Starting phenix.real_space_refine on Fri Feb 6 12:59:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oot_70672/02_2026/9oot_70672.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oot_70672/02_2026/9oot_70672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oot_70672/02_2026/9oot_70672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oot_70672/02_2026/9oot_70672.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oot_70672/02_2026/9oot_70672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oot_70672/02_2026/9oot_70672.map" } resolution = 3.13 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= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 150 5.16 5 C 15986 2.51 5 N 4076 2.21 5 O 4609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s 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: 24825 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6200 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 35, 'TRANS': 764} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6039 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 746} Chain breaks: 4 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 3, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 6196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6196 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 35, 'TRANS': 764} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 6044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6044 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 746} Chain breaks: 4 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 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: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'A8W': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'A8W': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.05, per 1000 atoms: 0.24 Number of scatterers: 24825 At special positions: 0 Unit cell: (144.725, 138.109, 181.113, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 4 15.00 O 4609 8.00 N 4076 7.00 C 15986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.02 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " 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=2.02 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 36 sheets defined 45.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.530A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.592A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.957A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.907A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.700A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 4.129A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.717A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.959A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.696A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 261' Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.626A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 removed outlier: 3.797A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.009A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 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 559 through 582 removed outlier: 3.579A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.749A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.549A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.682A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.512A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 809 through 841 removed outlier: 5.092A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.580A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 106 through 120 removed outlier: 4.080A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.744A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 4.381A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.532A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.599A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 3.570A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.719A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.515A pdb=" N GLY B 499 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 555 through 576 removed outlier: 3.652A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 625 through 656 Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.933A pdb=" N GLN B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.619A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 706 Processing helix chain 'B' and resid 713 through 723 removed outlier: 3.538A pdb=" N LEU B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 4.055A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.274A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.591A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 845 removed outlier: 5.268A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.816A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.606A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.657A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.855A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 4.018A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.529A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.603A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.751A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.516A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.906A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 