=" C 6RM B 908 " -0.107 2.00e-02 2.50e+03 pdb=" O 6RM B 908 " -0.064 2.00e-02 2.50e+03 pdb=" C1 6RM B 908 " -0.014 2.00e-02 2.50e+03 pdb=" C14 6RM B 908 " 0.083 2.00e-02 2.50e+03 pdb=" C2 6RM B 908 " 0.011 2.00e-02 2.50e+03 pdb=" C3 6RM B 908 " -0.008 2.00e-02 2.50e+03 pdb=" C4 6RM B 908 " 0.005 2.00e-02 2.50e+03 pdb=" C5 6RM B 908 " 0.029 2.00e-02 2.50e+03 pdb=" C6 6RM B 908 " 0.046 2.00e-02 2.50e+03 pdb=" C7 6RM B 908 " -0.091 2.00e-02 2.50e+03 pdb=" N1 6RM B 908 " 0.066 2.00e-02 2.50e+03 pdb=" S 6RM B 908 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 6RM C 902 " 0.006 2.00e-02 2.50e+03 2.08e-02 8.68e+00 pdb=" C11 6RM C 902 " -0.011 2.00e-02 2.50e+03 pdb=" C12 6RM C 902 " -0.002 2.00e-02 2.50e+03 pdb=" C13 6RM C 902 " 0.024 2.00e-02 2.50e+03 pdb=" C8 6RM C 902 " 0.021 2.00e-02 2.50e+03 pdb=" C9 6RM C 902 " 0.018 2.00e-02 2.50e+03 pdb=" F 6RM C 902 " -0.016 2.00e-02 2.50e+03 pdb=" O1 6RM C 902 " -0.041 2.00e-02 2.50e+03 ... (remaining 4300 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4433 2.77 - 3.31: 25007 3.31 - 3.84: 40310 3.84 - 4.37: 44899 4.37 - 4.90: 77198 Nonbonded interactions: 191847 Sorted by model distance: nonbonded pdb=" O GLN A 703 " pdb=" OG1 THR A 706 " model vdw 2.243 3.040 nonbonded pdb=" O GLN C 703 " pdb=" OG1 THR C 706 " model vdw 2.244 3.040 nonbonded pdb=" O ASN C 404 " pdb=" OG1 THR C 474 " model vdw 2.262 3.040 nonbonded pdb=" O ASN A 404 " pdb=" OG1 THR A 474 " model vdw 2.271 3.040 nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.273 3.040 ... (remaining 191842 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 34 through 901) selection = (chain 'C' and resid 34 through 901) } ncs_group { reference = (chain 'B' and resid 25 through 907) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.930 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 0.108 25189 Z= 0.116 Angle : 0.451 6.725 34192 Z= 0.231 Chirality : 0.041 0.157 3880 Planarity : 0.003 0.055 4287 Dihedral : 9.119 87.186 9344 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 1.92 % Allowed : 6.11 % Favored : 91.97 % 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: 0.78 (0.16), residues: 3040 helix: 2.21 (0.15), residues: 1220 sheet: 0.11 (0.32), residues: 306 loop : -0.85 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.007 0.001 TYR A 321 PHE 0.005 0.001 PHE D 753 TRP 0.006 0.001 TRP D 636 HIS 0.002 0.000 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00219 (25157) covalent geometry : angle 0.44971 (34112) SS BOND : bond 0.00109 ( 16) SS BOND : angle 0.47345 ( 32) hydrogen bonds : bond 0.14727 ( 981) hydrogen bonds : angle 6.04519 ( 2889) link_NAG-ASN : bond 0.00262 ( 16) link_NAG-ASN : angle 1.03040 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 485 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8751 (tpp) cc_final: 0.8509 (mmm) REVERT: A 200 MET cc_start: 0.6986 (tpt) cc_final: 0.6746 (tpt) REVERT: A 491 ASN cc_start: 0.8402 (m-40) cc_final: 0.8150 (t0) REVERT: A 787 GLU cc_start: 0.8305 (mp0) cc_final: 0.7916 (mp0) REVERT: B 41 MET cc_start: 0.8493 (ptp) cc_final: 0.7989 (ptm) REVERT: B 123 THR cc_start: 0.8514 (m) cc_final: 0.8169 (p) REVERT: B 514 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.8719 (m) REVERT: B 607 MET cc_start: 0.2926 (ptt) cc_final: 0.2306 (ptt) REVERT: B 611 TRP cc_start: 0.7340 (m-10) cc_final: 0.6833 (m100) REVERT: B 730 ILE cc_start: 0.8435 (mp) cc_final: 0.8170 (tp) REVERT: C 82 LEU cc_start: 0.8602 (mt) cc_final: 0.8150 (mt) REVERT: C 113 LEU cc_start: 0.9443 (mt) cc_final: 0.8695 (mt) REVERT: C 200 MET cc_start: 0.7148 (tpt) cc_final: 0.6716 (tpt) REVERT: C 252 ASP cc_start: 0.8752 (p0) cc_final: 0.8238 (p0) REVERT: C 320 CYS cc_start: 0.2525 (OUTLIER) cc_final: 0.1683 (m) REVERT: C 509 VAL cc_start: 0.8898 (t) cc_final: 0.8619 (t) REVERT: C 782 PHE cc_start: 0.8440 (m-10) cc_final: 0.7792 (m-10) REVERT: D 240 MET cc_start: 0.8620 (mmp) cc_final: 0.7857 (mmm) REVERT: D 249 VAL cc_start: 0.7434 (t) cc_final: 0.6813 (p) REVERT: D 386 THR cc_start: 0.8183 (p) cc_final: 0.7530 (p) REVERT: D 427 ASN cc_start: 0.8249 (m-40) cc_final: 0.8005 (t0) REVERT: D 616 ASN cc_start: 0.6723 (m-40) cc_final: 0.6145 (p0) REVERT: D 639 PHE cc_start: 0.9312 (t80) cc_final: 0.9003 (t80) REVERT: D 736 LEU cc_start: 0.8524 (mt) cc_final: 0.8252 (mt) outliers start: 51 outliers final: 21 residues processed: 531 average time/residue: 0.1684 time to fit residues: 137.9553 Evaluate side-chains 324 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 301 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 111 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN B 28 ASN B 40 GLN ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 GLN B 525 GLN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 111 GLN C 154 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 GLN D 28 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 375 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.069488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.053608 restraints weight = 150663.