Starting phenix.real_space_refine on Fri Feb 6 21:20:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzw_72084/02_2026/9pzw_72084.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzw_72084/02_2026/9pzw_72084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pzw_72084/02_2026/9pzw_72084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzw_72084/02_2026/9pzw_72084.map" model { file = "/net/cci-nas-00/data/ceres_data/9pzw_72084/02_2026/9pzw_72084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzw_72084/02_2026/9pzw_72084.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 158 5.16 5 C 17599 2.51 5 N 4583 2.21 5 O 5185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27525 Number of models: 1 Model: "" Number of chains: 16 Chain: "J" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 815 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5973 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 31, 'TRANS': 732} Chain breaks: 4 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 5852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5852 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 724} Chain breaks: 6 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 6011 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 729} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5936 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 733} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "L" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "M" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 820 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" 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: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.43, per 1000 atoms: 0.23 Number of scatterers: 27525 At special positions: 0 Unit cell: (121.18, 219.12, 182.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 158 16.00 O 5185 8.00 N 4583 7.00 C 17599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 115 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 112 " distance=2.04 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.02 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 800 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 115 " distance=2.04 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 61 " " NAG A 903 " - " ASN A 239 " " NAG A 904 " - " ASN A 350 " " NAG A 905 " - " ASN A 771 " " NAG B 902 " - " ASN B 75 " " NAG B 903 " - " ASN B 340 " " NAG B 904 " - " ASN B 380 " " NAG B 905 " - " ASN B 687 " " NAG C 902 " - " ASN C 61 " " NAG C 903 " - " ASN C 203 " " NAG C 904 " - " ASN C 239 " " NAG C 905 " - " ASN C 276 " " NAG C 906 " - " ASN C 350 " " NAG C 907 " - " ASN C 771 " " NAG D 902 " - " ASN D 75 " " NAG D 903 " - " ASN D 687 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6508 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 44 sheets defined 38.3% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'J' and resid 47 through 51 removed outlier: 4.263A pdb=" N TYR J 51 " --> pdb=" O PHE J 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 53 removed outlier: 4.138A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.931A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.042A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.206A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.631A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.694A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 561 through 584 Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.882A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 657 removed outlier: 3.842A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 668 removed outlier: 4.204A pdb=" N ASN A 668 " --> pdb=" O THR A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.623A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.551A pdb=" N GLU A 707 " --> pdb=" O TYR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 812 through 838 removed outlier: 4.033A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.745A pdb=" N VAL B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.695A pdb=" N GLU B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.540A pdb=" N MET B 338 " --> pdb=" O HIS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.512A pdb=" N GLY B 498 " --> pdb=" O ASN B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 556 through 579 Processing helix chain 'B' and resid 603 through 613 removed outlier: 3.941A pdb=" N PHE B 613 " --> pdb=" O TRP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 655 Processing helix chain 'B' and resid 667 through 672 removed outlier: 4.118A pdb=" N ARG B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 723 removed outlier: 3.629A pdb=" N VAL B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 771 through 784 Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 813 through 836 removed outlier: 4.109A pdb=" N ILE B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.711A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.684A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.595A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.573A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 172 through 188 removed outlier: 3.778A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.775A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 277 through 296 Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.089A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 584 Processing helix chain 'C' and resid 606 through 616 removed outlier: 3.884A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 657 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 769 through 782 removed outlier: 3.618A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 813 through 838 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 54 through 59 removed outlier: 3.946A pdb=" N GLU D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 128 through 133 removed outlier: 4.154A pdb=" N ALA D 131 " --> pdb=" O HIS D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 166 Processing helix chain 'D' and resid 179 through 193 removed outlier: 4.182A pdb=" N PHE D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.625A pdb=" N GLN D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.617A pdb=" N LEU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 310 removed outlier: 3.742A pdb=" N LYS D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.601A pdb=" N MET D 338 " --> pdb=" O HIS D 335 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL D 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 339' Processing helix chain 'D' and resid 458 through 472 removed outlier: 3.594A pdb=" N ASP D 462 " --> pdb=" O GLY D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 502 Processing helix chain 'D' and resid 516 through 522 Processing helix chain 'D' and resid 556 through 579 Processing helix chain 'D' and resid 603 through 614 removed outlier: 3.628A pdb=" N LEU D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 613 " --> pdb=" O TRP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 655 Processing helix chain 'D' and resid 667 