4.130A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.996A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.762A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.992A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.516A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.612A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.673A pdb=" N ARG C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.636A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.594A pdb=" N ARG C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.507A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 809 through 841 removed outlier: 5.160A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 57 removed outlier: 3.656A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.777A pdb=" N ILE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.761A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.858A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.956A pdb=" N MET D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.534A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 288 through 310 removed outlier: 3.544A pdb=" N ARG D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.536A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 330' Processing helix chain 'D' and resid 332 through 341 removed outlier: 3.851A pdb=" N ASN D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 555 through 576 Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.518A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 Processing helix chain 'D' and resid 668 through 673 removed outlier: 4.147A pdb=" N GLN D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 706 Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.842A pdb=" N LYS D 722 " --> pdb=" O LEU D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 Processing helix chain 'D' and resid 744 through 746 No H-bonds generated for 'chain 'D' and resid 744 through 746' Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.284A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 814 through 845 removed outlier: 5.087A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.656A pdb=" N ASN A 61 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.740A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.336A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.693A pdb=" N ILE A 353 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.105A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.650A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.044A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 72 removed outlier: 6.456A pdb=" N ILE B 35 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU B 69 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 37 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 98 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.449A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 257 through 258 removed outlier: 6.906A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.625A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU B 480 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN B 437 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB5, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.607A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AB7, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.800A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 163 through 165 removed outlier: 6.185A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 270 through 271 Processing sheet with id=AC1, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.483A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AC3, first strand: chain 'C' and resid 365 through 367 Processing sheet with id=AC4, first strand: chain 'C' and resid 474 through 478 removed outlier: 7.065A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 410 through 413 Processing sheet with id=AC6, first strand: chain 'C' and resid 487 through 488 removed outlier: 3.720A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AC8, first strand: chain 'C' and resid 681 through 682 Processing sheet with id=AC9, first strand: chain 'D' and resid 66 through 72 removed outlier: 6.517A pdb=" N ILE D 35 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU D 69 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 168 through 169 Processing sheet with id=AD2, first strand: chain 'D' and resid 171 through 173 removed outlier: 6.628A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 257 through 259 Processing sheet with id=AD4, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD5, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AD6, first strand: chain 'D' and resid 405 through 410 removed outlier: 8.072A pdb=" N LEU D 480 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN D 437 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 488 through 490 removed outlier: 3.779A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 495 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 683 through 685 removed outlier: 5.006A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 538 through 539 1028 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4755 1.33 - 1.45: 6208 1.45 - 1.57: 14153 1.57 - 1.70: 12 1.70 - 1.82: 254 Bond restraints: 25382 Sorted by residual: bond pdb=" O1 A8W B1001 " pdb=" S A8W B1001 " ideal model delta sigma weight residual 1.636 1.590 0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" O1 A8W D1001 " pdb=" S A8W D1001 " ideal model delta sigma weight residual 1.636 1.591 0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C3 A8W D1002 " pdb=" O1 A8W D1002 " ideal model delta sigma weight residual 1.432 1.473 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C3 A8W B1002 " pdb=" O1 A8W B1002 " ideal model delta sigma weight residual 1.432 1.473 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" O1 A8W B1002 " pdb=" S A8W B1002 " ideal model delta sigma weight residual 1.636 1.596 0.040 2.00e-02 2.50e+03 4.01e+00 ... (remaining 25377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 34020 2.17 - 4.35: 357 4.35 - 6.52: 53 6.52 - 8.69: 6 8.69 - 10.86: 2 Bond angle restraints: 34438 Sorted by residual: angle pdb=" CB MET A 209 " pdb=" CG MET A 209 " pdb=" SD MET A 209 " ideal model delta sigma weight residual 112.70 123.56 -10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C GLN D 662 " pdb=" N VAL D 663 " pdb=" CA VAL D 663 " ideal model delta sigma weight residual 121.97 128.44 -6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA VAL D 202 " pdb=" CB VAL D 202 " pdb=" CG1 VAL D 202 " ideal model delta sigma weight residual 110.40 116.24 -5.84 1.70e+00 3.46e-01 1.18e+01 angle pdb=" N VAL D 376 " pdb=" CA VAL D 376 " pdb=" C VAL D 376 " ideal model delta sigma weight residual 112.96 109.58 3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" C VAL D 202 " pdb=" CA VAL D 202 " pdb=" CB VAL D 202 " ideal model delta sigma weight residual 111.29 116.80 -5.51 1.64e+00 3.72e-01 1.13e+01 ... (remaining 34433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 14357 29.44 - 58.88: 905 58.88 - 88.32: 50 88.32 - 117.76: 2 117.76 - 147.20: 8 Dihedral angle restraints: 15322 sinusoidal: 6195 harmonic: 9127 Sorted by residual: dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual 93.00 171.74 -78.74 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS A 744 " pdb=" SG CYS A 744 " pdb=" SG CYS A 798 " pdb=" CB CYS A 798 " ideal model delta sinusoidal sigma weight residual -86.00 -19.39 -66.61 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS B 746 " pdb=" SG CYS B 746 " pdb=" SG CYS B 801 " pdb=" CB CYS B 801 " ideal model delta sinusoidal sigma weight residual -86.00 -141.40 55.40 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 15319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2308 0.032 - 0.064: 1075 0.064 - 0.095: 317 0.095 - 0.127: 165 0.127 - 0.159: 20 Chirality restraints: 3885 Sorted by residual: chirality pdb=" CB VAL D 663 " pdb=" CA VAL D 663 " pdb=" CG1 VAL D 663 " pdb=" CG2 VAL D 663 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA VAL B 202 " pdb=" N VAL B 202 " pdb=" C VAL B 202 " pdb=" CB VAL B 202 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA THR A 105 " pdb=" N THR A 105 " pdb=" C THR A 105 " pdb=" CB THR A 105 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 3882 not shown) Planarity restraints: 4341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 315 " -0.014 2.00e-02 2.50e+03 1.12e-02 3.15e+00 pdb=" CG TRP A 315 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 315 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 315 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 315 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 315 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 315 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 315 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 315 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 315 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 494 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C ASN A 494 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN A 494 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 495 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO C 319 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " -0.024 5.00e-02 4.00e+02 ... (remaining 4338 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3792 2.75 - 3.29: 24516 3.29 - 3.83: 41187 3.83 - 4.36: 49832 4.36 - 4.90: 85689 Nonbonded interactions: 205016 Sorted by model distance: nonbonded pdb=" OG1 THR D 76 " pdb=" OG SER D 80 " model vdw 2.215 3.040 nonbonded pdb=" O HIS C 146 " pdb=" OG SER C 149 " model vdw 2.229 3.040 nonbonded pdb=" N GLU C 497 " pdb=" OE1 GLU C 497 " model vdw 2.245 3.120 nonbonded pdb=" O ARG A 179 " pdb=" OG1 THR A 182 " model vdw 2.246 3.040 nonbonded pdb=" O ARG A 763 " pdb=" OG SER A 766 " model vdw 2.252 3.040 ... (remaining 205011 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 192 or (resid 193 and (name N or name CA or nam \ e C or name O or name CB )) or resid 194 through 661 or (resid 662 and (name N o \ r name CA or name C or name O or name CB )) or resid 663 through 677 or (resid 6 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 679 through \ 1002)) selection = (chain 'C' and (resid 25 through 798 or (resid 799 through 804 and (name N or na \ me CA or name C or name O or name CB )) or resid 805 through 837 or (resid 838 a \ nd (name N or name CA or name C or name O or name CB )) or resid 839 through 100 \ 2)) } ncs_group { reference = (chain 'B' and (resid 34 through 659 or (resid 660 through 661 and (name N or na \ me CA or name C or name O or name CB )) or resid 662 through 802 or (resid 803 t \ hrough 804 and (name N or name CA or name C or name O or name CB )) or resid 808 \ through 1002)) selection = (chain 'D' and (resid 34 through 388 or (resid 389 and (name N or name CA or nam \ e C