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.054890 restraints weight = 93734.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.055764 restraints weight = 66230.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056379 restraints weight = 51490.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.056789 restraints weight = 43001.023| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25189 Z= 0.288 Angle : 0.771 9.564 34192 Z= 0.397 Chirality : 0.048 0.265 3880 Planarity : 0.005 0.064 4287 Dihedral : 5.501 85.396 3672 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % 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: -0.51 (0.16), residues: 3040 helix: 0.86 (0.14), residues: 1290 sheet: -1.49 (0.25), residues: 390 loop : -1.10 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 52 TYR 0.026 0.003 TYR A 321 PHE 0.031 0.003 PHE B 533 TRP 0.047 0.002 TRP D 151 HIS 0.009 0.002 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00617 (25157) covalent geometry : angle 0.76191 (34112) SS BOND : bond 0.00589 ( 16) SS BOND : angle 2.31911 ( 32) hydrogen bonds : bond 0.04065 ( 981) hydrogen bonds : angle 5.26991 ( 2889) link_NAG-ASN : bond 0.00592 ( 16) link_NAG-ASN : angle 2.66601 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.6177 (ptm) cc_final: 0.5852 (tpt) REVERT: A 200 MET cc_start: 0.8017 (tpt) cc_final: 0.7607 (tpt) REVERT: A 252 ASP cc_start: 0.9014 (p0) cc_final: 0.8746 (p0) REVERT: A 472 LYS cc_start: 0.8579 (ptpp) cc_final: 0.8064 (ptmt) REVERT: A 491 ASN cc_start: 0.8770 (m-40) cc_final: 0.8281 (t0) REVERT: B 316 LYS cc_start: 0.8580 (pttp) cc_final: 0.8166 (tptp) REVERT: B 354 MET cc_start: 0.8995 (mmp) cc_final: 0.8587 (mmm) REVERT: B 616 ASN cc_start: 0.5284 (m-40) cc_final: 0.4354 (p0) REVERT: B 639 PHE cc_start: 0.9311 (t80) cc_final: 0.8917 (t80) REVERT: B 667 ILE cc_start: 0.8602 (pt) cc_final: 0.8251 (mm) REVERT: B 755 ARG cc_start: 0.8002 (tmm160) cc_final: 0.7792 (ttt-90) REVERT: C 82 LEU cc_start: 0.9179 (mt) cc_final: 0.8916 (mt) REVERT: C 113 LEU cc_start: 0.9738 (mt) cc_final: 0.9090 (mt) REVERT: C 200 MET cc_start: 0.7752 (tpt) cc_final: 0.7235 (tmm) REVERT: C 558 TRP cc_start: 0.6191 (t60) cc_final: 0.5373 (t-100) REVERT: D 119 LEU cc_start: 0.8492 (mm) cc_final: 0.8240 (mt) REVERT: D 240 MET cc_start: 0.8857 (mmp) cc_final: 0.8530 (mmm) REVERT: D 316 LYS cc_start: 0.8502 (pttm) cc_final: 0.8013 (tptt) REVERT: D 512 MET cc_start: 0.8921 (ttm) cc_final: 0.8627 (ttm) REVERT: D 639 PHE cc_start: 0.9435 (t80) cc_final: 0.9027 (t80) REVERT: D 706 MET cc_start: 0.8826 (mmm) cc_final: 0.8446 (mmp) REVERT: D 785 MET cc_start: 0.9486 (mmm) cc_final: 0.9283 (mmm) REVERT: D 787 ASP cc_start: 0.9041 (t0) cc_final: 0.8807 (t0) outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.1607 time to fit residues: 76.4317 Evaluate side-chains 214 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 264 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 301 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN B 40 GLN B 162 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN D 40 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.070999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.054581 restraints weight = 146846.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055940 restraints weight = 90840.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.056883 restraints weight = 64111.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.057523 restraints weight = 49581.