Starting phenix.real_space_refine on Sun Jan 26 14:11:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eou_31231/01_2025/7eou_31231_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eou_31231/01_2025/7eou_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_31231/01_2025/7eou_31231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eou_31231/01_2025/7eou_31231.map" model { file = "/net/cci-nas-00/data/ceres_data/7eou_31231/01_2025/7eou_31231_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eou_31231/01_2025/7eou_31231_trim.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP: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: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP: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: 13.81, per 1000 atoms: 0.56 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: 5.92 Conformation dependent library (CDL) restraints added in 3.0 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: 3.18 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: 9.04 Time building geometry restraints manager: 6.83 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 837 or resid 901)) selection = (chain 'C' and (resid 34 through 837 or resid 901)) } ncs_group { reference = (chain 'B' and (resid 25 through 844 or resid 901 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 52.330 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.120 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.290 ------------------------------------------------------------------------------- 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 25157 Z= 0.149 Angle : 0.450 6.725 34112 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 : 9.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP D 636 HIS 0.002 0.000 HIS C 119 PHE 0.005 0.001 PHE D 753 TYR 0.007 0.001 TYR A 321 ARG 0.002 0.000 ARG C 52 *********************** 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 : 2.613 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: 0.8752 (tpp) cc_final: 0.8508 (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: 0.4033 time to fit residues: 329.2720 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 : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 79 optimal weight: 0.0670 chunk 156 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 0.1980 chunk 178 optimal weight: 1.9990 chunk 277 optimal weight: 0.5980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN B 40 GLN B 404 HIS B 405 GLN B 477 HIS ** B 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN B 525 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN D 40 GLN D 134 HIS ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.080350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.064906 restraints weight = 158234.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.066367 restraints weight = 97659.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.067354 restraints weight = 67937.196| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 25157 Z= 0.159 Angle : 0.528 6.333 34112 Z= 0.270 Chirality : 0.043 0.252 3880 Planarity : 0.004 0.054 4287 Dihedral : 4.699 84.924 3672 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 0.04 % Allowed : 2.53 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 3040 helix: 1.63 (0.15), residues: 1266 sheet: -0.24 (0.31), residues: 324 loop : -0.73 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 151 HIS 0.005 0.001 HIS C 85 PHE 0.025 0.001 PHE A 183 TYR 0.015 0.001 TYR A 321 ARG 0.006 0.000 ARG A 52 *********************** 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 364 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 2.674 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 491 ASN cc_start: 0.8466 (m-40) cc_final: 0.8195 (t0) REVERT: A 564 MET cc_start: 0.3808 (mpp) cc_final: 0.3584 (ptp) REVERT: A 781 GLN cc_start: 0.8915 (pt0) cc_final: 0.8218 (pt0) REVERT: A 782 PHE cc_start: 0.7164 (m-10) cc_final: 0.6527 (m-10) REVERT: B 41 MET cc_start: 0.8230 (ptp) cc_final: 0.7971 (ptm) REVERT: B 123 THR cc_start: 0.8478 (m) cc_final: 0.8169 (p) REVERT: B 185 GLU cc_start: 0.8737 (pp20) cc_final: 0.8531 (pp20) REVERT: B 459 CYS cc_start: 0.8069 (m) cc_final: 0.7682 (m) REVERT: B 470 MET cc_start: 0.8634 (ptp) cc_final: 0.6779 (ptp) REVERT: B 607 MET cc_start: 0.3024 (ptt) cc_final: 0.2350 (ptt) REVERT: B 611 TRP cc_start: 0.7239 (m-10) cc_final: 0.6658 (m100) REVERT: B 616 ASN cc_start: 0.5488 (m-40) cc_final: 0.4805 (p0) REVERT: B 639 PHE cc_start: 0.9159 (t80) cc_final: 0.8881 (t80) REVERT: B 730 ILE cc_start: 0.8937 (mp) cc_final: 0.8354 (tt) REVERT: C 55 TRP cc_start: 0.8286 (t-100) cc_final: 0.8029 (t-100) REVERT: C 82 LEU cc_start: 0.8748 (mt) cc_final: 0.8510 (mt) REVERT: C 113 LEU cc_start: 0.9431 (mt) cc_final: 0.8836 (mt) REVERT: C 135 MET cc_start: 0.4957 (pmm) cc_final: 0.3741 (pmm) REVERT: C 200 MET cc_start: 0.7588 (tpt) cc_final: 0.6884 (tmm) REVERT: C 252 ASP cc_start: 0.8814 (p0) cc_final: 0.8323 (p0) REVERT: C 558 TRP cc_start: 0.6227 (t60) cc_final: 0.5592 (t-100) REVERT: D 240 MET cc_start: 0.8565 (mmp) cc_final: 0.8300 (mmm) REVERT: D 249 VAL cc_start: 0.6936 (t) cc_final: 0.6666 (p) REVERT: D 316 LYS cc_start: 0.8298 (pttm) cc_final: 0.7744 (tptt) REVERT: D 354 MET cc_start: 0.8710 (mmp) cc_final: 0.8324 (mmm) REVERT: D 427 ASN cc_start: 0.8560 (m-40) cc_final: 0.8288 (t0) REVERT: D 470 MET cc_start: 0.8308 (ptp) cc_final: 0.7306 (ptp) REVERT: D 639 PHE cc_start: 0.9326 (t80) cc_final: 0.8991 (t80) REVERT: D 706 MET cc_start: 0.8749 (mmm) cc_final: 0.8383 (mmp) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.3711 time to fit residues: 210.7952 Evaluate side-chains 255 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 74 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.0270 chunk 144 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: