Starting phenix.real_space_refine on Fri Feb 6 12:18:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oos_70671/02_2026/9oos_70671.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oos_70671/02_2026/9oos_70671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oos_70671/02_2026/9oos_70671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oos_70671/02_2026/9oos_70671.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oos_70671/02_2026/9oos_70671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oos_70671/02_2026/9oos_70671.map" } resolution = 3.03 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= 0.003 sd= 0.011 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 147 5.16 5 C 15854 2.51 5 N 4032 2.21 5 O 4592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 24629 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6123 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 3 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 8, 'ASP:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 6025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6025 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 747} Chain breaks: 4 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 88 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 1, 'GLU:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 6109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6109 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 34, 'TRANS': 762} Chain breaks: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 8, 'ASP:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "D" Number of atoms: 6026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6026 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 28, 'TRANS': 746} Chain breaks: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'TYR:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 70 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: 4.33, per 1000 atoms: 0.18 Number of scatterers: 24629 At special positions: 0 Unit cell: (149.687, 138.109, 182.767, 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 147 16.00 P 4 15.00 O 4592 8.00 N 4032 7.00 C 15854 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=2.03 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=2.03 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: 1.98 Conformation dependent library (CDL) restraints added in 894.5 milliseconds 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5870 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 34 sheets defined 46.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.879A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 removed outlier: 4.076A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.859A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.690A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 129 " --> pdb=" O SER A 126 " (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: 3.592A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.556A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.677A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.284A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.540A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 256' Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.693A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 removed outlier: 3.503A pdb=" N ALA A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.554A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.077A 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 removed outlier: 3.578A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.800A 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 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.701A 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: 3.986A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.773A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 809 through 840 removed outlier: 5.117A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.669A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 3.534A pdb=" N ILE B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.578A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.799A pdb=" N GLN B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.538A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.778A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 3.614A pdb=" N ARG B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 removed outlier: 4.272A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.827A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.527A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (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: 3.685A 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 removed outlier: 3.528A pdb=" N ASN B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.945A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 708 removed outlier: 4.481A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 removed outlier: 3.549A pdb=" N LYS B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 743 through 746 Processing helix chain 'B' and resid 751 through 755 Processing helix chain 'B' and resid 772 through 786 Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.710A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 845 removed outlier: 5.514A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.929A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 4.675A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 removed outlier: 