Starting phenix.real_space_refine on Sat Jun 21 04:51:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eor_31228/06_2025/7eor_31228_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eor_31228/06_2025/7eor_31228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eor_31228/06_2025/7eor_31228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eor_31228/06_2025/7eor_31228.map" model { file = "/net/cci-nas-00/data/ceres_data/7eor_31228/06_2025/7eor_31228_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eor_31228/06_2025/7eor_31228_trim.cif" } resolution = 4.0 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 150 5.16 5 C 15544 2.51 5 N 4040 2.21 5 O 4468 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24204 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5886 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 6093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 6215 Chain: "C" Number of atoms: 5886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5886 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 6093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 6215 Chain: "A" 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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.25, per 1000 atoms: 0.80 Number of scatterers: 24204 At special positions: 0 Unit cell: (116.61, 145.002, 185.562, 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 150 16.00 F 2 9.00 O 4468 8.00 N 4040 7.00 C 15544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " 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 C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " 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 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=2, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 276 " " NAG B 903 " - " ASN B 239 " " NAG B 904 " - " ASN B 203 " " NAG B 905 " - " ASN B 771 " " NAG B 906 " - " ASN B 471 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 276 " " NAG D 903 " - " ASN D 239 " " NAG D 904 " - " ASN D 203 " " NAG D 905 " - " ASN D 771 " " NAG D 906 " - " ASN D 471 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 4.7 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 31 sheets defined 45.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 45 through 60 removed outlier: 3.747A pdb=" N GLY A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Proline residue: A 57 - end of helix removed outlier: 3.678A pdb=" N ALA A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.676A pdb=" N PHE A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 152 through 165 removed outlier: 4.135A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.527A pdb=" N SER A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.822A pdb=" N SER A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 310 removed outlier: 3.920A pdb=" N LYS A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 4.157A pdb=" N THR A 382 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 472 removed outlier: 3.565A pdb=" N ARG A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.848A pdb=" N TYR A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.871A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.718A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 601 through 612 removed outlier: 4.060A pdb=" N VAL A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 627 No H-bonds generated for 'chain 'A' and resid 625 through 627' Processing helix chain 'A' and resid 628 through 653 removed outlier: 3.698A pdb=" N TRP A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.888A pdb=" N GLN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.677A pdb=" N ASN A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 707 through 709 No H-bonds generated for 'chain 'A' and resid 707 through 709' Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.972A pdb=" N ALA A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.649A pdb=" N CYS A 745 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS A 746 " --> pdb=" O GLU A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 746' Processing helix chain 'A' and resid 771 through 785 removed outlier: 4.075A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 796 removed outlier: 4.175A pdb=" N THR A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 837 Processing helix chain 'B' and resid 35 through 53 removed outlier: 3.618A pdb=" N GLU B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 84 removed outlier: 3.693A pdb=" N SER B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.693A pdb=" N SER B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.543A pdb=" N TYR B 128 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.873A pdb=" N SER B 148 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.722A pdb=" N LEU B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 238 removed outlier: 3.920A pdb=" N MET B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 4.279A pdb=" N SER B 255 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 4.147A pdb=" N ARG B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 296 removed outlier: 3.867A pdb=" N GLN B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.540A pdb=" N LYS B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.621A 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 525 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 562 through 583 removed outlier: 3.913A pdb=" N VAL B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 567 " --> pdb=" O TRP B 563 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 575 " --> pdb=" O HIS B 571 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 627 through 658 removed outlier: 3.745A pdb=" N VAL B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 4.244A pdb=" N ARG B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 669 through 674' Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.579A pdb=" N ILE B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) 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 710 removed outlier: 5.461A pdb=" N LYS B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 768 through 782 removed outlier: 3.552A pdb=" N VAL B 772 " --> pdb=" O TRP B 768 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 775 " --> pdb=" O ASN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 810 through 844 removed outlier: 3.860A pdb=" N ALA B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 829 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.752A pdb=" N GLY C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Proline residue: C 57 - end of helix removed outlier: 3.684A pdb=" N ALA C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 113 through 121 removed outlier: 3.594A pdb=" N PHE C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 152 through 165 removed outlier: 4.124A pdb=" N THR C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.528A pdb=" N SER C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.777A pdb=" N SER C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 removed outlier: 3.908A pdb=" N LYS C 309 " --> pdb=" O SER C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 removed outlier: 4.175A pdb=" N MET C 338 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 383 removed outlier: 4.180A pdb=" N THR C 382 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 472 removed outlier: 3.571A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.828A pdb=" N TYR C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 removed outlier: 3.865A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.674A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 600 through 612 removed outlier: 4.110A pdb=" N ALA C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 653 removed outlier: 3.630A pdb=" N TRP C 634 " --> pdb=" O MET C 630 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.925A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 698 removed outlier: 3.670A pdb=" N ASN C 693 " --> pdb=" O SER C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 706 Processing helix chain 'C' and resid 707 through 709 No H-bonds generated for 'chain 'C' and resid 707 through 709' Processing helix chain 'C' and resid 712 through 722 removed outlier: 3.979A pdb=" N ALA C 716 " --> pdb=" O GLY C 712 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 717 " --> pdb=" O VAL C 713 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.594A pdb=" N TYR C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 746 removed outlier: 3.506A pdb=" N CYS C 745 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS C 746 " --> pdb=" O GLU C 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 742 through 746' Processing helix chain 'C' and resid 771 through 785 removed outlier: 4.121A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 796 removed outlier: 4.177A pdb=" N THR C 793 " --> pdb=" O GLU C 789 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 837 Processing helix chain 'D' and resid 35 through 53 removed outlier: 3.629A pdb=" N GLU D 39 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 84 removed outlier: 3.853A pdb=" N ALA D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.602A pdb=" N SER D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.532A pdb=" N TYR D 128 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.873A pdb=" N SER D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 213 removed outlier: 3.714A pdb=" N LEU D 208 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 238 removed outlier: 3.917A pdb=" N MET D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.583A pdb=" N GLU D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER D 255 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 4.162A pdb=" N ARG D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 296 removed outlier: 3.867A pdb=" N GLN D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.536A pdb=" N LYS D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.635A 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 525 Processing helix chain 'D' and resid 559 through 561 No H-bonds generated for 'chain 'D' and resid 559 through 561' Processing helix chain 'D' and resid 562 through 583 removed outlier: 3.951A pdb=" N VAL D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 567 " --> pdb=" O TRP D 563 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL D 575 " --> pdb=" O HIS D 571 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 658 removed outlier: 3.798A pdb=" N VAL D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 674 removed outlier: 4.208A pdb=" N ARG D 673 " --> pdb=" O ASP D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 removed outlier: 3.568A pdb=" N ILE D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) 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 710 removed outlier: 5.373A pdb=" N LYS D 708 " --> pdb=" O ARG D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 768 through 782 removed outlier: 3.564A pdb=" N VAL D 772 " --> pdb=" O TRP D 768 " (cutoff:3.500A) removed outlier: 3.673A 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 844 removed outlier: 3.800A pdb=" N ALA D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 829 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 836 " --> pdb=" O PHE D 832 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.655A pdb=" N VAL A 99 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 98 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.524A pdb=" N PHE A 170 " --> pdb=" O ASP A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.554A pdb=" N THR A 174 " --> pdb=" O ILE A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 removed outlier: 3.727A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 479 removed outlier: 6.357A pdb=" N LEU A 406 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A 478 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE A 408 " --> pdb=" O TYR A 478 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER A 407 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 508 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 419 Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 440 removed outlier: 3.563A pdb=" N CYS A 436 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 452 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 536 removed outlier: 3.501A pdb=" N SER A 534 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 730 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 536 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 728 " --> pdb=" O MET A 536 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 683 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N ASP A 731 " --> pdb=" O GLY