through 672 Processing helix chain 'D' and resid 689 through 698 Processing helix chain 'D' and resid 698 through 708 removed outlier: 4.248A pdb=" N PHE D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 723 Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 771 through 784 Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 813 through 837 removed outlier: 4.028A pdb=" N ILE D 836 " --> pdb=" O LEU D 832 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP D 837 " --> pdb=" O ILE D 833 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 removed outlier: 4.158A pdb=" N TYR L 51 " --> pdb=" O PHE L 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 23 through 24 removed outlier: 3.598A pdb=" N ILE J 39 " --> pdb=" O MET J 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 29 through 30 removed outlier: 4.225A pdb=" N GLY J 68 " --> pdb=" O TRP J 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 29 through 30 Processing sheet with id=AA4, first strand: chain 'K' and resid 24 through 27 removed outlier: 3.527A pdb=" N THR K 25 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER K 42 " --> pdb=" O SER K 27 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE K 95 " --> pdb=" O CYS K 43 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER K 87 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'K' and resid 50 through 51 Processing sheet with id=AA7, first strand: chain 'K' and resid 77 through 78 removed outlier: 6.622A pdb=" N TRP K 59 " --> pdb=" O LEU K 71 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET K 109 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.301A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 193 through 196 removed outlier: 4.056A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.511A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A 354 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 476 through 478 removed outlier: 3.511A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 753 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG A 755 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN A 536 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 476 through 478 removed outlier: 3.511A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 753 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG A 755 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN A 536 " --> pdb=" O ARG A 755 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 409 through 413 Processing sheet with id=AB5, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 74 removed outlier: 6.925A pdb=" N VAL B 38 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N MET B 74 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 40 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.619A pdb=" N PHE B 170 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.619A pdb=" N PHE B 170 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 228 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 361 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS B 377 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AC1, first strand: chain 'B' and resid 474 through 479 removed outlier: 3.756A pdb=" N MET B 507 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 508 " --> pdb=" O ALA B 764 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 764 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AC3, first strand: chain 'B' and resid 438 through 441 Processing sheet with id=AC4, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AC5, first strand: chain 'B' and resid 682 through 683 removed outlier: 3.632A pdb=" N ILE B 729 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 730 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 537 " --> pdb=" O VAL B 748 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 66 removed outlier: 3.659A pdb=" N ASN C 61 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR C 63 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 193 through 195 removed outlier: 7.122A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AC9, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.608A pdb=" N ILE C 366 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN C 368 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 477 through 478 removed outlier: 6.134A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE C 754 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 538 " --> pdb=" O PHE C 754 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 477 through 478 removed outlier: 6.134A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE C 754 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 538 " --> pdb=" O PHE C 754 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.610A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 451 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AD5, first strand: chain 'D' and resid 67 through 74 removed outlier: 7.429A pdb=" N ASN D 35 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL D 99 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA D 37 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLY D 101 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU D 39 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 204 through 205 removed outlier: 8.963A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 228 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 256 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 279 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU D 361 " --> pdb=" O TRP D 378 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP D 378 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY D 376 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 365 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LYS D 374 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AD8, first strand: chain 'D' and resid 474 through 479 removed outlier: 3.514A pdb=" N ILE D 408 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET D 507 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 764 " --> pdb=" O ALA D 508 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.571A pdb=" N LYS D 454 " --> pdb=" O CYS D 436 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 728 through 731 removed outlier: 3.576A pdb=" N TYR D 730 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER D 534 " --> pdb=" O TYR D 730 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 537 " --> pdb=" O VAL D 748 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.590A pdb=" N GLN L 24 " --> pdb=" O LYS L 42 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL L 37 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU L 102 " --> pdb=" O VAL L 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 29 through 30 removed outlier: 4.201A pdb=" N GLY L 68 " --> pdb=" O TRP L 55 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AE5, first strand: chain 'M' and resid 26 through 27 removed outlier: 3.551A pdb=" N PHE M 95 " --> pdb=" O CYS M 43 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP M 94 " --> pdb=" O SER M 91 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER M 91 " --> pdb=" O ASP M 94 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER M 89 " --> pdb=" O SER M 96 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 30 through 32 Processing sheet with id=AE7, first strand: chain 'M' and resid 50 through 51 removed outlier: 3.549A pdb=" N THR M 54 " --> pdb=" O TYR M 51 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 77 through 78 removed outlier: 6.565A pdb=" N TRP M 59 " --> pdb=" O LEU M 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN M 114 " --> pdb=" O THR M 121 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR M 121 " --> pdb=" O GLN M 114 " (cutoff:3.500A) 1169 hydrogen bonds defined for protein. 3330 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: 6.20 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8791 1.34 - 1.46: 4886 1.46 - 1.58: 14186 1.58 - 1.69: 0 1.69 - 1.81: 270 Bond restraints: 28133 Sorted by residual: bond pdb=" C1 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" N ILE B 95 " pdb=" CA ILE B 95 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.36e+00 bond pdb=" N ILE B 750 " pdb=" CA ILE B 750 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 7.83e+00 bond pdb=" N GLN A 405 " pdb=" CA GLN A 405 " ideal model delta sigma weight residual 1.452 1.486 -0.033 1.22e-02 6.72e+03 7.51e+00 bond pdb=" N MET B 90 " pdb=" CA MET B 90 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 7.18e+00 ... (remaining 28128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 37093 1.51 - 3.02: 918 3.02 - 4.53: 132 4.53 - 6.04: 28 6.04 - 7.56: 5 Bond angle restraints: 38176 Sorted by residual: angle pdb=" CA ARG B 94 " pdb=" C ARG B 94 " pdb=" O ARG B 94 " ideal model delta sigma weight residual 122.64 117.80 4.84 1.25e+00 6.40e-01 1.50e+01 angle pdb=" N GLY D 688 " pdb=" CA GLY D 688 " pdb=" C GLY D 688 " ideal model delta sigma weight residual 111.20 116.26 -5.06 1.39e+00 5.18e-01 1.33e+01 angle pdb=" CA GLY B 753 " pdb=" C GLY B 753 " pdb=" O GLY B 753 " ideal model delta sigma weight residual 122.43 117.86 4.57 1.39e+00 5.18e-01 1.08e+01 angle pdb=" N TYR B 754 " pdb=" CA TYR B 754 " pdb=" C TYR B 754 " ideal model delta sigma weight residual 111.30 106.88 4.42 1.36e+00 5.41e-01 1.06e+01 angle pdb=" CA GLN A 405 " pdb=" C GLN A 405 " pdb=" O GLN A 405 " ideal model delta sigma weight residual 121.88 117.89 3.99 1.30e+00 5.92e-01 9.40e+00 ... (remaining 38171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 16286 22.90 - 45.81: 522 45.81 - 68.71: 56 68.71 - 91.62: 14 91.62 - 114.52: 7 Dihedral angle restraints: 16885 sinusoidal: 6791 harmonic: 10094 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 308 " pdb=" CB CYS C 308 " ideal model delta sinusoidal sigma weight residual 93.00 126.86 -33.86 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" C3 NAG B 902 " pdb=" C1 NAG B 902 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sinusoidal sigma weight residual -55.55 58.97 -114.52 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" N2 NAG B 902 " pdb=" C1 NAG B 902 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sinusoidal sigma weight residual -178.19 -64.91 -113.28 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 16882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3853 0.070 - 0.140: 495 0.140 - 0.210: 14 0.210 - 0.280: 4 0.280 - 0.350: 2 Chirality restraints: 4368 Sorted by residual: chirality pdb=" C1 NAG C 903 " pdb=" ND2 ASN C 203 " pdb=" C2 NAG C 903 " pdb=" O5 NAG C 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 380 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 4365 not shown) Planarity restraints: 4840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 903 " 0.331 2.00e-02 2.50e+03 2.82e-01 9.91e+02 pdb=" C7 NAG D 903 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG D 903 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NAG D 903 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG D 903 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 103 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO C 104 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 56 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO D 57 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " -0.035 5.00e-02 4.00e+02 ... (remaining 4837 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3477 2.75 - 3.29: 25665 3.29 - 3.83: 41545 3.83 - 4.36: 46060 4.36 - 4.90: 84096 Nonbonded interactions: 200843 Sorted by model distance: nonbonded pdb=" NE2 GLN D 154 " pdb=" OG SER D 259 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASP D 114 " pdb=" OG SER D 142 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 93 " pdb=" OE2 GLU A 277 " model vdw 2.230 3.040 nonbonded pdb=" N ASN C 161 " pdb=" OH TYR C 392 " model vdw 2.230 3.120 nonbonded pdb=" O GLY C 567 " pdb=" ND1 HIS C 571 " model vdw 2.233 3.120 ... (remaining 200838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 322 or (resid 323 and (name N or \ name CA or name C or name O or name CB )) or resid 324 through 585 or resid 605 \ through 629 or (resid 630 and (name N or name CA or name C or name O or name CB \ )) or resid 631 through 905)) selection = (chain 'C' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 35 or (resid 36 through 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 42 or (resid 43 through 45 and (n \ ame N or name CA or name C or name O or name CB )) or resid 46 through 51 or (re \ sid 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 55 or (resid 56 through 57 and (name N or name CA or name C or name O or nam \ e CB )) or resid 58 through 98 or (resid 99 through 100 and (name N or name CA o \ r name C or name O or name CB )) or resid 101 through 201 or (resid 202 and (nam \ e N or name CA or name C or name O or name CB )) or resid 203 through 256 or (re \ sid 257 through 258 and (name N or name CA or name C or name O or name CB )) or \ resid 259 through 328 or (resid 329 and (name N or name CA or name C or name O o \ r name CB )) or resid 330 through 336 or (resid 337 and (name N or name CA or na \ me C or name O or name CB )) or resid 338 through 377 or (resid 378 and (name N \ or name CA or name C or name O or name CB )) or resid 379 through 405 or (resid \ 406 and (name N or name CA or name C or name O or name CB )) or resid 407 throug \ h 698 or (resid 699 and (name N or name CA or name C or name O or name CB )) or \ resid 700 through 905)) } ncs_group { reference = (chain 'B' and (resid 31 through 206 or (resid 207 and (name N or name CA or nam \ e C or name O or name CB )) or resid 208 through 213 or (resid 214 and (name N o \ r name CA or name C or name O or name CB )) or resid 215 through 351 or (resid 3 \ 52 through 353 and (name N or name CA or name C or name O or name CB )) or resid \ 354 through 664 or (resid 665 and (name N or name CA or name C or name O or nam \ e CB )) or resid 666 through 706 or (resid 707 and (name N or name CA or name C \ or name O or name CB )) or resid 708 through 710 or (resid 711 and (name N or na \ me CA or name C or name O or name CB )) or resid 712 through 723 or (resid 724 a \ nd (name N or name CA or name C or name O or name CB )) or resid 