4.065A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.019A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.741A 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: 3.611A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 181 Processing helix chain 'C' and resid 182 through 183 No H-bonds generated for 'chain 'C' and resid 182 through 183' Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.737A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 removed outlier: 3.501A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.841A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 4.075A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.829A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 323 Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.078A 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 499 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.663A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 583 removed outlier: 3.721A pdb=" N LEU C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 3.973A 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: 3.579A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.809A pdb=" N ASN C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 694 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.747A pdb=" N TYR C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.571A 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: 3.888A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.671A pdb=" N SER C 779 " --> pdb=" O SER C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 809 through 821 removed outlier: 5.643A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 841 removed outlier: 4.331A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 841 " --> pdb=" O TYR C 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 57 removed outlier: 3.644A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.678A pdb=" N THR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.879A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.747A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.584A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.702A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.683A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.611A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 306 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 329 removed outlier: 3.934A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 340 removed outlier: 4.043A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (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 516 through 521 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 576 Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.580A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 656 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.566A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 706 removed outlier: 4.033A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 710 removed outlier: 3.767A pdb=" N ASN D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 707 through 710' Processing helix chain 'D' and resid 713 through 724 removed outlier: 3.548A pdb=" N LEU D 719 " --> pdb=" O ASP D 715 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER D 720 " --> pdb=" O ASP D 716 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 721 " --> pdb=" O ALA D 717 " (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 751 through 755 Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.507A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.808A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 845 removed outlier: 3.640A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.662A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 197 removed outlier: 7.296A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 5.960A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.358A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.677A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.844A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 540 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU A 751 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A 542 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR A 749 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 73 removed outlier: 5.756A pdb=" N ILE B 35 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU B 69 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 37 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AB3, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.247A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.529A pdb=" N LEU B 406 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU B 480 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLN B 437 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 490 removed outlier: 3.547A pdb=" N LYS B 488 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 524 through 525 Processing sheet with id=AB7, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.510A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.510A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 26 through 28 removed outlier: 5.798A pdb=" N GLN C 59 " --> pdb=" O VAL C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 90 through 92 removed outlier: 7.292A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.316A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.533A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 362 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 473 through 478 removed outlier: 3.594A