or name O or name CB )) or resid 390 through 660 or (resid 661 and (name N o \ r name CA or name C or name O or name CB )) or resid 662 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.730 Find NCS groups from input model: 0.510 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.005 0.060 25396 Z= 0.211 Angle : 0.569 10.864 34466 Z= 0.285 Chirality : 0.043 0.159 3885 Planarity : 0.004 0.043 4341 Dihedral : 17.547 147.201 9396 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.43 % Rotamer: Outliers : 0.42 % Allowed : 26.14 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.99 (0.15), residues: 3118 helix: 0.22 (0.14), residues: 1260 sheet: -1.17 (0.29), residues: 354 loop : -1.24 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.021 0.001 TYR D 479 PHE 0.027 0.002 PHE C 472 TRP 0.031 0.002 TRP A 315 HIS 0.003 0.001 HIS C 571 Details of bonding type rmsd covalent geometry : bond 0.00516 (25382) covalent geometry : angle 0.56887 (34438) SS BOND : bond 0.00331 ( 14) SS BOND : angle 0.82341 ( 28) hydrogen bonds : bond 0.26337 ( 1028) hydrogen bonds : angle 8.27746 ( 2952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 271 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8466 (mtp) cc_final: 0.8214 (ttp) REVERT: C 501 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8600 (ttp) outliers start: 11 outliers final: 7 residues processed: 276 average time/residue: 0.1699 time to fit residues: 75.8000 Evaluate side-chains 276 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 268 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain C residue 501 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN A 147 GLN A 499 ASN A 520 ASN ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN B 54 HIS B 105 GLN B 127 HIS B 336 ASN B 359 HIS B 486 HIS B 703 HIS B 782 GLN C 38 HIS C 61 ASN C 70 ASN C 101 HIS C 146 HIS C 147 GLN C 171 HIS C 355 ASN C 509 GLN ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN C 571 HIS C 696 GLN D 359 HIS D 486 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.113072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.091712 restraints weight = 63813.768| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.39 r_work: 0.3240 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25396 Z= 0.154 Angle : 0.558 9.207 34466 Z= 0.291 Chirality : 0.043 0.160 3885 Planarity : 0.004 0.046 4341 Dihedral : 9.157 129.515 3801 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 3.45 % Allowed : 22.80 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3118 helix: 0.82 (0.14), residues: 1310 sheet: -1.20 (0.29), residues: 324 loop : -1.37 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 115 TYR 0.014 0.001 TYR D 479 PHE 0.018 0.002 PHE D 416 TRP 0.022 0.001 TRP A 315 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00355 (25382) covalent geometry : angle 0.55760 (34438) SS BOND : bond 0.00278 ( 14) SS BOND : angle 1.03020 ( 28) hydrogen bonds : bond 0.05498 ( 1028) hydrogen bonds : angle 5.48847 ( 2952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 286 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8499 (mtp) cc_final: 0.8247 (ttp) REVERT: A 664 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6591 (mt) REVERT: C 139 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.3601 (mtm110) REVERT: C 158 TYR cc_start: 0.8353 (m-10) cc_final: 0.8151 (m-80) REVERT: C 494 ASN cc_start: 0.7011 (t0) cc_final: 0.6665 (t0) REVERT: C 501 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8839 (mtp) outliers start: 91 outliers final: 45 residues processed: 360 average time/residue: 0.1665 time to fit residues: 97.2715 Evaluate side-chains 320 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 295 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 0.0870 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN C 70 ASN C 101 HIS C 134 HIS C 293 HIS C 355 ASN C 520 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.112782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091538 restraints weight = 63503.532| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.34 r_work: 0.3228 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25396 Z= 0.192 Angle : 0.559 9.835 34466 Z= 0.288 Chirality : 0.044 0.161 3885 Planarity : 0.004 0.050 4341 Dihedral : 8.769 114.445 3789 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 4.36 % Allowed : 22.19 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.55 (0.15), residues: 3118 helix: 0.96 (0.14), residues: 1320 sheet: -1.35 (0.28), residues: 328 loop : -1.37 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.017 0.001 TYR D 479 PHE 0.024 0.002 PHE C 472 TRP 0.017 0.001 TRP A 315 HIS 0.007 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00465 (25382) covalent geometry : angle 0.55853 (34438) SS BOND : bond 0.00359 ( 14) SS BOND : angle 1.08447 ( 28) hydrogen bonds : bond 0.04776 ( 1028) hydrogen bonds : angle 5.17583 ( 2952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 296 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 330 TYR cc_start: 0.5736 (OUTLIER) cc_final: 0.4837 (t80) REVERT: A 664 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6626 (mt) REVERT: C 139 ARG cc_start: 0.6076 (OUTLIER) cc_final: 0.3450 (mtm110) REVERT: C 489 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6768 (mmm160) REVERT: C 494 ASN cc_start: 0.6961 (t0) cc_final: 0.6364 (t0) REVERT: D 69 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.6000 (pt0) outliers start: 115 outliers final: 72 residues processed: 385 average time/residue: 0.1662 time to fit residues: 103.9075 Evaluate side-chains 353 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 275 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 449 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 146 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 284 optimal weight: 0.0570 chunk 155 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 overall best weight: 0.