A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.917A pdb=" N ASN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA B 89 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 32 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 119 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 118 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.575A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 267 through 270 removed outlier: 6.528A pdb=" N TYR B 351 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 366 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 353 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 402 removed outlier: 7.399A pdb=" N LEU B 398 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N HIS B 477 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 400 " --> pdb=" O HIS B 477 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE B 435 " --> pdb=" O TYR B 474 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 476 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 438 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 451 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 487 through 488 removed outlier: 3.574A pdb=" N GLU B 488 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 497 " --> pdb=" O GLU B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 513 through 518 removed outlier: 5.084A pdb=" N ALA B 515 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 759 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 681 through 682 removed outlier: 7.296A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N ASP B 732 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU B 538 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLU B 751 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.668A pdb=" N VAL C 99 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 98 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.514A pdb=" N PHE C 170 " --> pdb=" O ASP C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 173 through 174 removed outlier: 3.569A pdb=" N THR C 174 " --> pdb=" O ILE C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.644A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 475 through 479 removed outlier: 6.387A pdb=" N LEU C 406 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR C 478 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE C 408 " --> pdb=" O TYR C 478 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER C 407 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 508 " --> pdb=" O ALA C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 417 through 419 Processing sheet with id=AC4, first strand: chain 'C' and resid 436 through 440 removed outlier: 3.516A pdb=" N CYS C 436 " --> pdb=" O LYS C 454 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 452 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 533 through 536 removed outlier: 3.546A pdb=" N TYR C 730 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 536 " --> pdb=" O PHE C 728 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 728 " --> pdb=" O MET C 536 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY C 683 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ASP C 731 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 60 through 65 removed outlier: 6.438A pdb=" N VAL D 27 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR D 63 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE D 29 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN D 28 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA D 89 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 32 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU D 119 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL D 118 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.575A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 267 through 270 removed outlier: 6.539A pdb=" N TYR D 351 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE D 366 " --> pdb=" O TYR D 351 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE D 353 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 397 through 402 removed outlier: 7.411A pdb=" N LEU D 398 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N HIS D 477 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE D 400 " --> pdb=" O HIS D 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 409 through 412 removed outlier: 3.582A pdb=" N VAL D 451 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 438 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 487 through 488 removed outlier: 3.583A pdb=" N GLU D 488 " --> pdb=" O GLU D 497 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 497 " --> pdb=" O GLU D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 513 through 518 removed outlier: 5.071A pdb=" N ALA D 515 " --> pdb=" O GLY D 759 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY D 759 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 681 through 682 removed outlier: 7.290A pdb=" N ALA D 682 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N ASP D 732 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2599 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: 8.36 Time building geometry restraints manager: 7.70 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: 3908 1.32 - 1.44: 6770 1.44 - 1.56: 13822 1.56 - 1.69: 0 1.69 - 1.81: 258 Bond restraints: 24758 Sorted by residual: bond pdb=" C1 NAG D 905 " pdb=" O5 NAG D 905 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG B 905 " pdb=" O5 NAG B 905 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N 6RM A 902 " pdb=" C2 6RM A 902 " ideal model delta sigma weight residual 1.412 1.371 0.041 2.00e-02 2.50e+03 4.21e+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 4.13e+00 bond pdb=" C1 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 ... (remaining 24753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 33171 1.57 - 3.14: 339 3.14 - 4.71: 29 4.71 - 6.28: 19 6.28 - 7.85: 8 Bond angle restraints: 33566 Sorted by residual: angle pdb=" C GLU A 211 " pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.06e+00 angle pdb=" C5 6RM A 902 " pdb=" C7 6RM A 902 " pdb=" O1 6RM A 902 " ideal model delta sigma weight residual 107.46 114.20 -6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" C CYS A 399 " pdb=" N GLU A 400 " pdb=" CA GLU A 400 