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.057868 restraints weight = 41270.223| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25189 Z= 0.150 Angle : 0.576 6.027 34192 Z= 0.298 Chirality : 0.044 0.257 3880 Planarity : 0.004 0.058 4287 Dihedral : 5.006 89.384 3672 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: -0.28 (0.16), residues: 3040 helix: 1.02 (0.15), residues: 1292 sheet: -1.29 (0.26), residues: 396 loop : -0.98 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 52 TYR 0.019 0.002 TYR D 578 PHE 0.024 0.001 PHE A 183 TRP 0.028 0.002 TRP A 255 HIS 0.004 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00326 (25157) covalent geometry : angle 0.56848 (34112) SS BOND : bond 0.00436 ( 16) SS BOND : angle 1.58768 ( 32) hydrogen bonds : bond 0.03230 ( 981) hydrogen bonds : angle 4.98380 ( 2889) link_NAG-ASN : bond 0.00242 ( 16) link_NAG-ASN : angle 2.19209 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.5859 (ptm) cc_final: 0.5572 (tpt) REVERT: A 162 MET cc_start: 0.9229 (mmm) cc_final: 0.8938 (tpp) REVERT: A 200 MET cc_start: 0.7882 (tpt) cc_final: 0.7512 (tpt) REVERT: A 472 LYS cc_start: 0.8819 (ptpp) cc_final: 0.7957 (ptmt) REVERT: A 491 ASN cc_start: 0.8813 (m-40) cc_final: 0.8338 (t0) REVERT: A 564 MET cc_start: 0.3823 (mpp) cc_final: 0.3543 (ptp) REVERT: A 817 MET cc_start: 0.2734 (mtt) cc_final: 0.2495 (mpp) REVERT: B 41 MET cc_start: 0.8537 (ptm) cc_final: 0.8152 (ptm) REVERT: B 316 LYS cc_start: 0.8610 (pttp) cc_final: 0.8117 (tptp) REVERT: B 354 MET cc_start: 0.8976 (mmp) cc_final: 0.8636 (mmm) REVERT: B 639 PHE cc_start: 0.9341 (t80) cc_final: 0.8872 (t80) REVERT: B 667 ILE cc_start: 0.8708 (pt) cc_final: 0.8268 (mm) REVERT: B 692 TYR cc_start: 0.8277 (m-80) cc_final: 0.7820 (m-80) REVERT: B 702 MET cc_start: 0.8819 (mmm) cc_final: 0.8127 (mmt) REVERT: C 82 LEU cc_start: 0.9130 (mt) cc_final: 0.8910 (mt) REVERT: C 112 MET cc_start: 0.8305 (ppp) cc_final: 0.8103 (ppp) REVERT: C 113 LEU cc_start: 0.9739 (mt) cc_final: 0.9134 (mt) REVERT: C 200 MET cc_start: 0.7538 (tpt) cc_final: 0.6921 (tmm) REVERT: C 783 VAL cc_start: 0.9488 (t) cc_final: 0.9238 (p) REVERT: D 240 MET cc_start: 0.8859 (mmp) cc_final: 0.8517 (mmm) REVERT: D 316 LYS cc_start: 0.8513 (pttm) cc_final: 0.7977 (tptt) REVERT: D 354 MET cc_start: 0.9141 (mmp) cc_final: 0.8849 (mmm) REVERT: D 512 MET cc_start: 0.8895 (ttm) cc_final: 0.8653 (ttm) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1518 time to fit residues: 67.4813 Evaluate side-chains 205 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 128 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS B 40 GLN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN D 40 GLN D 146 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.068190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051834 restraints weight = 147949.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053097 restraints weight = 92591.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.053974 restraints weight = 65831.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054497 restraints weight = 51533.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.054958 restraints weight = 43737.788| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25189 Z= 0.215 Angle : 0.637 7.107 34192 Z= 0.330 Chirality : 0.045 0.247 3880 Planarity : 0.004 0.054 4287 Dihedral : 5.221 88.865 3672 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 3040 helix: 0.74 (0.14), residues: 1302 sheet: -1.63 (0.24), residues: 420 loop : -1.14 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 179 TYR 0.019 0.002 TYR A 321 PHE 0.031 0.002 PHE A 183 TRP 0.035 0.002 TRP A 255 HIS 0.009 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00463 (25157) covalent geometry : angle 0.62930 (34112) SS BOND : bond 0.00605 ( 16) SS BOND : angle 1.60475 ( 32) hydrogen bonds : bond 0.03502 ( 981) hydrogen bonds : angle 5.04224 ( 2889) link_NAG-ASN : bond 0.00385 ( 16) link_NAG-ASN : angle 2.35184 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.6327 (ptm) cc_final: 0.5943 (tpt) REVERT: A 200 MET cc_start: 0.8029 (tpt) cc_final: 0.7591 (tpt) REVERT: A 255 TRP cc_start: 0.7800 (m100) cc_final: 0.7451 (m100) REVERT: A 530 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 564 MET cc_start: 0.3827 (mpp) cc_final: 0.3617 (ptp) REVERT: B 41 MET cc_start: 0.8667 (ptm) cc_final: 0.8365 (ptm) REVERT: B 316 LYS cc_start: 0.8742 (pttp) cc_final: 0.8269 (tptt) REVERT: B 354 MET cc_start: 0.8987 (mmp) cc_final: 0.8679 (mmm) REVERT: B 470 MET cc_start: 0.8811 (ptp) cc_final: 0.8506 (ptp) REVERT: B 512 MET cc_start: 0.9165 (ttm) cc_final: 0.8948 (ttm) REVERT: B 527 ILE cc_start: 0.9045 (mp) cc_final: 0.8820 (mp) REVERT: B 639 PHE cc_start: 0.9396 (t80) cc_final: 0.8903 (t80) REVERT: B 667 ILE cc_start: 0.8882 (pt) cc_final: 0.8593 (mm) REVERT: B 692 TYR cc_start: 0.8432 (m-80) cc_final: 0.7875 (m-80) REVERT: B 785 MET cc_start: 0.9424 (mmm) cc_final: 0.9052 (tpp) REVERT: C 82 LEU cc_start: 0.9276 (mt) cc_final: 0.9015 (mt) REVERT: C 112 MET cc_start: 0.8634 (ppp) cc_final: 0.8420 (ppp) REVERT: C 113 LEU cc_start: 0.9797 (mt) cc_final: 0.9177 (mt) REVERT: C 200 MET cc_start: 0.7640 (tpt) cc_final: 0.6982 (tmm) REVERT: C 406 LEU cc_start: 0.8833 (pt) cc_final: 0.8572 (pt) REVERT: D 41 MET cc_start: 0.8488 (ptp) cc_final: 0.8282 (ptm) REVERT: D 185 GLU cc_start: 0.8578 (pp20) cc_final: 0.8062 (pp20) REVERT: D 193 LYS cc_start: 0.9370 (tppt) cc_final: 0.9164 (tppt) REVERT: D 240 MET cc_start: 0.8824 (mmp) cc_final: 0.8511 (mmm) REVERT: D 316 LYS cc_start: 0.8691 (pttm) cc_final: 0.8041 (tptt) REVERT: D 354 MET cc_start: 0.9274 (mmp) cc_final: 0.9036 (mmm) REVERT: D 706 MET cc_start: 0.9260 (mmp) cc_final: 0.8969 (mmm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1482 time to fit residues: 60.0216 Evaluate side-chains 200 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 276 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 129 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.067886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051584 restraints weight = 149523.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052885 restraints weight = 92350.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053776 restraints weight = 65234.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054384 restraints weight = 50782.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.054779 restraints weight = 42559.652| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25189 Z= 0.182 Angle : 0.612 10.600 34192 Z= 0.316 Chirality : 0.045 0.252 3880 Planarity : 0.004 0.050 4287 Dihedral : 5.219 86.683 3672 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -0.61 (0.16), residues: 3040 helix: 0.82 (0.15), residues: 1292 sheet: -1.45 (0.26), residues: 390 loop : -1.24 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 244 TYR 0.017 0.002 TYR A 251 PHE 0.021 0.001 PHE A 183 TRP 0.026 0.002 TRP C 255 HIS 0.005 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00390 (25157) covalent geometry : angle 0.60490 (34112) SS BOND : bond 0.00672 ( 16) SS BOND : angle 1.60883 ( 32) hydrogen bonds : bond 0.03295 ( 981) hydrogen bonds : angle 4.97271 ( 2889) link_NAG-ASN : bond 0.00275 ( 16) link_NAG-ASN : angle 2.25268 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7984 (tpt) cc_final: 0.7579 (tpt) REVERT: A 255 TRP cc_start: 0.7854 (m100) cc_final: 0.7601 (m100) REVERT: A 564 MET cc_start: 0.4026 (mpp) cc_final: 0.3698 (ptp) REVERT: A 792 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8711 (mt-10) REVERT: A 817 MET cc_start: 0.2599 (mtt) cc_final: 0.2338 (mpp) REVERT: B 41 MET cc_start: 0.8607 (ptm) cc_final: 0.8297 (ptm) REVERT: B 316 LYS cc_start: 0.8623 (pttp) cc_final: 0.8113 (tptt) REVERT: B 461 ASP cc_start: 0.9015 (m-30) cc_final: 0.8719 (m-30) REVERT: B 470 MET cc_start: 0.8759 (ptp) cc_final: 0.8558 (ptp) REVERT: B 667 ILE cc_start: 0.8935 (pt) cc_final: 0.8674 (mm) REVERT: B 692 TYR cc_start: 0.8391 (m-80) cc_final: 0.7852 (m-80) REVERT: B 785 MET cc_start: 0.9350 (mmm) cc_final: 0.9031 (tpp) REVERT: C 82 LEU cc_start: 0.9314 (mt) cc_final: 0.9113 (mt) REVERT: C 112 MET cc_start: 0.8631 (ppp) cc_final: 0.8425 (ppp) REVERT: C 113 LEU cc_start: 0.9811 (mt) cc_final: 0.9179 (mt) REVERT: C 200 MET cc_start: 0.7527 (tpt) cc_final: 0.6954 (tmm) REVERT: D 181 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8815 (mm-30) REVERT: D 185 GLU cc_start: 0.8571 (pp20) cc_final: 0.8039 (pp20) REVERT: D 240 MET cc_start: 0.8787 (mmp) cc_final: 0.8529 (mmm) REVERT: D 354 MET cc_start: 0.9284 (mmp) cc_final: 0.9064 (mmm) REVERT: D 512 MET cc_start: 0.8923 (ttm) cc_final: 0.8695 (ttm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1537 time to fit residues: 63.1857 Evaluate side-chains 199 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 107 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 ASN D 812 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.070026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.053647 restraints weight = 145810.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.054987 restraints weight = 90425.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.055898 restraints weight = 63739.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.056512 restraints weight = 49613.