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.113735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092183 restraints weight = 63264.803| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.36 r_work: 0.3262 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25396 Z= 0.120 Angle : 0.517 8.921 34466 Z= 0.266 Chirality : 0.042 0.171 3885 Planarity : 0.004 0.051 4341 Dihedral : 8.408 110.100 3786 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 3.76 % Allowed : 22.27 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3118 helix: 1.20 (0.14), residues: 1326 sheet: -1.32 (0.28), residues: 328 loop : -1.36 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 260 TYR 0.013 0.001 TYR D 252 PHE 0.015 0.001 PHE D 836 TRP 0.016 0.001 TRP A 315 HIS 0.012 0.001 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00282 (25382) covalent geometry : angle 0.51692 (34438) SS BOND : bond 0.00201 ( 14) SS BOND : angle 0.92898 ( 28) hydrogen bonds : bond 0.04071 ( 1028) hydrogen bonds : angle 4.88567 ( 2952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 289 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8250 (mtt) cc_final: 0.8046 (mtp) REVERT: A 180 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 238 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 330 TYR cc_start: 0.5727 (OUTLIER) cc_final: 0.4833 (t80) REVERT: A 494 ASN cc_start: 0.6984 (t0) cc_final: 0.6727 (t0) REVERT: A 632 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 664 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6635 (mt) REVERT: B 514 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.7361 (p) REVERT: C 113 PHE cc_start: 0.7675 (t80) cc_final: 0.7443 (t80) REVERT: C 139 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.3484 (mtm110) REVERT: C 489 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5519 (mmm160) REVERT: C 494 ASN cc_start: 0.7070 (t0) cc_final: 0.6474 (t0) REVERT: C 496 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6972 (mttt) REVERT: D 69 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5936 (pt0) REVERT: D 202 VAL cc_start: 0.8779 (t) cc_final: 0.8576 (t) REVERT: D 791 GLU cc_start: 0.8300 (pt0) cc_final: 0.7988 (pt0) REVERT: D 842 PHE cc_start: 0.7562 (t80) cc_final: 0.7340 (t80) outliers start: 99 outliers final: 57 residues processed: 368 average time/residue: 0.1739 time to fit residues: 103.1553 Evaluate side-chains 339 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 272 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 449 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 308 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS C 293 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.113141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.091877 restraints weight = 63544.265| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.40 r_work: 0.3257 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25396 Z= 0.146 Angle : 0.529 9.153 34466 Z= 0.270 Chirality : 0.042 0.163 3885 Planarity : 0.004 0.051 4341 Dihedral : 8.372 109.070 3786 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 4.25 % Allowed : 22.12 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 3118 helix: 1.26 (0.14), residues: 1326 sheet: -1.26 (0.28), residues: 324 loop : -1.36 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 489 TYR 0.013 0.001 TYR D 479 PHE 0.017 0.001 PHE A 472 TRP 0.019 0.001 TRP A 315 HIS 0.009 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00354 (25382) covalent geometry : angle 0.52862 (34438) SS BOND : bond 0.00240 ( 14) SS BOND : angle 0.93719 ( 28) hydrogen bonds : bond 0.04031 ( 1028) hydrogen bonds : angle 4.82265 ( 2952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 289 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 278 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7840 (t) REVERT: A 330 TYR cc_start: 0.5750 (OUTLIER) cc_final: 0.4843 (t80) REVERT: A 494 ASN cc_start: 0.6969 (t0) cc_final: 0.6704 (t0) REVERT: A 632 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 664 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6610 (mt) REVERT: B 514 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.7355 (p) REVERT: B 601 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.7947 (m) REVERT: C 113 PHE cc_start: 0.7741 (t80) cc_final: 0.7529 (t80) REVERT: C 139 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.3414 (mtm110) REVERT: C 238 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8372 (mp) REVERT: C 494 ASN cc_start: 0.6991 (t0) cc_final: 0.6467 (t0) REVERT: C 496 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6989 (mttt) REVERT: D 202 VAL cc_start: 0.8734 (t) cc_final: 0.8525 (t) REVERT: D 334 MET cc_start: 0.7795 (mpp) cc_final: 0.7568 (mpp) REVERT: D 727 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.4568 (m-30) REVERT: D 791 GLU cc_start: 0.8277 (pt0) cc_final: 0.7959 (pt0) outliers start: 112 outliers final: 78 residues processed: 377 average time/residue: 0.1595 time to