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.96e+00 angle pdb=" C5 6RM C 902 " pdb=" C7 6RM C 902 " pdb=" O1 6RM C 902 " ideal model delta sigma weight residual 107.46 114.13 -6.67 3.00e+00 1.11e-01 4.95e+00 angle pdb=" C CYS C 399 " pdb=" N GLU C 400 " pdb=" CA GLU C 400 " ideal model delta sigma weight residual 121.80 127.22 -5.42 2.44e+00 1.68e-01 4.93e+00 ... (remaining 33561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 14551 24.44 - 48.89: 316 48.89 - 73.33: 17 73.33 - 97.77: 4 97.77 - 122.21: 6 Dihedral angle restraints: 14894 sinusoidal: 6110 harmonic: 8784 Sorted by residual: dihedral pdb=" C2 NAG D 905 " pdb=" C1 NAG D 905 " pdb=" O5 NAG D 905 " pdb=" C5 NAG D 905 " ideal model delta sinusoidal sigma weight residual -62.96 59.25 -122.21 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C2 NAG B 905 " pdb=" C1 NAG B 905 " pdb=" O5 NAG B 905 " pdb=" C5 NAG B 905 " ideal model delta sinusoidal sigma weight residual -62.96 59.18 -122.14 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1 NAG D 905 " pdb=" C5 NAG D 905 " pdb=" O5 NAG D 905 " pdb=" C6 NAG D 905 " ideal model delta sinusoidal sigma weight residual 171.16 -88.80 -100.04 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 14891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3296 0.058 - 0.116: 503 0.116 - 0.174: 25 0.174 - 0.233: 0 0.233 - 0.291: 2 Chirality restraints: 3826 Sorted by residual: chirality pdb=" C1 NAG D 902 " pdb=" ND2 ASN D 276 " pdb=" C2 NAG D 902 " pdb=" O5 NAG D 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1 NAG B 905 " pdb=" ND2 ASN B 771 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 3823 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 6RM C 902 " 0.020 2.00e-02 2.50e+03 5.51e-02 9.87e+01 pdb=" C 6RM C 902 " -0.106 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 " -0.008 2.00e-02 2.50e+03 pdb=" C4 6RM C 902 " 0.006 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 A 902 " 0.021 2.00e-02 2.50e+03 5.50e-02 9.84e+01 pdb=" C 6RM A 902 " -0.107 2.00e-02 2.50e+03 pdb=" O 6RM A 902 " -0.064 2.00e-02 2.50e+03 pdb=" C1 6RM A 902 " -0.014 2.00e-02 2.50e+03 pdb=" C14 6RM A 902 " 0.083 2.00e-02 2.50e+03 pdb=" C2 6RM A 902 " 0.011 2.00e-02 2.50e+03 pdb=" C3 6RM A 902 " -0.008 2.00e-02 2.50e+03 pdb=" C4 6RM A 902 " 0.005 2.00e-02 2.50e+03 pdb=" C5 6RM A 902 " 0.029 2.00e-02 2.50e+03 pdb=" C6 6RM A 902 " 0.045 2.00e-02 2.50e+03 pdb=" C7 6RM A 902 " -0.091 2.00e-02 2.50e+03 pdb=" N1 6RM A 902 " 0.065 2.00e-02 2.50e+03 pdb=" S 6RM A 902 " 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 8.69e+00 pdb=" C11 6RM C 902 " -0.010 2.00e-02 2.50e+03 pdb=" C12 6RM C 902 " -0.001 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 " -0.017 2.00e-02 2.50e+03 pdb=" O1 6RM C 902 " -0.041 2.00e-02 2.50e+03 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3652 2.76 - 3.30: 23794 3.30 - 3.83: 38636 3.83 - 4.37: 42318 4.37 - 4.90: 73288 Nonbonded interactions: 181688 Sorted by model distance: nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR C 446 " pdb=" OE1 GLU C 448 " model vdw 2.228 3.040 nonbonded pdb=" O THR D 396 " pdb=" OG1 THR D 473 " model vdw 2.229 3.040 nonbonded pdb=" O GLU A 577 " pdb=" OG SER A 580 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A 446 " pdb=" OE1 GLU A 448 " model vdw 2.231 3.040 ... (remaining 181683 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 25 through 775 or resid 777 through 844 or resid 901 throu \ gh 906)) selection = (chain 'D' and (resid 25 through 775 or resid 777 through 844 or resid 901 throu \ gh 906)) } 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=0.50 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: 1.140 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: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 61.220 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.140 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 0.076 24784 Z= 0.109 Angle : 0.446 8.792 33628 Z= 0.220 Chirality : 0.041 0.291 3826 Planarity : 0.003 0.055 4206 Dihedral : 9.476 122.215 9188 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.64 % Allowed : 4.72 % Favored : 93.64 % 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: 0.66 (0.17), residues: 2980 helix: 2.18 (0.16), residues: 1162 sheet: -0.18 (0.32), residues: 344 loop : -0.86 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 606 HIS 0.002 0.000 HIS A 42 PHE 0.008 0.001 PHE C 599 TYR 0.004 0.000 TYR C 761 ARG 0.001 0.000 ARG D 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 14) link_NAG-ASN : angle 2.17627 ( 42) hydrogen bonds : bond 0.14639 ( 892) hydrogen bonds : angle 5.67454 ( 2599) SS BOND : bond 0.00041 ( 10) SS BOND : angle 0.47386 ( 20) covalent geometry : bond 0.00211 (24758) covalent geometry : angle 0.43963 (33566) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 546 time to evaluate : 2.948 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: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9302 (mt) cc_final: 0.8991 (mm) REVERT: A 99 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8056 (m) REVERT: A 100 PHE cc_start: 0.7144 (m-10) cc_final: 0.6520 (m-10) REVERT: A 147 PHE cc_start: 0.8232 (m-80) cc_final: 0.7914 (m-80) REVERT: A 188 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8837 (mmmm) REVERT: A 192 ASP cc_start: 0.8844 (m-30) cc_final: 0.8631 (m-30) REVERT: A 255 TRP cc_start: 0.8338 (m100) cc_final: 0.8035 (m100) REVERT: A 455 CYS cc_start: 0.7235 (t) cc_final: 0.6823 (t) REVERT: A 641 PHE cc_start: 0.6585 (t80) cc_final: 0.6371 (t80) REVERT: B 41 MET cc_start: 0.9028 (ptp) cc_final: 0.7765 (ptp) REVERT: B 74 MET cc_start: 0.7495 (ppp) cc_final: 0.6918 (ttt) REVERT: B 90 ILE cc_start: 0.8552 (mm) cc_final: 0.8254 (mm) REVERT: B 116 ILE cc_start: 0.8957 (mm) cc_final: 0.8398 (mt) REVERT: B 127 ILE cc_start: 0.8730 (mt) cc_final: 0.8322 (pt) REVERT: B 136 SER cc_start: 0.8040 (m) cc_final: 0.7410 (p) REVERT: B 163 ILE cc_start: 0.9200 (mt) cc_final: 0.8992 (mp) REVERT: B 226 ASP cc_start: 0.7963 (p0) cc_final: 0.7746 (p0) REVERT: B 254 ILE cc_start: 0.8475 (mm) cc_final: 0.8204 (mm) REVERT: B 724 ASN cc_start: 0.9153 (m-40) cc_final: 0.8882 (m110) REVERT: C 40 LEU cc_start: 0.9286 (mt) cc_final: 0.9034 (mm) REVERT: C 99 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.7983 (m) REVERT: C 100 PHE cc_start: 0.7156 (m-10) cc_final: 0.6814 (m-10) REVERT: C 188 