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.056955 restraints weight = 41425.533| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25189 Z= 0.109 Angle : 0.574 8.837 34192 Z= 0.292 Chirality : 0.044 0.321 3880 Planarity : 0.004 0.051 4287 Dihedral : 4.955 89.506 3672 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 0.04 % Allowed : 1.70 % Favored : 98.27 % 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: -0.43 (0.16), residues: 3040 helix: 0.95 (0.15), residues: 1278 sheet: -1.38 (0.25), residues: 416 loop : -1.08 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 431 TYR 0.017 0.001 TYR A 251 PHE 0.019 0.001 PHE A 183 TRP 0.026 0.001 TRP C 255 HIS 0.008 0.001 HIS C 405 Details of bonding type rmsd covalent geometry : bond 0.00237 (25157) covalent geometry : angle 0.56701 (34112) SS BOND : bond 0.00288 ( 16) SS BOND : angle 1.24661 ( 32) hydrogen bonds : bond 0.03000 ( 981) hydrogen bonds : angle 4.86749 ( 2889) link_NAG-ASN : bond 0.00330 ( 16) link_NAG-ASN : angle 2.35871 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.9399 (mm) cc_final: 0.9048 (tt) REVERT: A 200 MET cc_start: 0.7876 (tpt) cc_final: 0.7433 (tpt) REVERT: A 255 TRP cc_start: 0.7361 (m100) cc_final: 0.7153 (m100) REVERT: A 564 MET cc_start: 0.3865 (mpp) cc_final: 0.3592 (ptp) REVERT: A 792 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8759 (mt-10) REVERT: A 817 MET cc_start: 0.2526 (mtt) cc_final: 0.2314 (mpp) REVERT: B 41 MET cc_start: 0.8684 (ptm) cc_final: 0.8366 (ptm) REVERT: B 119 LEU cc_start: 0.8313 (mm) cc_final: 0.8110 (mt) REVERT: B 316 LYS cc_start: 0.8563 (pttp) cc_final: 0.7940 (tptt) REVERT: B 461 ASP cc_start: 0.9140 (m-30) cc_final: 0.8850 (m-30) REVERT: B 470 MET cc_start: 0.8737 (ptp) cc_final: 0.8530 (ptp) REVERT: B 501 MET cc_start: 0.9463 (ptm) cc_final: 0.8992 (ppp) REVERT: B 639 PHE cc_start: 0.9209 (t80) cc_final: 0.8981 (t80) REVERT: B 667 ILE cc_start: 0.8964 (pt) cc_final: 0.8619 (mm) REVERT: B 692 TYR cc_start: 0.8237 (m-80) cc_final: 0.7597 (m-80) REVERT: B 785 MET cc_start: 0.9310 (mmm) cc_final: 0.8941 (tpp) REVERT: C 113 LEU cc_start: 0.9819 (mt) cc_final: 0.9245 (mt) REVERT: C 200 MET cc_start: 0.7315 (tpt) cc_final: 0.6695 (tmm) REVERT: C 252 ASP cc_start: 0.9116 (p0) cc_final: 0.8781 (p0) REVERT: D 41 MET cc_start: 0.8531 (ptp) cc_final: 0.8228 (ptp) REVERT: D 181 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8843 (mm-30) REVERT: D 185 GLU cc_start: 0.8539 (pp20) cc_final: 0.7989 (pp20) REVERT: D 240 MET cc_start: 0.8822 (mmp) cc_final: 0.8427 (mmm) REVERT: D 316 LYS cc_start: 0.8415 (pttp) cc_final: 0.8021 (tptt) REVERT: D 354 MET cc_start: 0.9180 (mmp) cc_final: 0.8871 (mmm) REVERT: D 512 MET cc_start: 0.8903 (ttm) cc_final: 0.8644 (ttm) REVERT: D 522 GLU cc_start: 0.8912 (pm20) cc_final: 0.8610 (pm20) REVERT: D 706 MET cc_start: 0.9041 (mmm) cc_final: 0.8829 (mmm) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.1477 time to fit residues: 65.1091 Evaluate side-chains 201 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 108 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 292 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN B 40 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.069399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053114 restraints weight = 146197.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.054456 restraints weight = 90464.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055374 restraints weight = 63714.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.055997 restraints weight = 49241.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.056359 restraints weight = 41121.104| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25189 Z= 0.127 Angle : 0.583 9.929 34192 Z= 0.295 Chirality : 0.044 0.326 3880 Planarity : 0.004 0.050 4287 Dihedral : 4.915 85.828 3672 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 3040 helix: 0.92 (0.15), residues: 1290 sheet: -1.35 (0.25), residues: 420 loop : -1.04 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 704 TYR 0.017 0.001 TYR A 281 PHE 0.020 0.001 PHE A 183 TRP 0.028 0.001 TRP C 255 HIS 0.005 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00277 (25157) covalent geometry : angle 0.57662 (34112) SS BOND : bond 0.00425 ( 16) SS BOND : angle 1.17693 ( 32) hydrogen bonds : bond 0.03004 ( 981) hydrogen bonds : angle 4.82971 ( 2889) link_NAG-ASN : bond 0.00314 ( 16) link_NAG-ASN : angle 2.21578 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9725 (mt) cc_final: 0.9468 (mt) REVERT: A 151 ILE cc_start: 0.9429 (mm) cc_final: 0.9145 (tt) REVERT: A 200 MET cc_start: 0.7843 (tpt) cc_final: 0.7407 (tpt) REVERT: A 220 LYS cc_start: 0.7983 (tttt) cc_final: 0.7354 (ptmt) REVERT: A 817 MET cc_start: 0.2731 (mtt) cc_final: 0.2455 (mpp) REVERT: B 41 MET cc_start: 0.8642 (ptm) cc_final: 0.8328 (ptm) REVERT: B 119 LEU cc_start: 0.8303 (mm) cc_final: 0.8082 (mt) REVERT: B 316 LYS cc_start: 0.8571 (pttp) cc_final: 0.7944 (tptt) REVERT: B 461 ASP cc_start: 0.9140 (m-30) cc_final: 0.8866 (m-30) REVERT: B 501 MET cc_start: 0.9496 (ptm) cc_final: 0.8993 (ppp) REVERT: B 502 MET cc_start: 0.8814 (tpp) cc_final: 0.8564 (tpp) REVERT: B 527 ILE cc_start: 0.8973 (mp) cc_final: 0.8767 (mp) REVERT: B 667 ILE cc_start: 0.8994 (pt) cc_final: 0.8690 (mm) REVERT: B 692 TYR cc_start: 0.8354 (m-80) cc_final: 0.7854 (m-80) REVERT: B 785 MET cc_start: 0.9313 (mmm) cc_final: 0.8979 (tpp) REVERT: C 112 MET cc_start: 0.8443 (ppp) cc_final: 0.8153 (ppp) REVERT: C 113 LEU cc_start: 0.9810 (mt) cc_final: 0.9273 (mt) REVERT: C 200 MET cc_start: 0.7238 (tpt) cc_final: 0.6658 (tmm) REVERT: C 252 ASP cc_start: 0.9060 (p0) cc_final: 0.8722 (p0) REVERT: C 783 VAL cc_start: 0.9534 (t) cc_final: 0.9289 (p) REVERT: D 41 MET cc_start: 0.8459 (ptp) cc_final: 0.8143 (ptp) REVERT: D 181 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8796 (mm-30) REVERT: D 185 GLU cc_start: 0.8598 (pp20) cc_final: 0.8053 (pp20) REVERT: D 240 MET cc_start: 0.8799 (mmp) cc_final: 0.8528 (mmm) REVERT: D 316 LYS cc_start: 0.8460 (pttp) cc_final: 0.8111 (tptt) REVERT: D 354 MET cc_start: 0.9169 (mmp) cc_final: 0.8827 (mmm) REVERT: D 501 MET cc_start: 0.9449 (ptp) cc_final: 0.9045 (ptp) REVERT: D 502 MET cc_start: 0.8780 (tpp) cc_final: 0.8534 (tpp) REVERT: D 512 MET cc_start: 0.8949 (ttm) cc_final: 0.8675 (ttm) REVERT: D 522 GLU cc_start: 0.8910 (pm20) cc_final: 0.8052 (pm20) REVERT: D 706 MET cc_start: 0.8964 (mmm) cc_final: 0.8758 (mmm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1439 time to fit residues: 61.0594 Evaluate side-chains 204 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 96 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.066668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.050442 restraints weight = 147952.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.051716 restraints weight = 90503.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.052587 restraints weight = 63985.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.053178 restraints weight = 49876.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.053575 restraints weight = 41936.881| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25189 Z= 0.214 Angle : 0.665 9.815 34192 Z= 0.342 Chirality : 0.046 0.341 3880 Planarity : 0.004 0.050 4287 Dihedral : 5.390 84.797 3672 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.73 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.70 (0.16), residues: 3040 helix: 0.70 (0.15), residues: 1290 sheet: -1.44 (0.24), residues: 428 loop : -1.23 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 181 TYR 0.024 0.002 TYR B 367 PHE 0.031 0.002 PHE A 183 TRP 0.027 0.002 TRP C 255 HIS 0.007 0.001 HIS C 381 Details of bonding type rmsd covalent geometry : bond 0.00459 (25157) covalent geometry : angle 0.65850 (34112) SS BOND : bond 0.00463 ( 16) SS BOND : angle 1.58930 ( 32) hydrogen bonds : bond 0.03532 ( 981) hydrogen bonds : angle 5.06426 ( 2889) link_NAG-ASN : bond 0.00387 ( 16) link_NAG-ASN : angle 2.34935 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9714 (mt) cc_final: 0.9408 (mt) REVERT: A 200 MET cc_start: 0.7911 (tpt) cc_final: 0.7600 (tpt) REVERT: A 255 TRP cc_start: 0.7943 (m100) cc_final: 0.7318 (m100) REVERT: A 787 GLU cc_start: 0.8307 (mp0) cc_final: 0.8027 (mp0) REVERT: A 792 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8739 (mt-10) REVERT: A 817 MET cc_start: 0.2709 (mtt) cc_final: 0.2404 (mpp) REVERT: B 41 MET cc_start: 0.8608 (ptm) cc_final: 0.8332 (ptm) REVERT: B 316 LYS cc_start: 0.8652 (pttp) cc_final: 0.8083 (tptt) REVERT: B 354 MET cc_start: 0.9194 (mmp) cc_final: 0.8881 (mmm) REVERT: B 461 ASP cc_start: 0.8968 (m-30) cc_final: 0.8750 (m-30) REVERT: B 470 MET cc_start: 0.8613 (ptp) cc_final: 0.6817 (ptp) REVERT: B 501 MET cc_start: 0.9445 (ptm) cc_final: 0.8868 (ppp) REVERT: B 692 TYR cc_start: 0.8372 (m-80) cc_final: 0.7931 (m-80) REVERT: B 785 MET cc_start: 0.9216 (mmm) cc_final: 0.8898 (tpp) REVERT: C 112 MET cc_start: 0.8611 (ppp) cc_final: 0.8360 (ppp) REVERT: C 113 LEU cc_start: 0.9815 (mt) cc_final: 0.9238 (mt) REVERT: C 200 MET cc_start: 0.7358 (tpt) cc_final: 0.6833 (tmm) REVERT: D 41 MET cc_start: 0.8401 (ptp) cc_final: 0.8141 (ptp) REVERT: D 181 