fit residues: 98.6574 Evaluate side-chains 364 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 275 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 449 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 213 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 247 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 249 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 279 optimal weight: 0.0970 chunk 280 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 782 GLN C 61 ASN C 293 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.113997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092270 restraints weight = 63653.027| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.33 r_work: 0.3278 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25396 Z= 0.107 Angle : 0.512 8.690 34466 Z= 0.261 Chirality : 0.042 0.163 3885 Planarity : 0.003 0.051 4341 Dihedral : 8.179 107.020 3785 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.80 % Rotamer: Outliers : 3.79 % Allowed : 22.53 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3118 helix: 1.43 (0.14), residues: 1326 sheet: -1.14 (0.29), residues: 320 loop : -1.36 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 794 TYR 0.011 0.001 TYR B 479 PHE 0.014 0.001 PHE B 182 TRP 0.020 0.001 TRP A 315 HIS 0.015 0.001 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00251 (25382) covalent geometry : angle 0.51121 (34438) SS BOND : bond 0.00160 ( 14) SS BOND : angle 0.92498 ( 28) hydrogen bonds : bond 0.03725 ( 1028) hydrogen bonds : angle 4.67032 ( 2952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 280 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 278 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7872 (t) REVERT: A 330 TYR cc_start: 0.5711 (OUTLIER) cc_final: 0.4810 (t80) REVERT: A 494 ASN cc_start: 0.6951 (t0) cc_final: 0.6669 (t0) REVERT: A 632 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8272 (tt) REVERT: A 664 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6596 (mt) REVERT: A 727 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6378 (m90) REVERT: B 514 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.7322 (p) REVERT: B 601 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.7954 (m) REVERT: B 818 MET cc_start: 0.8869 (mmm) cc_final: 0.8292 (mmm) REVERT: C 113 PHE cc_start: 0.7686 (t80) cc_final: 0.7486 (t80) REVERT: C 139 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.3526 (mtm110) REVERT: C 293 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.5754 (m-70) REVERT: C 494 ASN cc_start: 0.6791 (t0) cc_final: 0.6436 (t0) REVERT: C 496 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6833 (mttt) REVERT: D 69 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5956 (pt0) REVERT: D 202 VAL cc_start: 0.8769 (t) cc_final: 0.8561 (t) REVERT: D 334 MET cc_start: 0.7796 (mpp) cc_final: 0.7569 (mpp) REVERT: D 727 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.4517 (m-30) REVERT: D 791 GLU cc_start: 0.8235 (pt0) cc_final: 0.7927 (pt0) outliers start: 100 outliers final: 63 residues processed: 362 average time/residue: 0.1555 time to fit residues: 92.4486 Evaluate side-chains 345 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 269 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 189 optimal weight: 9.9990 chunk 13 optimal weight: 0.0980 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 2 optimal weight: 20.0000 chunk 257 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN C 94 HIS C 293 HIS C 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.113265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.092043 restraints weight = 63385.152| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.30 r_work: 0.3242 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25396 Z= 0.167 Angle : 0.546 9.522 34466 Z= 0.277 Chirality : 0.043 0.170 3885 Planarity : 0.004 0.052 4341 Dihedral : 8.303 107.089 3785 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 4.51 % Allowed : 21.89 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3118 helix: 1.35 (0.14), residues: 1328 sheet: -1.27 (0.28), residues: 340 loop : -1.35 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 794 TYR 0.016 0.001 TYR D 479 PHE 0.020 0.002 PHE A 472 TRP 0.020 0.001 TRP A 315 HIS 0.010 0.001 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00409 (25382) covalent geometry : angle 0.54572 (34438) SS BOND : bond 0.00282 ( 14) SS BOND : angle 1.01163 ( 28) hydrogen bonds : bond 0.03966 ( 1028) hydrogen bonds : angle 4.75039 ( 2952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 280 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 209 MET cc_start: 0.8014 (mmm) cc_final: 0.7777 (tpp) REVERT: A 278 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7906 (t) REVERT: A 330 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.4821 (t80) REVERT: A 494 ASN cc_start: 0.6906 (t0) cc_final: 0.6633 (t0) REVERT: A 632 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 664 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6615 (mt) REVERT: A 727 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6288 (m170) REVERT: B 293 VAL cc_start: 0.8840 (t) cc_final: 0.8620 (m) REVERT: B 514 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.7364 (p) REVERT: B 601 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7935 (m) REVERT: C 139 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.3457 (mtm110) REVERT: C 238 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 