725 through 903 \ )) selection = (chain 'D' and (resid 31 through 54 or resid 61 through 323 or resid 330 through \ 393 or (resid 394 and (name N or name CA or name C or name O or name CB )) or r \ esid 395 through 399 or (resid 400 and (name N or name CA or name C or name O or \ name CB )) or resid 401 through 430 or (resid 431 and (name N or name CA or nam \ e C or name O or name CB )) or resid 432 through 618 or resid 621 through 670 or \ (resid 671 through 672 and (name N or name CA or name C or name O or name CB )) \ or resid 673 or (resid 674 and (name N or name CA or name C or name O or name C \ B )) or resid 675 through 699 or (resid 700 and (name N or name CA or name C or \ name O or name CB )) or resid 701 through 834 or (resid 835 and (name N or name \ CA or name C or name O or name CB )) or resid 836 through 903)) } ncs_group { reference = chain 'J' selection = (chain 'L' and (resid 20 through 92 or (resid 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 through 138)) } ncs_group { reference = chain 'K' selection = (chain 'M' and ((resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 81 or (resid 82 and (name N or name CA or name C or name \ O or name CB )) or resid 83 through 129)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.290 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.310 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.004 0.076 28164 Z= 0.205 Angle : 0.611 21.574 38254 Z= 0.325 Chirality : 0.045 0.350 4368 Planarity : 0.006 0.282 4824 Dihedral : 11.695 114.521 10332 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.44 % Allowed : 6.98 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3441 helix: 1.78 (0.15), residues: 1264 sheet: -1.28 (0.20), residues: 644 loop : -1.74 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 392 TYR 0.016 0.001 TYR B 478 PHE 0.022 0.002 PHE B 459 TRP 0.015 0.001 TRP C 768 HIS 0.007 0.001 HIS D 702 Details of bonding type rmsd covalent geometry : bond 0.00446 (28133) covalent geometry : angle 0.58816 (38176) SS BOND : bond 0.00316 ( 15) SS BOND : angle 0.74922 ( 30) hydrogen bonds : bond 0.16526 ( 1151) hydrogen bonds : angle 6.12091 ( 3330) link_NAG-ASN : bond 0.00961 ( 16) link_NAG-ASN : angle 4.68062 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 330 time to evaluate : 1.147 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: J 42 LYS cc_start: 0.9228 (mttt) cc_final: 0.8937 (tptm) REVERT: J 109 ASP cc_start: 0.9105 (m-30) cc_final: 0.8735 (p0) REVERT: K 77 ASN cc_start: 0.9159 (m110) cc_final: 0.8923 (t0) REVERT: K 94 ASP cc_start: 0.9242 (t0) cc_final: 0.8829 (m-30) REVERT: B 476 ASP cc_start: 0.8351 (t0) cc_final: 0.7937 (p0) REVERT: B 793 THR cc_start: 0.9021 (m) cc_final: 0.8588 (p) REVERT: C 203 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8404 (t0) REVERT: C 354 MET cc_start: 0.8591 (mmm) cc_final: 0.8317 (mmm) REVERT: C 495 LYS cc_start: 0.8256 (tttm) cc_final: 0.7895 (mmmt) REVERT: D 564 MET cc_start: 0.6092 (ttt) cc_final: 0.5806 (ptt) outliers start: 13 outliers final: 7 residues processed: 343 average time/residue: 0.2370 time to fit residues: 120.0114 Evaluate side-chains 207 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 321 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 25 GLN K 37 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN A 48 GLN A 73 GLN A 146 HIS A 449 HIS A 477 HIS B 85 HIS B 201 GLN B 336 GLN B 358 HIS B 405 HIS B 451 ASN B 655 GLN B 693 ASN B 709 ASN C 70 ASN C 449 HIS C 477 HIS ** D 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 615 ASN D 671 GLN D 702 HIS L 25 GLN L 58 GLN M 26 GLN M 66 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.085573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.054418 restraints weight = 99506.251| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 4.70 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28164 Z= 0.152 Angle : 0.603 20.940 38254 Z= 0.302 Chirality : 0.044 0.367 4368 Planarity : 0.004 0.066 4824 Dihedral : 7.431 103.952 4077 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.48 % Allowed : 9.45 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3441 helix: 1.98 (0.15), residues: 1272 sheet: -1.03 (0.20), residues: 656 loop : -1.58 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 704 TYR 0.014 0.001 TYR B 478 PHE 0.014 0.001 PHE B 459 TRP 0.021 0.001 TRP B 609 HIS 0.007 0.001 HIS D 702 Details of bonding type rmsd covalent geometry : bond 0.00350 (28133) covalent geometry : angle 0.57949 (38176) SS BOND : bond 0.00327 ( 15) SS BOND : angle 0.82311 ( 30) hydrogen bonds : bond 0.04245 ( 1151) hydrogen bonds : angle 4.87786 ( 3330) link_NAG-ASN : bond 0.00788 ( 16) link_NAG-ASN : angle 4.71017 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 1.254 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: J 81 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8974 (tm-30) REVERT: J 109 ASP cc_start: 0.9255 (m-30) cc_final: 0.8627 (p0) REVERT: K 85 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6898 (mtp180) REVERT: K 94 ASP cc_start: 0.9038 (t0) cc_final: 0.8614 (m-30) REVERT: A 502 MET cc_start: 0.9223 (mmm) cc_final: 0.8851 (mmt) REVERT: A 695 ARG cc_start: 0.8621 (ttm170) cc_final: 0.8349 (ttm170) REVERT: B 199 ASP cc_start: 0.8701 (t0) cc_final: 0.8456 (t0) REVERT: B 476 ASP cc_start: 0.8307 (t0) cc_final: 0.7399 (p0) REVERT: B 701 MET cc_start: 0.8537 (tpp) cc_final: 0.8320 (tpp) REVERT: C 203 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8392 (t0) REVERT: C 237 MET cc_start: 0.8596 (tmm) cc_final: 0.8263 (tmm) REVERT: C 354 MET cc_start: 0.7972 (mmm) cc_final: 0.7472 (mmm) REVERT: C 672 LEU cc_start: 0.8844 (mp) cc_final: 0.8566 (mt) REVERT: D 564 MET cc_start: 0.5986 (ttt) cc_final: 0.5766 (ptt) REVERT: L 54 GLU cc_start: 0.8069 (mp0) cc_final: 0.7766 (mt-10) REVERT: L 65 GLU cc_start: 0.8497 (mp0) cc_final: 0.7689 (mp0) REVERT: L 92 ASP cc_start: 0.8363 (t0) cc_final: 0.8146 (t0) outliers start: 44 outliers final: 24 residues processed: 252 average time/residue: 0.1949 time to fit residues: 78.6297 Evaluate side-chains 214 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain M residue 33 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 258 optimal weight: 0.9980 chunk 284 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 336 optimal weight: 0.0670 chunk 302 optimal weight: 30.0000 chunk 71 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 343 optimal weight: 7.