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8748 (mmmm) REVERT: C 192 ASP cc_start: 0.8866 (m-30) cc_final: 0.8645 (m-30) REVERT: C 255 TRP cc_start: 0.8333 (m100) cc_final: 0.8083 (m100) REVERT: C 455 CYS cc_start: 0.7466 (t) cc_final: 0.7007 (t) REVERT: D 41 MET cc_start: 0.9078 (ptp) cc_final: 0.7828 (ptp) REVERT: D 74 MET cc_start: 0.7835 (ppp) cc_final: 0.6663 (ttp) REVERT: D 136 SER cc_start: 0.7993 (m) cc_final: 0.7400 (p) REVERT: D 818 MET cc_start: -0.0370 (mmt) cc_final: -0.0929 (ttm) outliers start: 43 outliers final: 8 residues processed: 587 average time/residue: 0.4452 time to fit residues: 396.2085 Evaluate side-chains 317 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 307 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 127 optimal weight: 40.0000 chunk 78 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 674 HIS A 774 GLN B 363 GLN B 477 HIS B 559 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 ASN C 674 HIS C 774 GLN D 363 GLN D 477 HIS D 650 ASN ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.091738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.068406 restraints weight = 116100.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.070199 restraints weight = 65786.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071313 restraints weight = 45392.021| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24784 Z= 0.269 Angle : 0.729 9.161 33628 Z= 0.370 Chirality : 0.048 0.259 3826 Planarity : 0.005 0.079 4206 Dihedral : 7.197 111.331 3586 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.40 % Allowed : 11.54 % Favored : 86.06 % 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: 0.14 (0.16), residues: 2980 helix: 1.57 (0.15), residues: 1184 sheet: -0.74 (0.30), residues: 338 loop : -0.95 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 55 HIS 0.009 0.002 HIS C 42 PHE 0.023 0.002 PHE C 473 TYR 0.026 0.002 TYR A 475 ARG 0.016 0.001 ARG A 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 14) link_NAG-ASN : angle 2.58433 ( 42) hydrogen bonds : bond 0.03463 ( 892) hydrogen bonds : angle 4.86078 ( 2599) SS BOND : bond 0.02162 ( 10) SS BOND : angle 0.80520 ( 20) covalent geometry : bond 0.00585 (24758) covalent geometry : angle 0.72329 (33566) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 3.351 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: A 99 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7716 (m) REVERT: A 188 LYS cc_start: 0.9360 (mmmm) cc_final: 0.9077 (mmmm) REVERT: A 192 ASP cc_start: 0.9149 (m-30) cc_final: 0.8918 (m-30) REVERT: A 413 GLU cc_start: 0.8358 (tp30) cc_final: 0.8024 (tm-30) REVERT: A 475 TYR cc_start: 0.5572 (m-10) cc_final: 0.5337 (m-80) REVERT: A 564 MET cc_start: 0.4706 (tmm) cc_final: 0.4321 (tmm) REVERT: A 701 MET cc_start: 0.8849 (mmm) cc_final: 0.8611 (mmm) REVERT: B 152 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: B 254 ILE cc_start: 0.8755 (mm) cc_final: 0.8491 (mm) REVERT: B 679 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7699 (t80) REVERT: B 785 MET cc_start: 0.9344 (mmt) cc_final: 0.8965 (mpp) REVERT: B 818 MET cc_start: -0.2521 (mtp) cc_final: -0.2983 (ttm) REVERT: C 99 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7773 (m) REVERT: C 188 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9069 (mmmm) REVERT: C 192 ASP cc_start: 0.9152 (m-30) cc_final: 0.8920 (m-30) REVERT: C 230 TYR cc_start: 0.7585 (m-10) cc_final: 0.7330 (m-80) REVERT: C 415 PRO cc_start: 0.7324 (Cg_exo) cc_final: 0.6981 (Cg_endo) REVERT: C 560 MET cc_start: 0.5317 (tmm) cc_final: 0.4724 (ttp) REVERT: C 701 MET cc_start: 0.8829 (mmm) cc_final: 0.8604 (mmm) REVERT: C 774 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8774 (mp10) REVERT: D 136 SER cc_start: 0.8292 (m) cc_final: 0.7635 (p) REVERT: D 152 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8549 (m-10) REVERT: D 679 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7699 (t80) REVERT: D 818 MET cc_start: -0.0409 (mmt) cc_final: -0.0949 (ttm) outliers start: 63 outliers final: 41 residues processed: 330 average time/residue: 0.4696 time to fit residues: 252.3192 Evaluate side-chains 289 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 477 HIS Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 261 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 278 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 167 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 274 optimal weight: 0.5980 chunk 218 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 477 HIS ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN D 477 HIS ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.092532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.069323 restraints weight = 115672.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.071095 restraints weight = 66214.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.072248 restraints weight = 45970.475| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24784 Z= 0.134 Angle : 0.618 10.730 33628 Z= 0.302 Chirality : 0.045 0.300 3826 Planarity : 0.003 0.041 4206 Dihedral : 6.886 108.933 3586 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.87 % Allowed : 12.99 % Favored : 85.15 % 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: 0.16 (0.16), residues: 2980 helix: 1.61 (0.16), residues: 1174 sheet: -0.82 (0.28), residues: 382 loop : -0.91 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 55 HIS 0.010 0.001 HIS D 477 PHE 0.023 0.001 PHE B 753 TYR 0.020 0.001 TYR B 692 ARG 0.007 0.001 ARG A 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 14) link_NAG-ASN : angle 2.61790 ( 42) hydrogen bonds : bond 0.02943 ( 892) hydrogen bonds : angle 4.51914 ( 2599) SS BOND : bond 0.00170 ( 10) SS BOND : angle 0.77330 ( 20) covalent geometry : bond 0.00302 (24758) covalent geometry : angle 0.61128 (33566) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 2.752 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 188 LYS cc_start: 0.9355 (mmmm) cc_final: 0.9060 (mmmm) REVERT: A 192 ASP cc_start: 0.9157 (m-30) cc_final: 0.8930 (m-30) REVERT: A 230 TYR cc_start: 0.7363 (m-10) cc_final: 0.7099 (m-80) REVERT: A 475 TYR cc_start: 0.5815 (m-80) cc_final: 0.5507 (m-80) REVERT: A 701 MET cc_start: 0.8865 (mmm) cc_final: 0.8584 (mmm) REVERT: B 152 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8250 (m-10) REVERT: B 254 ILE cc_start: 