pdb=" N VAL C 514 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (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 Processing sheet with id=AC7, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.210A pdb=" N ILE C 540 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU C 751 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 542 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR C 749 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 66 through 73 removed outlier: 6.389A pdb=" N ILE D 35 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU D 69 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 96 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 168 through 169 Processing sheet with id=AD1, first strand: chain 'D' and resid 171 through 173 removed outlier: 6.203A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 380 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD3, first strand: chain 'D' and resid 405 through 410 removed outlier: 7.558A pdb=" N LEU D 480 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN D 437 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD5, first strand: chain 'D' and resid 513 through 514 removed outlier: 4.510A pdb=" N LEU D 513 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY D 761 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE D 530 " --> pdb=" O GLY D 761 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 513 through 514 removed outlier: 4.510A pdb=" N LEU D 513 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY D 761 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE D 530 " --> pdb=" O GLY D 761 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 524 through 525 1044 hydrogen bonds defined for protein. 2961 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: 4.60 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4331 1.32 - 1.45: 6464 1.45 - 1.57: 14117 1.57 - 1.69: 12 1.69 - 1.82: 248 Bond restraints: 25172 Sorted by residual: bond pdb=" O1 A8W D1002 " pdb=" S A8W D1002 " ideal model delta sigma weight residual 1.636 1.590 0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" O1 A8W D1001 " pdb=" S A8W D1001 " ideal model delta sigma weight residual 1.636 1.592 0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C3 A8W B1002 " pdb=" O1 A8W B1002 " ideal model delta sigma weight residual 1.432 1.474 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" O1 A8W B1001 " pdb=" S A8W B1001 " ideal model delta sigma weight residual 1.636 1.595 0.041 2.00e-02 2.50e+03 4.16e+00 bond pdb=" C3 A8W B1001 " pdb=" O1 A8W B1001 " ideal model delta sigma weight residual 1.432 1.472 -0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 25167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 33402 1.59 - 3.17: 626 3.17 - 4.76: 106 4.76 - 6.34: 36 6.34 - 7.93: 2 Bond angle restraints: 34172 Sorted by residual: angle pdb=" C SER A 802 " pdb=" N ASN A 803 " pdb=" CA ASN A 803 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.13e+00 angle pdb=" N VAL A 656 " pdb=" CA VAL A 656 " pdb=" C VAL A 656 " ideal model delta sigma weight residual 111.81 109.30 2.51 8.60e-01 1.35e+00 8.50e+00 angle pdb=" C PHE C 558 " pdb=" N GLN C 559 " pdb=" CA GLN C 559 " ideal model delta sigma weight residual 120.89 117.09 3.80 1.50e+00 4.44e-01 6.41e+00 angle pdb=" N GLU D 552 " pdb=" CA GLU D 552 " pdb=" C GLU D 552 " ideal model delta sigma weight residual 109.81 115.30 -5.49 2.21e+00 2.05e-01 6.17e+00 angle pdb=" CB LYS D 382 " pdb=" CG LYS D 382 " pdb=" CD LYS D 382 " ideal model delta sigma weight residual 111.30 116.91 -5.61 2.30e+00 1.89e-01 5.96e+00 ... (remaining 34167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 14811 33.52 - 67.04: 345 67.04 - 100.56: 21 100.56 - 134.09: 1 134.09 - 167.61: 7 Dihedral angle restraints: 15185 sinusoidal: 6080 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual 93.00 27.79 65.21 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual -86.00 -128.91 42.91 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CA PRO B 679 " pdb=" C PRO B 679 " pdb=" N PRO B 680 " pdb=" CA PRO B 680 " ideal model delta harmonic sigma weight residual 180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 15182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2479 0.038 - 0.075: 990 0.075 - 0.113: 336 0.113 - 0.151: 72 0.151 - 0.188: 2 Chirality restraints: 3879 Sorted by residual: chirality pdb=" CB ILE A 29 " pdb=" CA ILE A 29 " pdb=" CG1 ILE A 29 " pdb=" CG2 ILE A 29 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CB VAL D 422 " pdb=" CA VAL D 422 " pdb=" CG1 VAL D 422 " pdb=" CG2 VAL D 422 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA GLU A 406 " pdb=" N GLU A 406 " pdb=" C GLU A 406 " pdb=" CB GLU A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 3876 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO D 553 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 194 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C VAL A 194 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL A 194 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 195 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 458 " -0.013 2.00e-02 2.50e+03 1.22e-02 2.61e+00 pdb=" CG PHE A 458 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 458 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 458 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 458 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 458 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 458 " -0.002 2.00e-02 2.50e+03 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2187 2.74 - 3.28: 25002 3.28 - 3.82: 40343 3.82 - 4.36: 50570 4.36 - 4.90: 86012 Nonbonded interactions: 204114 Sorted by model distance: nonbonded pdb=" OD2 ASP B 732 " pdb=" OH TYR B 762 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR D 691 " pdb=" OE2 GLU D1000 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLU C 834 " model vdw 2.208 3.040 nonbonded pdb=" O THR C 791 " pdb=" OH TYR C 795 " model vdw 2.222 3.040 nonbonded pdb=" O ILE C 664 " pdb=" OG1 THR C 749 " model vdw 2.226 3.040 ... (remaining 204109 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 114 or (resid 115 and (name N or n \ ame CA or name C or name O or name CB )) or resid 116 through 325 or (resid 326 \ and (name N or name CA or name C or name O or name CB )) or resid 327 through 49 \ 3 or (resid 494 through 495 and (name N or name CA or name C or name O or name C \ B )) or resid 496 through 707 or (resid 708 and (name N or name CA or name C or \ name O or name CB )) or resid 709 through 795 or (resid 796 through 797 and (nam \ e N or name CA or name C or name O or name CB )) or resid 798 through 1002)) selection = (chain 'C' and (resid 25 through 544 or resid 549 through 586 or resid 600 throu \ gh 673 or (resid 674 and (name N or name CA or name C or name O or name CB )) or \ resid 675 through 1002)) } ncs_group { reference = (chain 'B' and (resid 34 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 104 or (resid 105 and (name N or n \ ame CA or name C or name O or name CB )) or resid 106 through 541 or (resid 542 \ and (name N or name CA or name C or name O or name CB )) or resid 543 through 65 \ 6 or (resid 657 through 659 and (name N or name CA or name C or name O or name C \ B )) or resid 660 or (resid 661 through 662 and (name N or name CA or name C or \ name O or name CB )) or resid 663 through 802 or (resid 803 through 804 and (nam \ e N or name CA or name C or name O or name CB )) or resid 808 through 841 or (re \ sid 842 through 845 and (name N or name CA or name C or name O or name CB )) or \ resid 1000 through 1002)) selection = (chain 'D' and (resid 34 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 293 or (resid 294 and (name N or n \ ame CA or name C or name O or name CB )) or resid 295 through 336 or (resid 337 \ and (name N or name CA or name C or name O or name CB )) or resid 338 through 37 \ 7 or (resid 378 and (name N or name CA or name C or name O or name CB )) or resi \ d 379 through 430 or (resid 431 and (name N or name CA or name C or name O or na \ me CB )) or resid 432 through 469 or (resid 470 and (name N or name CA or name C \ or name O or name CB )) or resid 471 through 472 or (resid 473 and (name N or n \ ame CA or name C or name O or name CB )) or resid 474 through 623 or (resid 624 \ and (name N or name CA or name C or name O or name CB )) or resid 625 through 71 \ 1 or (resid 712 and (name N or name CA or name C or name O or name CB )) or resi \ d 713 through 790 or (resid 791 and (name N or name CA or name C or name O or na \ me CB )) or resid 792 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.870 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.006 0.075 25186 Z= 0.244 Angle : 0.573 7.925 34200 Z= 0.290 Chirality : 0.045 0.188 3879 Planarity : 0.004 0.048 4308 Dihedral : 14.947 167.607 9273 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -1.04 (0.15), residues: 3107 helix: -0.32 (0.14), residues: 1258 sheet: -0.96 (0.28), residues: 356 loop : -0.83 (0.17), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 694 TYR 0.014 0.001 TYR B 164 PHE 0.028 0.002 PHE A 458 TRP 0.023 0.002 TRP D 197 HIS 0.008 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00603 (25172) covalent geometry : angle 0.57265 (34172) SS BOND : bond 0.00348 ( 14) SS BOND : angle 0.92867 ( 28) hydrogen bonds : bond 0.25267 ( 1037) hydrogen bonds : angle 8.40726 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8295 (tptm) cc_final: 0.6769 (ttpt) REVERT: A 233 ARG cc_start: 0.8086 (ptp-110) cc_final: 0.7861 (ptp90) REVERT: A 237 MET cc_start: 0.8132 (ppp) cc_final: 0.7814 (ppp) REVERT: D 349 LEU cc_start: 0.8101 (mp) cc_final: 0.7835 (mp) REVERT: D 385 GLN cc_start: 0.6927 (mp10) cc_final: 0.6508 (mp10) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1552 time to fit residues: 66.3123 Evaluate side-chains 244 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 GLN A 273 ASN A 311 ASN A 375 ASN A 477 HIS A 494 ASN A 521 ASN A 812 ASN B 218 ASN B 325 HIS B 688 ASN B 817 ASN C 70 ASN C 73 GLN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN C 477 HIS C 742 GLN C 780 HIS D 152 GLN D 217 GLN D 311 HIS D 336 ASN D 622 ASN D 697 ASN D 840 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.131359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095405 restraints weight = 52272.297| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.27 r_work: 0.3239 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25186 Z= 0.136 Angle : 0.540 7.518 34200 Z= 0.285 Chirality : 0.043 0.153 3879 Planarity : 0.004 0.048 4308 Dihedral : 9.876 156.418 3771 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 0.35 % Allowed : 5.92 % Favored : 93.73 % 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: -0.42 (0.15), residues: 3107 helix: 0.55 (0.14), residues: 1295 sheet: -0.97 (0.27), residues: 372 loop : -0.78 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 36 TYR 0.024 0.001 TYR D 179 PHE 0.022 0.002 PHE C 627 TRP 0.012 0.001 TRP A 563 HIS 0.004 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00307 (25172) covalent geometry : angle 