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS B 696 ASN C 70 ASN ** D 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 HIS ** 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 = 0.3674 r_free = 0.3674 target = 0.084270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053013 restraints weight = 100274.494| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.69 r_work: 0.2738 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28164 Z= 0.172 Angle : 0.590 20.950 38254 Z= 0.295 Chirality : 0.044 0.358 4368 Planarity : 0.004 0.071 4824 Dihedral : 6.794 100.773 4077 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.92 % Allowed : 10.46 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 3441 helix: 1.96 (0.15), residues: 1284 sheet: -0.87 (0.21), residues: 642 loop : -1.52 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 704 TYR 0.014 0.001 TYR B 478 PHE 0.014 0.001 PHE C 533 TRP 0.025 0.001 TRP B 609 HIS 0.003 0.001 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00403 (28133) covalent geometry : angle 0.56642 (38176) SS BOND : bond 0.00270 ( 15) SS BOND : angle 0.65324 ( 30) hydrogen bonds : bond 0.04150 ( 1151) hydrogen bonds : angle 4.67495 ( 3330) link_NAG-ASN : bond 0.00759 ( 16) link_NAG-ASN : angle 4.65328 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 1.239 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: J 81 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9024 (tm-30) REVERT: J 109 ASP cc_start: 0.9296 (m-30) cc_final: 0.8627 (p0) REVERT: K 85 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7242 (ptm160) REVERT: K 94 ASP cc_start: 0.9141 (t0) cc_final: 0.8751 (m-30) REVERT: K 113 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: A 502 MET cc_start: 0.9299 (mmm) cc_final: 0.8893 (mmt) REVERT: B 199 ASP cc_start: 0.9029 (t0) cc_final: 0.8770 (t0) REVERT: B 381 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.9030 (mm-40) REVERT: B 788 MET cc_start: 0.8512 (tpp) cc_final: 0.8248 (tpp) REVERT: C 203 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8440 (t0) REVERT: C 237 MET cc_start: 0.8876 (tmm) cc_final: 0.8572 (tmm) REVERT: C 354 MET cc_start: 0.8496 (mmm) cc_final: 0.7955 (mmm) REVERT: D 428 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8851 (p) REVERT: D 561 MET cc_start: 0.2023 (mmt) cc_final: 0.1788 (mmt) REVERT: D 564 MET cc_start: 0.6103 (ttt) cc_final: 0.5863 (ptp) REVERT: L 54 GLU cc_start: 0.8243 (mp0) cc_final: 0.7957 (mt-10) REVERT: L 65 GLU cc_start: 0.8813 (mp0) cc_final: 0.8020 (mp0) REVERT: L 81 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9058 (mm-30) REVERT: L 84 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8732 (ttpp) REVERT: L 92 ASP cc_start: 0.8420 (t0) cc_final: 0.8118 (t0) outliers start: 57 outliers final: 27 residues processed: 239 average time/residue: 0.1826 time to fit residues: 71.5429 Evaluate side-chains 209 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 119 ARG Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 75 optimal weight: 40.0000 chunk 234 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 257 optimal weight: 0.4980 chunk 303 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 405 GLN B 53 ASN ** D 42 HIS ** 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 = 0.3660 r_free = 0.3660 target = 0.083493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052115 restraints weight = 100109.174| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.66 r_work: 0.2719 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28164 Z= 0.184 Angle : 0.581 20.966 38254 Z= 0.293 Chirality : 0.044 0.361 4368 Planarity : 0.004 0.070 4824 Dihedral : 6.394 96.574 4075 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.23 % Allowed : 10.70 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3441 helix: 1.97 (0.15), residues: 1276 sheet: -0.84 (0.20), residues: 657 loop : -1.48 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 469 TYR 0.014 0.001 TYR B 478 PHE 0.015 0.001 PHE C 533 TRP 0.023 0.001 TRP B 609 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00434 (28133) covalent geometry : angle 0.55674 (38176) SS BOND : bond 0.00289 ( 15) SS BOND : angle 0.70780 ( 30) hydrogen bonds : bond 0.04142 ( 1151) hydrogen bonds : angle 4.60823 ( 3330) link_NAG-ASN : bond 0.00722 ( 16) link_NAG-ASN : angle 4.69758 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 1.134 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: J 81 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8971 (tm-30) REVERT: J 109 ASP cc_start: 0.9309 (m-30) cc_final: 0.8611 (p0) REVERT: K 85 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6324 (ptm160) REVERT: K 94 ASP cc_start: 0.9137 (t0) cc_final: 0.8764 (m-30) REVERT: K 113 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: A 502 MET cc_start: 0.9328 (mmm) cc_final: 0.8925 (mmt) REVERT: A 762 MET cc_start: 0.8638 (mtm) cc_final: 0.8420 (mtp) REVERT: B 199 ASP cc_start: 0.9114 (t0) cc_final: 0.8800 (t0) REVERT: B 381 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.9075 (mm-40) REVERT: C 94 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8436 (m-70) REVERT: C 203 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8506 (t0) REVERT: C 237 MET cc_start: 0.8898 (tmm) cc_final: 0.8603 (tmm) REVERT: C 354 MET cc_start: 0.8487 (mmm) cc_final: 0.7976 (mmm) REVERT: C 672 LEU cc_start: 0.8732 (mp) cc_final: 0.8182 (mt) REVERT: C 702 MET cc_start: 0.8981 (mmm) cc_final: 0.8648 (mmt) REVERT: C 818 MET cc_start: -0.1799 (tpt) cc_final: -0.2325 (ppp) REVERT: D 55 TRP cc_start: 0.8031 (OUTLIER) cc_final: 0.7449 (t60) REVERT: D 428 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8844 (p) REVERT: D 564 MET cc_start: 0.6060 (ttt) cc_final: 0.5737 (ptp) REVERT: D 788 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8468 (mpp) REVERT: L 54 GLU cc_start: 0.8239 (mp0) cc_final: 0.7975 (mt-10) REVERT: L 65 GLU cc_start: 0.8822 (mp0) cc_final: 0.8014 (mp0) REVERT: L 84 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8803 (ttpp) REVERT: L 92 ASP cc_start: 0.8437 (t0) cc_final: 0.8075 (t0) REVERT: L 121 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9205 (t) outliers start: 66 outliers final: 34 residues processed: 234 average time/residue: 0.1739 time to fit residues: 67.7192 Evaluate side-chains 215 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 55 TRP Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 15 optimal weight: 4.9990 chunk 272 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 236 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 336 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS B 106 GLN D 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.084341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053084 restraints weight = 99155.161| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.61 r_work: 0.2748 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28164 Z= 0.108 Angle : 0.540 20.801 38254 Z= 0.268 Chirality : 0.043 0.370 4368 Planarity : 0.004 0.068 4824 Dihedral : 6.041 94.727 4073 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.92 % Allowed : 11.50 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3441 helix: 2.11 (0.15), residues: 1272 sheet: -0.74 (0.20), residues: 670 loop : -1.36 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 469 TYR 0.013 0.001 TYR B 478 PHE 0.010 0.001 PHE B 459 TRP 0.023 0.001 TRP B 609 HIS 0.003 0.001 HIS K 100 Details of bonding type rmsd covalent geometry : bond 0.00244 (28133) covalent geometry : angle 0.51459 (38176) SS BOND : bond 0.00204 ( 15) SS BOND : angle 0.61289 ( 30) hydrogen bonds : bond 0.03374 ( 1151) hydrogen bonds : angle 4.34569 ( 3330) link_NAG-ASN : bond 0.00799 ( 16) link_NAG-ASN : angle 4.61171 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 1.140 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: J 109 ASP cc_start: 0.9310 (m-30) cc_final: 0.8566 (p0) REVERT: J 122 MET cc_start: 0.9066 (mtt) cc_final: 0.8853 (mtt) REVERT: K 85 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8162 (mtm180) REVERT: K 94 ASP cc_start: 0.9127 (t0) cc_final: 0.8685 (m-30) REVERT: A 237 MET cc_start: 0.9296 (tpp) cc_final: 0.8964 (tmm) REVERT: A 429 ASP cc_start: 0.7788 (t0) cc_final: 0.7536 (t0) REVERT: A 502 MET cc_start: 0.9306 (mmm) cc_final: 0.8920 (mmt) REVERT: A 762 MET cc_start: 0.8657 (mtm) cc_final: 0.8439 (mtp) REVERT: B 199 ASP cc_start: 0.9146 (t0) cc_final: 0.8825 (t0) REVERT: B 381 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8986 (mm-40) REVERT: C 94 HIS cc_start: 0.8672 (OUTLIER) cc_final: 0.8460 (m-70) REVERT: C 203 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8519 (t0) REVERT: C 237 MET cc_start: 0.8905 (tmm) cc_final: 0.8585 (tmm) REVERT: C 354 MET cc_start: 0.8476 (mmm) cc_final: 0.7947 (mmm) REVERT: C 672 LEU cc_start: 0.8758 (mp) cc_final: 0.8207 (mt) REVERT: C 702 MET cc_start: 0.8972 (mmm) cc_final: 0.8640 (mmt) REVERT: C 818 MET cc_start: -0.1813 (tpt) cc_final: -0.2327 (ppp) REVERT: D 428 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8864 (p) REVERT: D 564 MET cc_start: 0.6043 (ttt) cc_final: 0.5817 (ptt) REVERT: D 788 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8641 (mpp) REVERT: L 54 GLU cc_start: 0.8203 (mp0) cc_final: 0.7958 (mt-10) REVERT: L 65 GLU cc_start: 0.8820 (mp0) cc_final: 0.8003 (mp0) REVERT: L 81 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9011 (mm-30) REVERT: L 84 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8759 (ttpp) REVERT: L 92 ASP cc_start: 0.8530 (t0) cc_final: 0.8177 (t0) REVERT: L 121 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9155 (t) REVERT: M 50 GLU cc_start: 0.8510 (mp0) cc_final: 0.8141 (mp0) REVERT: M 109 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.7000 (mmp) outliers start: 57 outliers final: 31 residues processed: 229 average time/residue: 0.1869 time to fit residues: 69.5752 Evaluate side-chains 212 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 119 ARG Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 777 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 795 TYR Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 109 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 110 optimal weight: 0.6980 chunk 343 optimal weight: 5.9990 chunk 235 optimal weight: 0.0000 chunk 299 optimal weight: 7.9990 chunk 292 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 139 optimal weight: 0.0570 chunk 191 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.083975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.052915 restraints weight = 100131.684| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 4.66 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28164 Z= 0.126 Angle : 0.552 20.682 38254 Z= 0.272 Chirality : 0.043 0.370 4368 Planarity : 0.004 0.066 4824 Dihedral : 5.863 96.050 4071 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.96 % Allowed : 11.64 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3441 helix: 2.09 (0.15), residues: 1284 sheet: -0.65 (0.20), residues: 673 loop : -1.34 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 704 TYR 0.017 0.001 TYR A 330 PHE 0.010 0.001 PHE C 533 TRP 0.015 0.001 TRP B 609 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00293 (28133) covalent geometry : angle 0.52842 (38176) SS BOND : bond 0.00297 ( 15) SS BOND : angle 0.92140 ( 30) hydrogen bonds : bond 0.03452 ( 1151) hydrogen bonds : angle 4.29692 ( 3330) link_NAG-ASN : bond 0.00792 ( 16) link_NAG-ASN : angle 4.54578 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 1.127 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: J 109 ASP cc_start: 0.9279 (m-30) cc_final: 0.8560 (p0) REVERT: K 94 ASP cc_start: 0.9138 (t0) cc_final: 0.8686 (m-30) REVERT: A 237 MET cc_start: 0.9276 (tpp) cc_final: 0.9002 (tmm) REVERT: A 429 ASP cc_start: 0.7787 (t0) cc_final: 0.7310 (p0) REVERT: A 502 MET cc_start: 0.9308 (mmm) cc_final: 0.8933 (mmt) REVERT: B 74 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7984 (pmm) REVERT: B 199 ASP cc_start: 0.9006 (t0) cc_final: 0.8649 (t0) REVERT: B 701 MET cc_start: 0.8786 (mmm) cc_final: 0.8514 (tpp) REVERT: C 94 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.8086 (m-70) REVERT: C 203 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8522 (t0) REVERT: C 237 MET cc_start: 0.8718 (tmm) cc_final: 0.8407 (tmm) REVERT: C 354 MET cc_start: 0.7967 (mmm) cc_final: 0.7457 (mmm) REVERT: C 818 MET cc_start: -0.1770 (tpt) cc_final: -0.2286 (ppp) REVERT: D 428 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8842 (p) REVERT: D 469 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8480 (ttp80) REVERT: D 564 MET cc_start: 0.6021 (ttt) cc_final: 0.5813 (ptt) REVERT: D 788 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8458 (mpp) REVERT: L 54 GLU cc_start: 0.8075 (mp0) cc_final: 0.7805 (mt-10) REVERT: L 65 GLU cc_start: 0.8552 (mp0) cc_final: 0.7728 (mp0) REVERT: L 81 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8774 (mm-30) REVERT: L 84 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8688 (ttpp) REVERT: L 92 ASP cc_start: 0.8511 (t0) cc_final: 0.8103 (t0) REVERT: L 121 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9160 (t) REVERT: M 50 GLU cc_start: 0.7940 (mp0) cc_final: 0.7611 (mp0) REVERT: M 109 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6988 (mmp) outliers start: 58 outliers final: 34 residues processed: 225 average time/residue: 0.1792 time to fit residues: 66.9140 Evaluate side-chains 210 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 119 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 109 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 328 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS B 332 HIS D 674 HIS ** L 132 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 = 0.3633 r_free = 0.3633 target = 0.082653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.051689 restraints weight = 99701.024| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.68 r_work: 0.2692 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28164 Z= 0.222 Angle : 0.618 20.869 38254 Z= 0.311 Chirality : 0.045 0.368 4368 Planarity : 0.004 0.067 4824 Dihedral : 5.940 91.963 4070 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.06 % Allowed : 12.25 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 3441 helix: 1.96 (0.15), residues: 1284 sheet: -0.71 (0.20), residues: 656 loop : -1.45 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 704 TYR 0.013 0.001 TYR A 330 PHE 0.020 0.001 PHE C 533 TRP 0.015 0.001 TRP B 609 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00526 (28133) covalent geometry : angle 0.59582 (38176) SS BOND : bond 0.00338 ( 15) SS BOND : angle 1.04154 ( 30) hydrogen bonds : bond 0.04478 ( 1151) hydrogen bonds : angle 4.57559 ( 3330) link_NAG-ASN : bond 0.00709 ( 16) link_NAG-ASN : angle 4.66400 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 0.878 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: J 109 ASP cc_start: 0.9303 (m-30) cc_final: 0.8578 (p0) REVERT: J 122 MET cc_start: 0.9093 (mtt) cc_final: 0.8804 (mtt) REVERT: K 85 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8037 (mtm180) REVERT: K 94 ASP cc_start: 0.9131 (t0) cc_final: 0.8792 (m-30) REVERT: K 113 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: A 429 ASP cc_start: 0.7943 (t0) cc_final: 0.7688 (t0) REVERT: B 74 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8179 (pmm) REVERT: B 199 ASP cc_start: 0.9194 (t0) cc_final: 0.8897 (t0) REVERT: C 94 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8510 (m-70) REVERT: C 237 MET cc_start: 0.8972 (tmm) cc_final: 0.8666 (tmm) REVERT: C 354 MET cc_start: 0.8375 (mmm) cc_final: 0.7861 (mmm) REVERT: C 406 GLU cc_start: 0.8787 (tp30) cc_final: 0.8478 (tp30) REVERT: C 672 LEU cc_start: 0.8307 (mt) cc_final: 0.8061 (mt) REVERT: C 818 MET cc_start: -0.1769 (tpt) cc_final: -0.2272 (ppp) REVERT: D 55 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.7381 (t60) REVERT: D 428 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8789 (p) REVERT: D 469 ARG cc_start: 0.9238 (ttp80) cc_final: 0.8689 (ttp80) REVERT: D 564 MET cc_start: 0.6002 (ttt) cc_final: 0.5774 (ptt) REVERT: D 788 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8541 (mpp) REVERT: L 54 GLU cc_start: 0.8320 (mp0) cc_final: 0.8098 (mt-10) REVERT: L 65 GLU cc_start: 0.8812 (mp0) cc_final: 0.8004 (mp0) REVERT: L 92 ASP cc_start: 0.8510 (t0) cc_final: 0.8123 (t0) REVERT: M 50 GLU cc_start: 0.8517 (mp0) cc_final: 0.8127 (mp0) REVERT: M 109 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7167 (mmp) outliers start: 61 outliers final: 42 residues processed: 219 average time/residue: 0.1601 time to fit residues: 58.5575 Evaluate side-chains 216 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 119 ARG Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 795 TYR Chi-restraints excluded: chain D residue 55 TRP Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 109 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 123 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 257 optimal weight: 0.5980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** D 332 HIS ** 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 = 0.3643 r_free = 0.3643 target = 0.083065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052120 restraints weight = 100097.908| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.61 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28164 Z= 0.173 Angle : 0.603 20.853 38254 Z= 0.297 Chirality : 0.044 0.364 4368 Planarity : 0.004 0.069 4824 Dihedral : 5.898 91.017 4070 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.92 % Allowed : 12.69 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3441 helix: 2.00 (0.15), residues: 1282 sheet: -0.69 (0.20), residues: 658 loop : -1.39 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 704 TYR 0.013 0.001 TYR C 681 PHE 0.014 0.001 PHE C 533 TRP 0.015 0.001 TRP C 56 HIS 0.005 0.001 HIS K 100 Details of bonding type rmsd covalent geometry : bond 0.00408 (28133) covalent geometry : angle 0.57954 (38176) SS BOND : bond 0.00265 ( 15) SS BOND : angle 0.89499 ( 30) hydrogen bonds : bond 0.03981 ( 1151) hydrogen bonds : angle 4.48263 ( 3330) link_NAG-ASN : bond 0.00708 ( 16) link_NAG-ASN : angle 4.66911 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 1.027 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: J 109 ASP cc_start: 0.9280 (m-30) cc_final: 0.8560 (p0) REVERT: J 122 MET cc_start: 0.8974 (mtt) cc_final: 0.8671 (mtt) REVERT: K 85 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7823 (mtm180) REVERT: K 94 ASP cc_start: 0.9134 (t0) cc_final: 0.8784 (m-30) REVERT: K 113 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: A 237 MET cc_start: 0.9205 (tpp) cc_final: 0.8880 (tmm) REVERT: A 429 ASP cc_start: 0.7948 (t0) cc_final: 0.7672 (t0) REVERT: A 502 MET cc_start: 0.8965 (mmt) cc_final: 0.8625 (mmt) REVERT: B 74 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8087 (pmm) REVERT: B 107 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8721 (pm20) REVERT: B 199 ASP cc_start: 0.9045 (t0) cc_final: 0.8718 (t0) REVERT: B 306 MET cc_start: 0.8021 (ttp) cc_final: 0.6921 (tmm) REVERT: C 94 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.8126 (m-70) REVERT: C 237 MET cc_start: 0.8803 (tmm) cc_final: 0.8504 (tmm) REVERT: C 354 MET cc_start: 0.7892 (mmm) cc_final: 0.7362 (mmm) REVERT: C 406 GLU cc_start: 0.8515 (tp30) cc_final: 0.8188 (tp30) REVERT: C 726 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8661 (tp) REVERT: C 818 MET cc_start: -0.1702 (tpt) cc_final: -0.2210 (ppp) REVERT: D 55 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.7357 (t60) REVERT: D 428 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8756 (p) REVERT: D 469 ARG cc_start: 0.9061 (ttp80) cc_final: 0.8499 (ttp80) REVERT: D 564 MET cc_start: 0.5937 (ttt) cc_final: 0.5720 (ptt) REVERT: D 705 MET cc_start: 0.8560 (ttm) cc_final: 0.8102 (ptm) REVERT: L 54 GLU cc_start: 0.8089 (mp0) cc_final: 0.7866 (mt-10) REVERT: L 65 GLU cc_start: 0.8547 (mp0) cc_final: 0.7674 (mp0) REVERT: L 84 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8811 (ttpp) REVERT: L 92 ASP cc_start: 0.8506 (t0) cc_final: 0.8102 (t0) REVERT: M 50 GLU cc_start: 0.7963 (mp0) cc_final: 0.7604 (mp0) REVERT: M 109 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7169 (mmp) outliers start: 57 outliers final: 41 residues processed: 217 average time/residue: 0.1734 time to fit residues: 61.5524 Evaluate side-chains 215 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 ARG Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 795 TYR Chi-restraints excluded: chain D residue 55 TRP Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 109 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 52 optimal weight: 2.9990 chunk 322 optimal weight: 40.0000 chunk 311 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** D 332 HIS ** 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 = 0.3641 r_free = 0.3641 target = 0.082950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052009 restraints weight = 99793.449| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.66 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28164 Z= 0.167 Angle : 0.608 20.871 38254 Z= 0.299 Chirality : 0.044 0.368 4368 Planarity : 0.004 0.069 4824 Dihedral : 5.896 93.272 4070 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.86 % Allowed : 12.96 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3441 helix: 2.02 (0.15), residues: 1275 sheet: -0.65 (0.20), residues: 654 loop : -1.36 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 704 TYR 0.013 0.001 TYR B 478 PHE 0.014 0.001 PHE C 533 TRP 0.014 0.001 TRP D 55 HIS 0.004 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00392 (28133) covalent geometry : angle 0.58557 (38176) SS BOND : bond 0.00244 ( 15) SS BOND : angle 0.79568 ( 30) hydrogen bonds : bond 0.03878 ( 1151) hydrogen bonds : angle 4.46562 ( 3330) link_NAG-ASN : bond 0.00725 ( 16) link_NAG-ASN : angle 4.58580 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.882 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: J 109 ASP cc_start: 