293 HIS cc_start: 0.6666 (OUTLIER) cc_final: 0.5994 (m-70) REVERT: C 330 TYR cc_start: 0.5647 (OUTLIER) cc_final: 0.4629 (t80) REVERT: C 494 ASN cc_start: 0.6783 (t0) cc_final: 0.6467 (t0) REVERT: C 496 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6858 (mttt) REVERT: D 202 VAL cc_start: 0.8755 (t) cc_final: 0.8542 (t) REVERT: D 334 MET cc_start: 0.7770 (mpp) cc_final: 0.7542 (mpp) REVERT: D 727 ASP cc_start: 0.6075 (OUTLIER) cc_final: 0.4682 (m-30) REVERT: D 791 GLU cc_start: 0.8258 (pt0) cc_final: 0.7964 (pt0) outliers start: 119 outliers final: 86 residues processed: 378 average time/residue: 0.1537 time to fit residues: 95.8577 Evaluate side-chains 370 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 270 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 449 HIS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 51 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 36 optimal weight: 0.0040 chunk 191 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 301 optimal weight: 0.0670 chunk 180 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 217 optimal weight: 0.5980 overall best weight: 0.2968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.114290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.093176 restraints weight = 63581.784| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.34 r_work: 0.3277 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25396 Z= 0.100 Angle : 0.516 9.640 34466 Z= 0.262 Chirality : 0.042 0.173 3885 Planarity : 0.003 0.052 4341 Dihedral : 8.070 104.760 3785 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 3.26 % Allowed : 23.14 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 3118 helix: 1.53 (0.14), residues: 1326 sheet: -1.10 (0.28), residues: 336 loop : -1.35 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 794 TYR 0.012 0.001 TYR C 410 PHE 0.014 0.001 PHE D 842 TRP 0.022 0.001 TRP A 315 HIS 0.011 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00229 (25382) covalent geometry : angle 0.51528 (34438) SS BOND : bond 0.00134 ( 14) SS BOND : angle 0.84790 ( 28) hydrogen bonds : bond 0.03533 ( 1028) hydrogen bonds : angle 4.56671 ( 2952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 276 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 209 MET cc_start: 0.8001 (mmm) cc_final: 0.7768 (tpp) REVERT: A 278 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7975 (t) REVERT: A 330 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.4748 (t80) REVERT: A 494 ASN cc_start: 0.6895 (t0) cc_final: 0.6616 (t0) REVERT: A 632 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8268 (tt) REVERT: B 207 MET cc_start: 0.4876 (mmp) cc_final: 0.4134 (mmp) REVERT: B 222 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8196 (mmtt) REVERT: B 601 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.7950 (m) REVERT: C 139 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.3521 (mtm110) REVERT: C 238 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (mp) REVERT: C 293 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.6047 (m-70) REVERT: C 330 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.4542 (t80) REVERT: C 494 ASN cc_start: 0.6831 (t0) cc_final: 0.6497 (t0) REVERT: C 496 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6804 (mttt) REVERT: D 69 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6260 (pt0) REVERT: D 73 MET cc_start: 0.5447 (ppp) cc_final: 0.5179 (ppp) REVERT: D 334 MET cc_start: 0.7783 (mpp) cc_final: 0.7557 (mpp) REVERT: D 727 ASP cc_start: 0.5899 (OUTLIER) cc_final: 0.4452 (m-30) REVERT: D 791 GLU cc_start: 0.8258 (pt0) cc_final: 0.7973 (pt0) outliers start: 86 outliers final: 61 residues processed: 346 average time/residue: 0.1649 time to fit residues: 93.1809 Evaluate side-chains 338 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 85 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 138 optimal weight: 0.0970 chunk 249 optimal weight: 0.8980 chunk 252 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.110711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.089232 restraints weight = 62654.242| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.41 r_work: 0.3266 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25396 Z= 0.131 Angle : 0.534 10.220 34466 Z= 0.271 Chirality : 0.043 0.180 3885 Planarity : 0.003 0.052 4341 Dihedral : 8.099 104.166 3785 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.29 % Favored : 94.61 % Rotamer: Outliers : 3.53 % Allowed : 22.88 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3118 helix: 1.49 (0.14), residues: 1330 sheet: -1.13 (0.28), residues: 338 loop : -1.35 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 179 TYR 0.014 0.001 TYR B 452 PHE 0.015 0.001 PHE D 614 TRP 0.022 0.001 TRP A 315 HIS 0.015 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00316 (25382) covalent geometry : angle 0.53367 (34438) SS BOND : bond 0.00186 ( 14) SS BOND : angle 1.12960 ( 28) hydrogen bonds : bond 0.03668 ( 1028) hydrogen bonds : angle 4.59374 ( 2952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 267 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.7996 (mmm) cc_final: 0.7763 (tpp) REVERT: A 278 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7992 (t) REVERT: A 330 TYR cc_start: 0.5751 (OUTLIER) cc_final: 0.4822 (t80) REVERT: A 494 ASN cc_start: 0.6810 (t0) cc_final: 0.6518 (t0) REVERT: A 632 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8262 (tt) REVERT: A 664 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6638 (mt) REVERT: B 222 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8251 (mmtt) REVERT: B 601 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7931 (m) REVERT: B 818 MET cc_start: 0.8866 (mmm) cc_final: 0.8293 (mmm) REVERT: B 843 TYR cc_start: 0.7109 (t80) cc_final: 0.6879 (t80) REVERT: C 139 ARG cc_start: 0.6076 (OUTLIER) cc_final: 0.3641 (mtm110) REVERT: C 238 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 293 HIS cc_start: 0.6517 (OUTLIER) cc_final: 0.6066 (m-70) REVERT: C 330 TYR cc_start: 0.5755 (OUTLIER) cc_final: 0.4645 (t80) REVERT: C 494 ASN cc_start: 0.6774 (t0) cc_final: 0.6440 (t0) REVERT: C 496 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6975 (mttt) REVERT: C 641 MET cc_start: 0.8853 (tmm) cc_final: 0.8400 (ttp) REVERT: D 334 MET cc_start: 0.7783 (mpp) cc_final: 0.7565 (mpp) REVERT: D 727 ASP cc_start: 0.5941 (OUTLIER) cc_final: 0.4535 (m-30) REVERT: D 791 GLU cc_start: 0.8222 (pt0) cc_final: 0.7930 (pt0) outliers start: 93 outliers final: 73 residues processed: 343 average time/residue: 0.1612 time to fit residues: 90.6146 Evaluate side-chains 345 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 261 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 64 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 280 optimal weight: 0.0770 chunk 94 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 253 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS C 94 HIS C 293 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.110511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.088876 restraints weight = 63109.627| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.20 r_work: 0.3291 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25396 Z= 0.113 Angle : 0.531 10.218 34466 Z= 0.270 Chirality : 0.042 0.194 3885 Planarity : 0.004 0.052 4341 Dihedral : 8.035 103.168 3785 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 3.30 % Allowed : 23.03 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3118 helix: 1.52 (0.14), residues: 1328 sheet: -1.07 (0.28), residues: 338 loop : -1.34 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 179 TYR 0.014 0.001 TYR B 452 PHE 0.015 0.001 PHE D 842 TRP 0.022 0.001 TRP A 315 HIS 0.018 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00268 (25382) covalent geometry : angle 0.53115 (34438) SS BOND : bond 0.00160 ( 14) SS BOND : angle 0.84103 ( 28) hydrogen bonds : bond 0.03571 ( 1028) hydrogen bonds : angle 4.55612 ( 2952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6236 Ramachandran restraints generated. 3118 Oldfield, 0 Emsley, 3118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 269 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.7990 (mmm) cc_final: 0.7753 (tpp) REVERT: A 278 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.8027 (t) REVERT: A 330 TYR cc_start: 0.5737 (OUTLIER) cc_final: 0.4807 (t80) REVERT: A 494 ASN cc_start: 0.6788 (t0) cc_final: 0.6498 (t0) REVERT: A 632 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8264 (tt) REVERT: B 222 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8226 (mmtt) REVERT: B 601 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7906 (m) REVERT: B 843 TYR cc_start: 0.7072 (t80) cc_final: 0.6846 (t80) REVERT: C 139 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.3530 (mtm110) REVERT: C 238 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8394 (mp) REVERT: C 293 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.5872 (m-70) REVERT: C 330 TYR cc_start: 0.5775 (OUTLIER) cc_final: 0.4662 (t80) REVERT: C 494 ASN cc_start: 0.6746 (t0) cc_final: 0.6414 (t0) REVERT: C 496 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6926 (mttt) REVERT: D 334 MET cc_start: 0.7759 (mpp) cc_final: 0.7544 (mpp) REVERT: D 727 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.4411 (m-30) REVERT: D 791 GLU cc_start: 0.8176 (pt0) cc_final: 0.7888 (pt0) outliers start: 87 outliers final: 72 residues processed: 339 average time/residue: 0.1616 time to fit residues: 90.1215 Evaluate side-chains 347 residues out of total 2732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 265 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain D residue 1000 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 118 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.107679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.086420 restraints weight = 63943.032| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.27 r_work: 0.3266 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25396 Z= 0.151 Angle : 0.549 10.227 34466 Z= 0.277 Chirality : 0.043 0.197 3885 Planarity : 0.004 0.061 4341 Dihedral : 8.121 103.041 3785 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 3.45 % Allowed : 22.76 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3118 helix: 1.45 (0.14), residues: 1330 sheet: -1.20 (0.27), residues: 354 loop : -1.34 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 179 TYR 0.015 0.001 TYR D 479 PHE 0.017 0.001 PHE A 472 TRP 0.020 0.001 TRP A 315 HIS 0.014 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00368 (25382) covalent geometry : angle 0.54918 (34438) SS BOND : bond 0.00219 ( 14) SS BOND : angle 0.83516 ( 28) hydrogen bonds : bond 0.03737 ( 1028) hydrogen bonds : angle 4.61192 ( 2952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6721.88 seconds wall clock time: 116 minutes 6.54 seconds (6966.54 seconds total)