0.8725 (mm) cc_final: 0.8453 (mm) REVERT: B 679 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7656 (t80) REVERT: B 818 MET cc_start: -0.2422 (mtp) cc_final: -0.2845 (ttm) REVERT: C 99 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (m) REVERT: C 188 LYS cc_start: 0.9351 (mmmm) cc_final: 0.9035 (mmmm) REVERT: C 192 ASP cc_start: 0.9115 (m-30) cc_final: 0.8897 (m-30) REVERT: C 701 MET cc_start: 0.8839 (mmm) cc_final: 0.8551 (mmm) REVERT: D 136 SER cc_start: 0.8331 (m) cc_final: 0.7678 (p) REVERT: D 152 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: D 679 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.7788 (t80) outliers start: 49 outliers final: 24 residues processed: 299 average time/residue: 0.4074 time to fit residues: 195.2869 Evaluate side-chains 255 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 234 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 276 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 228 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.092007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068604 restraints weight = 117643.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070313 restraints weight = 67121.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.071519 restraints weight = 46605.989| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24784 Z= 0.126 Angle : 0.626 10.119 33628 Z= 0.302 Chirality : 0.045 0.306 3826 Planarity : 0.003 0.043 4206 Dihedral : 6.830 108.619 3584 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.13 % Allowed : 13.25 % Favored : 84.62 % 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: 0.01 (0.16), residues: 2980 helix: 1.44 (0.15), residues: 1206 sheet: -0.80 (0.27), residues: 404 loop : -1.03 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 55 HIS 0.004 0.001 HIS B 477 PHE 0.030 0.001 PHE B 754 TYR 0.018 0.001 TYR D 692 ARG 0.007 0.001 ARG A 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 14) link_NAG-ASN : angle 2.59554 ( 42) hydrogen bonds : bond 0.02766 ( 892) hydrogen bonds : angle 4.43248 ( 2599) SS BOND : bond 0.00236 ( 10) SS BOND : angle 1.51836 ( 20) covalent geometry : bond 0.00285 (24758) covalent geometry : angle 0.61917 (33566) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 2.830 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 74 MET cc_start: 0.7544 (pmm) cc_final: 0.7327 (pmm) REVERT: A 188 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9059 (mmmm) REVERT: A 192 ASP cc_start: 0.9195 (m-30) cc_final: 0.8981 (m-30) REVERT: A 475 TYR cc_start: 0.5697 (m-80) cc_final: 0.5439 (m-80) REVERT: A 701 MET cc_start: 0.8866 (mmm) cc_final: 0.8622 (mmm) REVERT: B 133 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8874 (tt) REVERT: B 254 ILE cc_start: 0.8778 (mm) cc_final: 0.8490 (mm) REVERT: B 679 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7718 (t80) REVERT: B 738 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6751 (t80) REVERT: C 188 LYS cc_start: 0.9363 (mmmm) cc_final: 0.9105 (mmmm) REVERT: C 560 MET cc_start: 0.5385 (tmm) cc_final: 0.4748 (ttp) REVERT: C 701 MET cc_start: 0.8871 (mmm) cc_final: 0.8580 (mmm) REVERT: D 136 SER cc_start: 0.8495 (m) cc_final: 0.7973 (p) REVERT: D 152 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8390 (m-10) REVERT: D 679 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7986 (t80) REVERT: D 738 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6886 (t80) REVERT: D 818 MET cc_start: -0.1598 (mmt) cc_final: -0.2056 (mtt) outliers start: 56 outliers final: 34 residues processed: 274 average time/residue: 0.4269 time to fit residues: 191.5767 Evaluate side-chains 259 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 738 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 135 optimal weight: 0.0020 chunk 300 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 292 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.091114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.067588 restraints weight = 116436.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.069293 restraints weight = 66515.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.070622 restraints weight = 46249.285| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24784 Z= 0.135 Angle : 0.622 9.394 33628 Z= 0.301 Chirality : 0.044 0.308 3826 Planarity : 0.003 0.045 4206 Dihedral : 6.795 108.554 3583 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.55 % Allowed : 13.14 % Favored : 84.31 % 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: 0.01 (0.16), residues: 2980 helix: 1.42 (0.15), residues: 1216 sheet: -0.78 (0.27), residues: 404 loop : -1.05 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 55 HIS 0.004 0.001 HIS B 134 PHE 0.029 0.001 PHE C 782 TYR 0.018 0.001 TYR A 321 ARG 0.005 0.001 ARG B 755 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 14) link_NAG-ASN : angle 2.62362 ( 42) hydrogen bonds : bond 0.02764 ( 892) hydrogen bonds : angle 4.37458 ( 2599) SS BOND : bond 0.00370 ( 10) SS BOND : angle 1.75951 ( 20) covalent geometry : bond 0.00305 (24758) covalent geometry : angle 0.61381 (33566) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 2.669 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 188 LYS cc_start: 0.9371 (mmmm) cc_final: 0.9115 (mmmm) REVERT: A 475 TYR cc_start: 0.5882 (m-80) cc_final: 0.5585 (m-80) REVERT: A 701 MET cc_start: 0.8925 (mmm) cc_final: 0.8688 (mmm) REVERT: A 776 ASP cc_start: 0.8512 (p0) cc_final: 0.8287 (p0) REVERT: B 209 MET cc_start: 0.9093 (ptp) cc_final: 0.8857 (mmm) REVERT: B 254 ILE cc_start: 0.8796 (mm) cc_final: 0.8512 (mm) REVERT: B 679 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8067 (t80) REVERT: B 738 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6973 (t80) REVERT: C 192 ASP cc_start: 0.9151 (m-30) cc_final: 0.8767 (p0) REVERT: C 389 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.7105 (m) REVERT: D 123 THR cc_start: 0.9030 (m) cc_final: 0.8757 (p) REVERT: D 136 SER cc_start: 0.8617 (m) cc_final: 0.8091 (p) REVERT: D 152 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8349 (m-10) REVERT: D 679 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8111 (t80) REVERT: D 818 MET cc_start: -0.1907 (mmt) cc_final: -0.2505 (mtt) outliers start: 67 outliers final: 45 residues processed: 275 average time/residue: 0.3667 time to fit residues: 166.9404 Evaluate side-chains 259 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain C residue 55 TRP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 259 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS C 736 ASN ** D 770 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 = 0.3837 r_free = 0.3837 target = 0.089677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066590 restraints weight = 113353.