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8816 (mm-30) REVERT: D 240 MET cc_start: 0.8797 (mmp) cc_final: 0.8478 (mmm) REVERT: D 316 LYS cc_start: 0.8438 (pttp) cc_final: 0.8133 (tptt) REVERT: D 354 MET cc_start: 0.9235 (mmp) cc_final: 0.8977 (mmm) REVERT: D 502 MET cc_start: 0.8818 (tpp) cc_final: 0.8611 (tpp) REVERT: D 512 MET cc_start: 0.8894 (ttm) cc_final: 0.8674 (ttm) REVERT: D 692 TYR cc_start: 0.8161 (m-80) cc_final: 0.7669 (m-80) REVERT: D 706 MET cc_start: 0.9027 (mmm) cc_final: 0.8815 (mmm) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1420 time to fit residues: 55.4143 Evaluate side-chains 184 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 248 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 146 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.067806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.051508 restraints weight = 147016.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052822 restraints weight = 90545.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053710 restraints weight = 63849.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.054307 restraints weight = 49636.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.054722 restraints weight = 41621.725| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25189 Z= 0.147 Angle : 0.633 11.924 34192 Z= 0.323 Chirality : 0.046 0.322 3880 Planarity : 0.004 0.050 4287 Dihedral : 5.264 86.533 3672 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 3040 helix: 0.73 (0.15), residues: 1288 sheet: -1.59 (0.24), residues: 446 loop : -1.04 (0.19), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 437 TYR 0.019 0.002 TYR A 281 PHE 0.021 0.001 PHE A 183 TRP 0.023 0.002 TRP A 255 HIS 0.004 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00324 (25157) covalent geometry : angle 0.62604 (34112) SS BOND : bond 0.00457 ( 16) SS BOND : angle 1.64265 ( 32) hydrogen bonds : bond 0.03295 ( 981) hydrogen bonds : angle 5.01846 ( 2889) link_NAG-ASN : bond 0.00308 ( 16) link_NAG-ASN : angle 2.23697 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9727 (mt) cc_final: 0.9471 (mt) REVERT: A 151 ILE cc_start: 0.9449 (mm) cc_final: 0.9207 (tt) REVERT: A 183 PHE cc_start: 0.7142 (m-80) cc_final: 0.6899 (m-80) REVERT: A 200 MET cc_start: 0.7869 (tpt) cc_final: 0.7494 (tpt) REVERT: A 255 TRP cc_start: 0.7865 (m100) cc_final: 0.7315 (m100) REVERT: A 792 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 817 MET cc_start: 0.2598 (mtt) cc_final: 0.2334 (mpp) REVERT: B 41 MET cc_start: 0.8758 (ptm) cc_final: 0.8446 (ptm) REVERT: B 316 LYS cc_start: 0.8685 (pttp) cc_final: 0.8025 (tptt) REVERT: B 354 MET cc_start: 0.9159 (mmp) cc_final: 0.8734 (mmm) REVERT: B 461 ASP cc_start: 0.9146 (m-30) cc_final: 0.8847 (m-30) REVERT: B 470 MET cc_start: 0.8690 (ptp) cc_final: 0.7387 (ptp) REVERT: B 501 MET cc_start: 0.9514 (ptm) cc_final: 0.8937 (ppp) REVERT: B 512 MET cc_start: 0.8989 (ttm) cc_final: 0.8780 (ttm) REVERT: B 692 TYR cc_start: 0.8453 (m-80) cc_final: 0.7903 (m-80) REVERT: B 785 MET cc_start: 0.9330 (mmm) cc_final: 0.9038 (tpp) REVERT: C 89 LEU cc_start: 0.9335 (pp) cc_final: 0.9123 (pp) REVERT: C 112 MET cc_start: 0.8701 (ppp) cc_final: 0.8435 (ppp) REVERT: C 113 LEU cc_start: 0.9822 (mt) cc_final: 0.9300 (mt) REVERT: C 200 MET cc_start: 0.7313 (tpt) cc_final: 0.6764 (tmm) REVERT: D 41 MET cc_start: 0.8647 (ptp) cc_final: 0.8324 (ptp) REVERT: D 181 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8786 (tm-30) REVERT: D 240 MET cc_start: 0.8902 (mmp) cc_final: 0.8508 (mmm) REVERT: D 316 LYS cc_start: 0.8465 (pttp) cc_final: 0.8109 (tptt) REVERT: D 354 MET cc_start: 0.9198 (mmp) cc_final: 0.8857 (mmm) REVERT: D 512 MET cc_start: 0.8999 (ttm) cc_final: 0.8755 (ttm) REVERT: D 692 TYR cc_start: 0.8115 (m-80) cc_final: 0.7603 (m-80) REVERT: D 706 MET cc_start: 0.9089 (mmm) cc_final: 0.8850 (mmm) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1416 time to fit residues: 54.9864 Evaluate side-chains 186 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 97 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.066658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050369 restraints weight = 146494.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.051654 restraints weight = 90471.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.052527 restraints weight = 63876.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.053131 restraints weight = 49810.