0.9234 (m-30) cc_final: 0.8526 (p0) REVERT: J 122 MET cc_start: 0.8934 (mtt) cc_final: 0.8617 (mtt) REVERT: K 85 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7880 (mtm180) REVERT: K 94 ASP cc_start: 0.9140 (t0) cc_final: 0.8803 (m-30) REVERT: K 113 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: A 237 MET cc_start: 0.9270 (tpp) cc_final: 0.8954 (tmm) REVERT: B 74 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8043 (pmm) REVERT: B 107 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8723 (pm20) REVERT: B 199 ASP cc_start: 0.9064 (t0) cc_final: 0.8767 (t0) REVERT: B 306 MET cc_start: 0.7973 (ttp) cc_final: 0.7626 (ttp) REVERT: C 74 MET cc_start: 0.8692 (tpp) cc_final: 0.8458 (tpp) REVERT: C 94 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.8179 (m-70) REVERT: C 237 MET cc_start: 0.8779 (tmm) cc_final: 0.8511 (tmm) REVERT: C 354 MET cc_start: 0.7841 (mmm) cc_final: 0.7310 (mmm) REVERT: C 406 GLU cc_start: 0.8548 (tp30) cc_final: 0.8223 (tp30) REVERT: C 726 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8677 (tp) REVERT: C 818 MET cc_start: -0.1780 (tpt) cc_final: -0.2271 (ppp) REVERT: D 55 TRP cc_start: 0.8018 (OUTLIER) cc_final: 0.7360 (t60) REVERT: D 428 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8719 (p) REVERT: D 469 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8504 (ttp80) REVERT: D 564 MET cc_start: 0.5948 (ttt) cc_final: 0.5721 (ptp) REVERT: D 705 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8146 (ptm) REVERT: L 54 GLU cc_start: 0.8012 (mp0) cc_final: 0.7790 (mt-10) REVERT: L 65 GLU cc_start: 0.8539 (mp0) cc_final: 0.7667 (mp0) REVERT: L 81 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8821 (mm-30) REVERT: L 84 LYS cc_start: 0.9049 (ttmm) cc_final: 0.8745 (ttpp) REVERT: L 92 ASP cc_start: 0.8375 (t0) cc_final: 0.7975 (t0) REVERT: M 50 GLU cc_start: 0.7975 (mp0) cc_final: 0.7608 (mp0) REVERT: M 109 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7257 (mmp) outliers start: 55 outliers final: 39 residues processed: 213 average time/residue: 0.1594 time to fit residues: 56.0437 Evaluate side-chains 214 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 ARG Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 795 TYR Chi-restraints excluded: chain D residue 55 TRP Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 325 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 290 optimal weight: 0.9980 chunk 74 optimal weight: 40.0000 chunk 292 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** D 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052960 restraints weight = 99813.137| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 4.72 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28164 Z= 0.108 Angle : 0.583 20.733 38254 Z= 0.284 Chirality : 0.043 0.372 4368 Planarity : 0.004 0.069 4824 Dihedral : 5.624 88.919 4070 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.35 % Allowed : 13.46 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3441 helix: 2.07 (0.15), residues: 1282 sheet: -0.58 (0.21), residues: 650 loop : -1.27 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 704 TYR 0.013 0.001 TYR C 681 PHE 0.013 0.001 PHE A 529 TRP 0.016 0.001 TRP B 609 HIS 0.003 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00245 (28133) covalent geometry : angle 0.56091 (38176) SS BOND : bond 0.00167 ( 15) SS BOND : angle 0.65524 ( 30) hydrogen bonds : bond 0.03249 ( 1151) hydrogen bonds : angle 4.30297 ( 3330) link_NAG-ASN : bond 0.00793 ( 16) link_NAG-ASN : angle 4.53998 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.147 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: J 109 ASP cc_start: 0.9196 (m-30) cc_final: 0.8498 (p0) REVERT: J 122 MET cc_start: 0.8881 (mtt) cc_final: 0.8555 (mtt) REVERT: K 85 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7879 (mtm180) REVERT: K 94 ASP cc_start: 0.9129 (t0) cc_final: 0.8716 (m-30) REVERT: A 237 MET cc_start: 0.9281 (tpp) cc_final: 0.8947 (tmm) REVERT: B 74 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8068 (pmm) REVERT: B 107 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: B 199 ASP cc_start: 0.9074 (t0) cc_final: 0.8783 (t0) REVERT: B 306 MET cc_start: 0.7896 (ttp) cc_final: 0.6704 (tmm) REVERT: C 94 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8204 (m-70) REVERT: C 237 MET cc_start: 0.8792 (tmm) cc_final: 0.8512 (tmm) REVERT: C 354 MET cc_start: 0.7837 (mmm) cc_final: 0.7315 (mmm) REVERT: C 818 MET cc_start: -0.1823 (tpt) cc_final: -0.2310 (ptt) REVERT: D 428 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8771 (p) REVERT: D 469 ARG cc_start: 0.9051 (ttp80) cc_final: 0.8513 (ttp80) REVERT: D 564 MET cc_start: 0.6136 (ttt) cc_final: 0.5915 (ptp) REVERT: D 705 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8105 (ptm) REVERT: D 708 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6988 (p90) REVERT: L 54 GLU cc_start: 0.8019 (mp0) cc_final: 0.7792 (mt-10) REVERT: L 65 GLU cc_start: 0.8531 (mp0) cc_final: 0.7669 (mp0) REVERT: L 81 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8833 (mm-30) REVERT: L 84 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8732 (ttpp) REVERT: L 92 ASP cc_start: 0.8389 (t0) cc_final: 0.8002 (t0) REVERT: M 50 GLU cc_start: 0.7977 (mp0) cc_final: 0.7590 (mp0) REVERT: M 109 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7271 (mmp) outliers start: 40 outliers final: 30 residues processed: 205 average time/residue: 0.1773 time to fit residues: 59.9677 Evaluate side-chains 203 residues out of total 3023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 119 ARG Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 286 TYR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 708 PHE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 239 optimal weight: 0.0980 chunk 333 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** D 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 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 = 0.3651 r_free = 0.3651 target = 0.083391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052194 restraints weight = 98961.096| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.68 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28164 Z= 0.133 Angle : 0.593 20.724 38254 Z= 0.289 Chirality : 0.043 0.361 4368 Planarity : 0.004 0.068 4824 Dihedral : 5.536 88.548 4070 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.45 % Allowed : 13.50 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3441 helix: 2.06 (0.15), residues: 1282 sheet: -0.55 (0.21), residues: 650 loop : -1.24 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 156 TYR 0.014 0.001 TYR C 681 PHE 0.011 0.001 PHE C 533 TRP 0.041 0.001 TRP C 56 HIS 0.004 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00312 (28133) covalent geometry : angle 0.57100 (38176) SS BOND : bond 0.00191 ( 15) SS BOND : angle 0.68196 ( 30) hydrogen bonds : bond 0.03502 ( 1151) hydrogen bonds : angle 4.33265 ( 3330) link_NAG-ASN : bond 0.00749 ( 16) link_NAG-ASN : angle 4.52170 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7290.76 seconds wall clock time: 125 minutes 34.31 seconds (7534.31 seconds total)