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068414 restraints weight = 63810.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.069568 restraints weight = 43643.761| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24784 Z= 0.153 Angle : 0.645 9.938 33628 Z= 0.312 Chirality : 0.044 0.309 3826 Planarity : 0.003 0.047 4206 Dihedral : 6.827 108.718 3583 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.36 % Allowed : 14.17 % Favored : 83.47 % 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: 0.00 (0.16), residues: 2980 helix: 1.47 (0.15), residues: 1204 sheet: -0.81 (0.28), residues: 372 loop : -1.08 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 55 HIS 0.006 0.001 HIS C 405 PHE 0.030 0.002 PHE A 641 TYR 0.015 0.001 TYR C 230 ARG 0.005 0.000 ARG B 755 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 14) link_NAG-ASN : angle 2.64601 ( 42) hydrogen bonds : bond 0.02830 ( 892) hydrogen bonds : angle 4.39563 ( 2599) SS BOND : bond 0.00310 ( 10) SS BOND : angle 1.72409 ( 20) covalent geometry : bond 0.00348 (24758) covalent geometry : angle 0.63709 (33566) Misc. bond : bond 0.00046 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 3.605 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: A 192 ASP cc_start: 0.9167 (m-30) cc_final: 0.8840 (p0) REVERT: A 475 TYR cc_start: 0.5872 (m-80) cc_final: 0.5403 (m-80) REVERT: B 254 ILE cc_start: 0.8821 (mm) cc_final: 0.8519 (mm) REVERT: B 679 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8125 (t80) REVERT: B 738 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6940 (t80) REVERT: C 403 ASP cc_start: 0.7566 (p0) cc_final: 0.7130 (p0) REVERT: C 560 MET cc_start: 0.5291 (tmm) cc_final: 0.4509 (ttp) REVERT: C 701 MET cc_start: 0.8892 (mmm) cc_final: 0.8608 (mmm) REVERT: D 136 SER cc_start: 0.8666 (m) cc_final: 0.8197 (p) REVERT: D 627 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6821 (p90) REVERT: D 679 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8167 (t80) REVERT: D 738 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7092 (t80) REVERT: D 813 MET cc_start: -0.3961 (mtt) cc_final: -0.4518 (mtt) outliers start: 62 outliers final: 44 residues processed: 269 average time/residue: 0.4316 time to fit residues: 186.1717 Evaluate side-chains 254 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 627 PHE Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 738 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 171 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 53 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 286 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.087978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064657 restraints weight = 114090.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066472 restraints weight = 63978.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.067733 restraints weight = 43684.193| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24784 Z= 0.200 Angle : 0.681 12.302 33628 Z= 0.332 Chirality : 0.045 0.302 3826 Planarity : 0.004 0.049 4206 Dihedral : 7.031 109.718 3582 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.63 % Allowed : 14.09 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.12 (0.16), residues: 2980 helix: 1.39 (0.15), residues: 1204 sheet: -0.88 (0.26), residues: 402 loop : -1.16 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 55 HIS 0.004 0.001 HIS A 42 PHE 0.025 0.002 PHE A 641 TYR 0.029 0.002 TYR A 230 ARG 0.016 0.001 ARG C 386 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 14) link_NAG-ASN : angle 2.74570 ( 42) hydrogen bonds : bond 0.03056 ( 892) hydrogen bonds : angle 4.48608 ( 2599) SS BOND : bond 0.00355 ( 10) SS BOND : angle 1.88364 ( 20) covalent geometry : bond 0.00444 (24758) covalent geometry : angle 0.67325 (33566) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 205 time to evaluate : 5.322 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: A 475 TYR cc_start: 0.5962 (m-80) cc_final: 0.5636 (m-80) REVERT: A 536 MET cc_start: 0.8684 (tpt) cc_final: 0.8454 (tpt) REVERT: B 679 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8177 (t80) REVERT: B 738 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7011 (t80) REVERT: C 183 PHE cc_start: 0.6745 (m-10) cc_final: 0.5479 (m-10) REVERT: C 230 TYR cc_start: 0.7784 (m-10) cc_final: 0.7552 (m-80) REVERT: C 536 MET cc_start: 0.8672 (tpt) cc_final: 0.8378 (tpt) REVERT: D 209 MET cc_start: 0.9196 (ptp) cc_final: 0.8984 (mmm) REVERT: D 627 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6712 (p90) REVERT: D 679 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8293 (t80) REVERT: D 738 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7294 (t80) REVERT: D 818 MET cc_start: -0.1822 (mmt) cc_final: -0.2798 (mtt) outliers start: 69 outliers final: 54 residues processed: 260 average time/residue: 0.4508 time to fit residues: 187.8834 Evaluate side-chains 255 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain C residue 55 TRP Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 627 PHE Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 738 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 59 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 53 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 198 optimal weight: 0.5980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.086921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.063527 restraints weight = 114048.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.065185 restraints weight = 64348.