0.53955 (34172) SS BOND : bond 0.00209 ( 14) SS BOND : angle 0.61955 ( 28) hydrogen bonds : bond 0.05155 ( 1037) hydrogen bonds : angle 5.47715 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 260 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8289 (tptm) cc_final: 0.7894 (tptp) REVERT: A 266 ILE cc_start: 0.7860 (mm) cc_final: 0.7640 (mt) REVERT: B 218 ASN cc_start: 0.7851 (m-40) cc_final: 0.7243 (t0) REVERT: B 562 MET cc_start: 0.8962 (tmm) cc_final: 0.8698 (tmm) REVERT: C 354 MET cc_start: 0.6232 (tmm) cc_final: 0.5817 (tmm) REVERT: C 576 MET cc_start: 0.8470 (ttm) cc_final: 0.8265 (ttt) REVERT: D 242 GLU cc_start: 0.8132 (tp30) cc_final: 0.7656 (pt0) REVERT: D 349 LEU cc_start: 0.8150 (mp) cc_final: 0.7861 (mp) REVERT: D 358 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.7130 (mmm) REVERT: D 385 GLN cc_start: 0.7496 (mp10) cc_final: 0.7199 (mp10) REVERT: D 706 MET cc_start: 0.8685 (mtm) cc_final: 0.8395 (mtp) outliers start: 9 outliers final: 4 residues processed: 265 average time/residue: 0.1469 time to fit residues: 62.9610 Evaluate side-chains 253 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 248 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 358 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 206 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 260 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.129974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092453 restraints weight = 52415.554| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.33 r_work: 0.3153 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 25186 Z= 0.279 Angle : 0.607 6.960 34200 Z= 0.313 Chirality : 0.047 0.195 3879 Planarity : 0.004 0.052 4308 Dihedral : 9.982 157.924 3771 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.88 % Allowed : 8.81 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.15), residues: 3107 helix: 0.62 (0.14), residues: 1284 sheet: -1.36 (0.26), residues: 381 loop : -0.84 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.031 0.002 TYR D 179 PHE 0.025 0.002 PHE C 458 TRP 0.015 0.002 TRP D 197 HIS 0.009 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00693 (25172) covalent geometry : angle 0.60683 (34172) SS BOND : bond 0.00397 ( 14) SS BOND : angle 0.80130 ( 28) hydrogen bonds : bond 0.05110 ( 1037) hydrogen bonds : angle 5.31878 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 1.138 Fit side-chains REVERT: A 132 SER cc_start: 0.8375 (m) cc_final: 0.8155 (m) REVERT: A 237 MET cc_start: 0.8234 (ppp) cc_final: 0.8032 (ppp) REVERT: B 218 ASN cc_start: 0.7916 (m-40) cc_final: 0.7283 (t0) REVERT: C 43 ARG cc_start: 0.5924 (tpp-160) cc_final: 0.5688 (ttm-80) REVERT: C 354 MET cc_start: 0.6320 (tmm) cc_final: 0.6068 (tmm) REVERT: D 349 LEU cc_start: 0.8296 (mp) cc_final: 0.8018 (mp) REVERT: D 356 TYR cc_start: 0.5246 (m-10) cc_final: 0.4786 (m-10) REVERT: D 358 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7274 (mmm) REVERT: D 385 GLN cc_start: 0.7502 (mp10) cc_final: 0.7132 (mp10) REVERT: D 545 VAL cc_start: 0.7099 (OUTLIER) cc_final: 0.6845 (t) outliers start: 23 outliers final: 10 residues processed: 287 average time/residue: 0.1470 time to fit residues: 68.3220 Evaluate side-chains 273 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 261 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 545 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 226 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 282 optimal weight: 0.6980 chunk 212 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 173 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 HIS B 180 GLN B 662 GLN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN C 375 ASN D 218 ASN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.131341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094439 restraints weight = 52339.333| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.29 r_work: 0.3186 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25186 Z= 0.128 Angle : 0.512 8.122 34200 Z= 0.266 Chirality : 0.042 0.184 3879 Planarity : 0.004 0.048 4308 Dihedral : 9.535 153.216 3771 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 0.73 % Allowed : 11.00 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 3107 helix: 0.97 (0.14), residues: 1292 sheet: -1.13 (0.27), residues: 355 loop : -0.84 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.031 0.001 TYR D 179 PHE 0.025 0.001 PHE C 627 TRP 0.011 0.001 TRP A 563 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00304 (25172) covalent geometry : angle 0.51205 (34172) SS BOND : bond 0.00330 ( 14) SS BOND : angle 0.84992 ( 28) hydrogen bonds : bond 0.03980 ( 1037) hydrogen bonds : angle 4.94924 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.932 Fit side-chains REVERT: A 233 ARG cc_start: 0.8229 (ptp90) cc_final: 0.7345 (ptp90) REVERT: A 237 MET cc_start: 0.8297 (ppp) cc_final: 0.8041 (ppp) REVERT: A 354 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7258 (ptp) REVERT: A 704 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8008 (mtp180) REVERT: B 218 ASN cc_start: 0.7855 (m-40) cc_final: 0.7282 (t0) REVERT: B 386 MET cc_start: 0.5653 (mmm) cc_final: 0.5058 (tpp) REVERT: C 36 ARG cc_start: 0.6939 (tpm170) cc_final: 0.6613 (tpm170) REVERT: C 354 MET cc_start: 0.6363 (tmm) cc_final: 0.6087 (tmm) REVERT: D 242 GLU cc_start: 0.8268 (tp30) cc_final: 0.7727 (pt0) REVERT: D 349 LEU cc_start: 0.8271 (mp) cc_final: 0.7989 (mp) REVERT: D 356 TYR cc_start: 0.5252 (m-10) cc_final: 0.4792 (m-10) REVERT: D 385 GLN cc_start: 0.7517 (mp10) cc_final: 0.7152 (mp10) REVERT: D 545 VAL cc_start: 0.7017 (OUTLIER) cc_final: 0.6749 (t) outliers start: 19 outliers final: 9 residues processed: 276 average time/residue: 0.1538 time to fit residues: 68.1017 Evaluate side-chains 260 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 248 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 545 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 30.0000 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 291 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN C 375 ASN D 127 HIS ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.131318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094176 restraints weight = 52141.255| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.31 r_work: 0.3193 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25186 Z= 0.131 Angle : 0.501 6.964 34200 Z= 0.260 Chirality : 0.042 0.160 3879 Planarity : 0.004 0.051 4308 Dihedral : 9.294 148.046 3771 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 1.19 % Allowed : 11.65 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3107 helix: 1.13 (0.14), residues: 1298 sheet: -1.11 (0.27), residues: 353 loop : -0.84 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.032 0.001 TYR D 179 PHE 0.023 0.002 PHE C 627 TRP 0.011 0.001 TRP A 563 HIS 0.004 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00316 (25172) covalent geometry : angle 0.50121 (34172) SS BOND : bond 0.00199 ( 14) SS BOND : angle 0.67299 ( 28) hydrogen bonds : bond 0.03809 ( 1037) hydrogen bonds : angle 4.80530 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.776 Fit side-chains REVERT: A 233 ARG cc_start: 0.8244 (ptp90) cc_final: 0.7318 (ptp90) REVERT: A 354 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7253 (ptp) REVERT: A 704 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7992 (mtp180) REVERT: B 218 ASN cc_start: 0.7841 (m-40) cc_final: 0.7261 (t0) REVERT: B 235 GLU cc_start: 0.7869 (pm20) cc_final: 0.7593 (pp20) REVERT: B 386 MET cc_start: 0.5720 (mmm) cc_final: 0.5305 (mmm) REVERT: B 491 ASN cc_start: 0.7437 (t0) cc_final: 0.7048 (t0) REVERT: B 604 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8515 (mttm) REVERT: C 215 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: C 354 MET cc_start: 0.6327 (tmm) cc_final: 0.6031 (tmm) REVERT: D 73 MET cc_start: 0.6142 (ptp) cc_final: 0.5913 (ptp) REVERT: D 242 GLU cc_start: 0.8249 (tp30) cc_final: 0.7703 (pt0) REVERT: D 349 LEU cc_start: 0.8256 (mp) cc_final: 0.8022 (mp) REVERT: D 356 TYR cc_start: 0.5276 (m-10) cc_final: 0.4852 (m-10) REVERT: D 385 GLN cc_start: 0.7483 (mp10) cc_final: 0.7119 (mp10) REVERT: D 545 VAL cc_start: 0.7065 (OUTLIER) cc_final: 0.6786 (t) outliers start: 31 outliers final: 12 residues processed: 286 average time/residue: 0.1543 time to fit residues: 71.2782 Evaluate side-chains 272 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 255 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 604 LYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 545 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 0.5980 chunk 212 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 281 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 672 GLN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.131601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094360 restraints weight = 52258.099| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.28 r_work: 0.3190 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25186 Z= 0.118 Angle : 0.496 7.703 34200 Z= 0.256 Chirality : 0.042 0.174 3879 Planarity : 0.004 0.052 4308 Dihedral : 9.105 142.812 3771 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 0.92 % Allowed : 12.69 % Favored : 86.38 % 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: 0.02 (0.15), residues: 3107 helix: 1.29 (0.15), residues: 1288 sheet: -1.09 (0.27), residues: 353 loop : -0.82 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.034 0.001 TYR D 179 PHE 0.024 0.001 PHE C 627 TRP 0.012 0.001 TRP B 197 HIS 0.004 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00280 (25172) covalent geometry : angle 0.49619 (34172) SS BOND : bond 0.00151 ( 14) SS BOND : angle 0.51814 ( 28) hydrogen bonds : bond 0.03603 ( 1037) hydrogen bonds : angle 4.69315 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 259 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8430 (tppt) cc_final: 0.8206 (ttpt) REVERT: A 233 ARG cc_start: 0.8269 (ptp90) cc_final: 0.7298 (ptp90) REVERT: A 354 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7287 (ptp) REVERT: A 704 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7991 (mtp180) REVERT: B 218 ASN cc_start: 0.7849 (m-40) cc_final: 0.7268 (t0) REVERT: B 386 MET cc_start: 0.5704 (mmm) cc_final: 0.5101 (tpp) REVERT: B 491 ASN cc_start: 0.7367 (t0) cc_final: 0.6996 (t0) REVERT: C 215 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: C 354 MET cc_start: 0.6316 (tmm) cc_final: 0.6010 (tmm) REVERT: D 73 MET cc_start: 0.6195 (ptp) cc_final: 0.5958 (ptp) REVERT: D 349 LEU cc_start: 0.8244 (mp) cc_final: 0.8012 (mp) REVERT: D 356 TYR cc_start: 0.5278 (m-10) cc_final: 0.4867 (m-10) REVERT: D 385 GLN cc_start: 0.7525 (mp10) cc_final: 0.7150 (mp10) REVERT: D 545 VAL cc_start: 0.7039 (OUTLIER) cc_final: 0.6761 (t) outliers start: 24 outliers final: 14 residues processed: 277 average time/residue: 0.1443 time to fit residues: 64.6498 Evaluate side-chains 271 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 583 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 304 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 chunk 183 