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.053472 restraints weight = 41729.078| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25189 Z= 0.196 Angle : 0.680 12.061 34192 Z= 0.348 Chirality : 0.046 0.319 3880 Planarity : 0.004 0.050 4287 Dihedral : 5.432 82.561 3672 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.76 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.75 (0.16), residues: 3040 helix: 0.66 (0.15), residues: 1280 sheet: -1.67 (0.24), residues: 430 loop : -1.16 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 386 TYR 0.019 0.002 TYR D 692 PHE 0.031 0.002 PHE B 639 TRP 0.033 0.002 TRP C 255 HIS 0.006 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00426 (25157) covalent geometry : angle 0.67367 (34112) SS BOND : bond 0.00607 ( 16) SS BOND : angle 1.67712 ( 32) hydrogen bonds : bond 0.03546 ( 981) hydrogen bonds : angle 5.13761 ( 2889) link_NAG-ASN : bond 0.00368 ( 16) link_NAG-ASN : angle 2.24661 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9727 (mt) cc_final: 0.9466 (mt) REVERT: A 135 MET cc_start: 0.5716 (mmp) cc_final: 0.5211 (ptp) REVERT: A 200 MET cc_start: 0.7863 (tpt) cc_final: 0.7545 (tpt) REVERT: A 220 LYS cc_start: 0.7989 (ttmt) cc_final: 0.6342 (tppt) REVERT: A 255 TRP cc_start: 0.8126 (m100) cc_final: 0.7331 (m100) REVERT: A 475 TYR cc_start: 0.6711 (m-80) cc_final: 0.6027 (m-80) REVERT: A 787 GLU cc_start: 0.8645 (pm20) cc_final: 0.8030 (pm20) REVERT: A 792 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8851 (mt-10) REVERT: A 817 MET cc_start: 0.2652 (mtt) cc_final: 0.2362 (mpp) REVERT: B 41 MET cc_start: 0.8752 (ptm) cc_final: 0.8450 (ptm) REVERT: B 240 MET cc_start: 0.9163 (mmm) cc_final: 0.8506 (mmm) REVERT: B 316 LYS cc_start: 0.8687 (pttp) cc_final: 0.8006 (tptt) REVERT: B 354 MET cc_start: 0.9204 (mmp) cc_final: 0.8805 (mmm) REVERT: B 461 ASP cc_start: 0.9054 (m-30) cc_final: 0.8818 (m-30) REVERT: B 470 MET cc_start: 0.8679 (ptp) cc_final: 0.7374 (ptp) REVERT: B 501 MET cc_start: 0.9484 (ptm) cc_final: 0.8921 (ppp) REVERT: B 692 TYR cc_start: 0.8420 (m-80) cc_final: 0.7864 (m-80) REVERT: B 785 MET cc_start: 0.9252 (mmm) cc_final: 0.9013 (tpp) REVERT: C 112 MET cc_start: 0.8711 (ppp) cc_final: 0.8495 (ppp) REVERT: C 113 LEU cc_start: 0.9822 (mt) cc_final: 0.9251 (mt) REVERT: C 200 MET cc_start: 0.7382 (tpt) cc_final: 0.6880 (tmm) REVERT: D 181 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8804 (mm-30) REVERT: D 240 MET cc_start: 0.8859 (mmp) cc_final: 0.8502 (mmm) REVERT: D 316 LYS cc_start: 0.8502 (pttp) cc_final: 0.8149 (tptt) REVERT: D 354 MET cc_start: 0.9216 (mmp) cc_final: 0.8949 (mmm) REVERT: D 502 MET cc_start: 0.8780 (tpp) cc_final: 0.8560 (tpp) REVERT: D 512 MET cc_start: 0.8971 (ttm) cc_final: 0.8737 (ttm) REVERT: D 692 TYR cc_start: 0.8179 (m-80) cc_final: 0.7614 (m-80) REVERT: D 706 MET cc_start: 0.9083 (mmm) cc_final: 0.8853 (mmm) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1451 time to fit residues: 53.7951 Evaluate side-chains 174 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 287 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 chunk 296 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.068017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051645 restraints weight = 145785.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.052988 restraints weight = 89589.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.053888 restraints weight = 62978.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.054505 restraints weight = 49010.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.054922 restraints weight = 40983.305| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25189 Z= 0.133 Angle : 0.636 12.127 34192 Z= 0.321 Chirality : 0.046 0.302 3880 Planarity : 0.004 0.051 4287 Dihedral : 5.234 81.587 3672 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.64 (0.16), residues: 3040 helix: 0.72 (0.15), residues: 1278 sheet: -1.67 (0.24), residues: 434 loop : -1.05 (0.19), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 386 TYR 0.019 0.001 TYR A 281 PHE 0.039 0.001 PHE B 639 TRP 0.025 0.002 TRP C 255 HIS 0.005 0.001 HIS B 727 Details of bonding type rmsd covalent geometry : bond 0.00294 (25157) covalent geometry : angle 0.63045 (34112) SS BOND : bond 0.00491 ( 16) SS BOND : angle 1.44578 ( 32) hydrogen bonds : bond 0.03251 ( 981) hydrogen bonds : angle 5.02653 ( 2889) link_NAG-ASN : bond 0.00300 ( 16) link_NAG-ASN : angle 2.11484 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3585.50 seconds wall clock time: 63 minutes 11.76 seconds (3791.76 seconds total)