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066452 restraints weight = 44357.605| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24784 Z= 0.205 Angle : 0.707 12.432 33628 Z= 0.347 Chirality : 0.046 0.311 3826 Planarity : 0.004 0.068 4206 Dihedral : 7.210 110.005 3582 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.36 % Allowed : 14.74 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.23 (0.16), residues: 2980 helix: 1.32 (0.15), residues: 1196 sheet: -1.02 (0.26), residues: 402 loop : -1.19 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 55 HIS 0.005 0.001 HIS C 42 PHE 0.062 0.002 PHE D 754 TYR 0.042 0.002 TYR D 692 ARG 0.010 0.001 ARG C 386 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 14) link_NAG-ASN : angle 2.83051 ( 42) hydrogen bonds : bond 0.03166 ( 892) hydrogen bonds : angle 4.57509 ( 2599) SS BOND : bond 0.00361 ( 10) SS BOND : angle 1.83340 ( 20) covalent geometry : bond 0.00455 (24758) covalent geometry : angle 0.69878 (33566) Misc. bond : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 2.928 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 475 TYR cc_start: 0.5947 (m-80) cc_final: 0.5595 (m-80) REVERT: A 701 MET cc_start: 0.8983 (mmm) cc_final: 0.8660 (mmm) REVERT: B 237 MET cc_start: 0.8681 (ppp) cc_final: 0.8334 (ppp) REVERT: B 679 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8235 (t80) REVERT: C 162 MET cc_start: 0.8604 (ttm) cc_final: 0.8335 (ttm) REVERT: C 701 MET cc_start: 0.8985 (mmm) cc_final: 0.8666 (mmm) REVERT: C 792 GLU cc_start: 0.8771 (tp30) cc_final: 0.8513 (tp30) REVERT: D 209 MET cc_start: 0.9182 (ptp) cc_final: 0.8961 (mmm) REVERT: D 627 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: D 679 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8363 (t80) REVERT: D 769 LYS cc_start: 0.8673 (mttt) cc_final: 0.8375 (mttm) outliers start: 62 outliers final: 50 residues processed: 253 average time/residue: 0.4596 time to fit residues: 185.9451 Evaluate side-chains 244 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 55 TRP Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 627 PHE Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 49 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 192 optimal weight: 0.0050 chunk 243 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN ** D 770 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 = 0.3802 r_free = 0.3802 target = 0.088100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064698 restraints weight = 113533.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066513 restraints weight = 63247.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067795 restraints weight = 42960.792| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24784 Z= 0.137 Angle : 0.675 12.554 33628 Z= 0.329 Chirality : 0.045 0.329 3826 Planarity : 0.004 0.047 4206 Dihedral : 6.974 108.674 3579 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.13 % Allowed : 15.08 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.07 (0.16), residues: 2980 helix: 1.43 (0.15), residues: 1186 sheet: -0.93 (0.27), residues: 384 loop : -1.07 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 55 HIS 0.004 0.001 HIS A 42 PHE 0.063 0.002 PHE D 754 TYR 0.017 0.001 TYR B 692 ARG 0.011 0.001 ARG C 386 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 14) link_NAG-ASN : angle 2.80187 ( 42) hydrogen bonds : bond 0.02925 ( 892) hydrogen bonds : angle 4.50850 ( 2599) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.63288 ( 20) covalent geometry : bond 0.00312 (24758) covalent geometry : angle 0.66737 (33566) Misc. bond : bond 0.00056 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 3.086 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 144 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: A 475 TYR cc_start: 0.5996 (m-80) cc_final: 0.5670 (m-80) REVERT: A 701 MET cc_start: 0.8958 (mmm) cc_final: 0.8631 (mmm) REVERT: A 754 TYR cc_start: 0.7581 (t80) cc_final: 0.7216 (t80) REVERT: B 237 MET cc_start: 0.8709 (ppp) cc_final: 0.8336 (ppp) REVERT: B 679 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8350 (t80) REVERT: C 701 MET cc_start: 0.8942 (mmm) cc_final: 0.8631 (mmm) REVERT: D 209 MET cc_start: 0.9230 (ptp) cc_final: 0.8967 (mmm) REVERT: D 679 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8395 (t80) REVERT: D 695 ARG cc_start: 0.8449 (ttp-110) cc_final: 0.8239 (ttm170) REVERT: D 769 LYS cc_start: 0.8764 (mttt) cc_final: 0.8431 (mttm) REVERT: D 794 ARG cc_start: 0.6651 (mtt90) cc_final: 0.6447 (mtt90) REVERT: D 813 MET cc_start: -0.3833 (mtt) cc_final: -0.4048 (mtt) outliers start: 56 outliers final: 44 residues processed: 252 average time/residue: 0.3620 time to fit residues: 144.7392 Evaluate side-chains 237 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.68 > 50: distance: 34 - 39: 3.226 distance: 35 - 60: 11.611 distance: 39 - 40: 9.430 distance: 40 - 43: 16.522 distance: 41 - 42: 13.386 distance: 41 - 44: 7.915 distance: 42 - 68: 19.064 distance: 44 - 45: 6.894 distance: 45 - 46: 6.471 distance: 45 - 48: 8.493 distance: 46 - 47: 10.542 distance: 46 - 52: 4.494 distance: 47 - 77: 14.489 distance: 48 - 49: 8.895 distance: 49 - 50: 6.378 distance: 49 - 51: 3.383 distance: 53 - 54: 6.715 distance: 53 - 56: 7.283 distance: 54 - 55: 10.039 distance: 55 - 82: 12.787 distance: 57 - 58: 6.049 distance: 57 - 59: 6.922 distance: 60 - 61: 9.512 distance: 61 - 62: 7.336 distance: 61 - 64: 18.051 distance: 62 - 63: 4.362 distance: 62 - 68: 6.548 distance: 63 - 91: 21.411 distance: 64 - 65: 22.598 distance: 65 - 66: 11.143 distance: 66 - 67: 8.738 distance: 68 - 69: 3.732 distance: 69 - 70: 11.076 distance: 69 - 72: 4.802 distance: 70 - 71: 11.269 distance: 70 - 77: 12.967 distance: 73 - 74: 6.560 distance: 74 - 75: 5.113 distance: 74 - 76: 4.691 distance: 77 - 78: 12.310 distance: 78 - 79: 12.717 distance: 78 - 81: 9.862 distance: 79 - 80: 24.717 distance: 79 - 82: 26.891 distance: 82 - 83: 16.479 distance: 83 - 84: 7.136 distance: 83 - 86: 8.184 distance: 84 - 85: 33.838 distance: 84 - 91: 5.570 distance: 87 - 88: 18.692 distance: 88 - 89: 20.740 distance: 89 - 90: 15.553 distance: 91 - 92: 7.769 distance: 92 - 93: 4.946 distance: 92 - 95: 6.041 distance: 93 - 94: 13.468 distance: 93 - 100: 7.643 distance: 95 - 96: 18.414 distance: 96 - 97: 24.983 distance: 97 - 98: 28.408 distance: 97 - 99: 20.019 distance: 100 - 101: 21.392 distance: 101 - 102: 13.867 distance: 101 - 104: 26.706 distance: 102 - 103: 15.642 distance: 102 - 108: 8.645 distance: 104 - 105: 9.769 distance: 105 - 106: 20.387 distance: 105 - 107: 29.516 distance: 108 - 109: 11.122 distance: 109 - 110: 5.203 distance: 109 - 112: 4.907 distance: 110 - 111: 3.355 distance: 110 - 117: 9.320 distance: 112 - 113: 13.640 distance: 113 - 114: 7.719 distance: 114 - 115: 10.285 distance: 114 - 116: 15.092