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN B 224 GLN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.131699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095091 restraints weight = 52300.450| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.26 r_work: 0.3202 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25186 Z= 0.118 Angle : 0.494 8.151 34200 Z= 0.254 Chirality : 0.042 0.158 3879 Planarity : 0.004 0.053 4308 Dihedral : 8.931 134.915 3771 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 0.96 % Allowed : 13.27 % Favored : 85.77 % 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: 0.07 (0.15), residues: 3107 helix: 1.36 (0.15), residues: 1287 sheet: -1.09 (0.27), residues: 355 loop : -0.82 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.036 0.001 TYR D 179 PHE 0.023 0.001 PHE C 627 TRP 0.010 0.001 TRP A 563 HIS 0.004 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00284 (25172) covalent geometry : angle 0.49393 (34172) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.47840 ( 28) hydrogen bonds : bond 0.03505 ( 1037) hydrogen bonds : angle 4.63223 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8431 (tppt) cc_final: 0.8197 (ttpt) REVERT: A 233 ARG cc_start: 0.8300 (ptp90) cc_final: 0.7357 (ptp90) REVERT: A 266 ILE cc_start: 0.7857 (mt) cc_final: 0.7373 (tt) REVERT: A 704 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: B 218 ASN cc_start: 0.7863 (m-40) cc_final: 0.7301 (t0) REVERT: B 235 GLU cc_start: 0.7863 (pm20) cc_final: 0.7610 (pp20) REVERT: B 386 MET cc_start: 0.5735 (mmm) cc_final: 0.5329 (tpp) REVERT: B 604 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8517 (mttm) REVERT: C 215 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: C 354 MET cc_start: 0.6315 (tmm) cc_final: 0.6008 (tmm) REVERT: D 73 MET cc_start: 0.6259 (ptp) cc_final: 0.6038 (ptp) REVERT: D 349 LEU cc_start: 0.8273 (mp) cc_final: 0.8025 (mp) REVERT: D 356 TYR cc_start: 0.5293 (m-10) cc_final: 0.4869 (m-10) REVERT: D 385 GLN cc_start: 0.7521 (mp10) cc_final: 0.7130 (mp10) REVERT: D 545 VAL cc_start: 0.7029 (OUTLIER) cc_final: 0.6751 (t) outliers start: 25 outliers final: 17 residues processed: 279 average time/residue: 0.1404 time to fit residues: 63.6071 Evaluate side-chains 273 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 604 LYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 223 optimal weight: 0.9990 chunk 272 optimal weight: 0.2980 chunk 208 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 310 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.132189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094024 restraints weight = 52322.134| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.23 r_work: 0.3212 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25186 Z= 0.105 Angle : 0.485 8.189 34200 Z= 0.249 Chirality : 0.041 0.157 3879 Planarity : 0.004 0.053 4308 Dihedral : 8.694 124.041 3771 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 1.00 % Allowed : 13.54 % Favored : 85.46 % 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: 3107 helix: 1.47 (0.15), residues: 1286 sheet: -1.02 (0.27), residues: 354 loop : -0.82 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.038 0.001 TYR D 179 PHE 0.021 0.001 PHE C 627 TRP 0.014 0.001 TRP B 197 HIS 0.003 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00249 (25172) covalent geometry : angle 0.48478 (34172) SS BOND : bond 0.00131 ( 14) SS BOND : angle 0.41658 ( 28) hydrogen bonds : bond 0.03319 ( 1037) hydrogen bonds : angle 4.54510 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.767 Fit side-chains REVERT: A 115 ARG cc_start: 0.7492 (mmt-90) cc_final: 0.7185 (mmt-90) REVERT: A 178 LYS cc_start: 0.8473 (tppt) cc_final: 0.8222 (ttpt) REVERT: A 233 ARG cc_start: 0.8320 (ptp90) cc_final: 0.7357 (ptp90) REVERT: B 218 ASN cc_start: 0.7870 (m-40) cc_final: 0.7312 (t0) REVERT: B 224 GLN cc_start: 0.8165 (mp10) cc_final: 0.7932 (mp10) REVERT: B 235 GLU cc_start: 0.7873 (pm20) cc_final: 0.7630 (pp20) REVERT: B 386 MET cc_start: 0.5852 (mmm) cc_final: 0.5575 (mmm) REVERT: B 604 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8489 (mttm) REVERT: C 74 MET cc_start: 0.5658 (tpp) cc_final: 0.5411 (tpp) REVERT: C 215 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: C 354 MET cc_start: 0.6322 (tmm) cc_final: 0.6018 (tmm) REVERT: D 73 MET cc_start: 0.6220 (ptp) cc_final: 0.6011 (ptp) REVERT: D 349 LEU cc_start: 0.8259 (mp) cc_final: 0.8017 (mp) REVERT: D 356 TYR cc_start: 0.5270 (m-10) cc_final: 0.4818 (m-10) REVERT: D 385 GLN cc_start: 0.7485 (mp10) cc_final: 0.7139 (mp10) REVERT: D 545 VAL cc_start: 0.6967 (OUTLIER) cc_final: 0.6686 (t) outliers start: 26 outliers final: 18 residues processed: 281 average time/residue: 0.1524 time to fit residues: 69.1127 Evaluate side-chains 278 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 604 LYS Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 164 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 177 optimal weight: 0.5980 chunk 311 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.131822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095412 restraints weight = 52450.682| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.37 r_work: 0.3206 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25186 Z= 0.120 Angle : 0.495 8.502 34200 Z= 0.252 Chirality : 0.042 0.156 3879 Planarity : 0.004 0.053 4308 Dihedral : 8.632 115.880 3771 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 0.88 % Allowed : 13.58 % Favored : 85.54 % 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: 0.17 (0.15), residues: 3107 helix: 1.49 (0.15), residues: 1285 sheet: -1.08 (0.26), residues: 367 loop : -0.79 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.042 0.001 TYR D 179 PHE 0.021 0.001 PHE C 627 TRP 0.013 0.001 TRP B 197 HIS 0.004 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00290 (25172) covalent geometry : angle 0.49483 (34172) SS BOND : bond 0.00156 ( 14) SS BOND : angle 0.46454 ( 28) hydrogen bonds : bond 0.03382 ( 1037) hydrogen bonds : angle 4.53850 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 0.937 Fit side-chains REVERT: A 74 MET cc_start: 0.5901 (mmt) cc_final: 0.5699 (mmp) REVERT: A 233 ARG cc_start: 0.8321 (ptp90) cc_final: 0.7337 (ptp90) REVERT: A 266 ILE cc_start: 0.7878 (mt) cc_final: 0.7448 (tt) REVERT: B 180 GLN cc_start: 0.7286 (pt0) cc_final: 0.6966 (tt0) REVERT: B 218 ASN cc_start: 0.7864 (m-40) cc_final: 0.7302 (t0) REVERT: B 235 GLU cc_start: 0.7824 (pm20) cc_final: 0.7614 (pp20) REVERT: B 386 MET cc_start: 0.5895 (mmm) cc_final: 0.5596 (mmm) REVERT: B 604 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8491 (mttm) REVERT: B 709 PHE cc_start: 0.8281 (m-10) cc_final: 0.8037 (m-10) REVERT: C 215 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: C 354 MET cc_start: 0.6337 (tmm) cc_final: 0.6043 (tmm) REVERT: D 73 MET cc_start: 0.6201 (ptp) cc_final: 0.5987 (ptp) REVERT: D 349 LEU cc_start: 0.8299 (mp) cc_final: 0.8060 (mp) REVERT: D 356 TYR cc_start: 0.5275 (m-10) cc_final: 0.4807 (m-10) REVERT: D 385 GLN cc_start: 0.7498 (mp10) cc_final: 0.7183 (mp10) REVERT: D 545 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6728 (t) outliers start: 23 outliers final: 18 residues processed: 280 average time/residue: 0.1587 time to fit residues: 71.4650 Evaluate side-chains 275 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 604 LYS Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 69 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 131 optimal weight: 0.0030 chunk 135 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN B 357 GLN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.132238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096525 restraints weight = 52384.453| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.39 r_work: 0.3218 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25186 Z= 0.104 Angle : 0.487 8.613 34200 Z= 0.248 Chirality : 0.041 0.156 3879 Planarity : 0.003 0.053 4308 Dihedral : 8.490 108.505 3771 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 0.81 % Allowed : 13.65 % Favored : 85.54 % 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: 0.20 (0.15), residues: 3107 helix: 1.56 (0.15), residues: 1288 sheet: -1.07 (0.26), residues: 369 loop : -0.83 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.041 0.001 TYR D 179 PHE 0.021 0.001 PHE C 627 TRP 0.013 0.001 TRP B 197 HIS 0.003 0.000 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00247 (25172) covalent geometry : angle 0.48733 (34172) SS BOND : bond 0.00133 ( 14) SS BOND : angle 0.41841 ( 28) hydrogen bonds : bond 0.03226 ( 1037) hydrogen bonds : angle 4.47922 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 260 time to evaluate : 0.899 Fit side-chains REVERT: A 233 ARG cc_start: 0.8322 (ptp90) cc_final: 0.7358 (ptp90) REVERT: A 266 ILE cc_start: 0.7823 (mt) cc_final: 0.7402 (tt) REVERT: B 218 ASN cc_start: 0.7853 (m-40) cc_final: 0.7288 (t0) REVERT: B 386 MET cc_start: 0.5867 (mmm) cc_final: 0.5364 (tpp) REVERT: B 604 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (mttm) REVERT: C 74 MET cc_start: 0.5683 (tpp) cc_final: 0.5428 (tpp) REVERT: C 215 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: C 233 ARG cc_start: 0.7127 (mpp80) cc_final: 0.6884 (mpp80) REVERT: C 354 MET cc_start: 0.6291 (tmm) cc_final: 0.5995 (tmm) REVERT: D 73 MET cc_start: 0.6222 (ptp) cc_final: 0.6002 (ptp) REVERT: D 222 LYS cc_start: 0.8214 (mttm) cc_final: 0.8009 (mtmt) REVERT: D 349 LEU cc_start: 0.8289 (mp) cc_final: 0.8053 (mp) REVERT: D 356 TYR cc_start: 0.5243 (m-10) cc_final: 0.4776 (m-10) REVERT: D 385 GLN cc_start: 0.7506 (mp10) cc_final: 0.7222 (mp10) REVERT: D 545 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6664 (t) outliers start: 21 outliers final: 16 residues processed: 278 average time/residue: 0.1628 time to fit residues: 72.6210 Evaluate side-chains 276 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 257 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 604 LYS Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 167 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 271 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 697 ASN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.130047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092677 restraints weight = 52090.344| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.16 r_work: 0.3161 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 25186 Z= 0.297 Angle : 0.620 8.387 34200 Z= 0.314 Chirality : 0.048 0.217 3879 Planarity : 0.004 0.052 4308 Dihedral : 9.133 111.964 3771 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 0.88 % Allowed : 13.92 % Favored : 85.19 % 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: -0.19 (0.15), residues: 3107 helix: 1.10 (0.14), residues: 1284 sheet: -1.30 (0.27), residues: 350 loop : -0.89 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 712 TYR 0.044 0.002 TYR D 179 PHE 0.034 0.003 PHE C 472 TRP 0.026 0.002 TRP D 197 HIS 0.008 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00735 (25172) covalent geometry : angle 0.62019 (34172) SS BOND : bond 0.00446 ( 14) SS BOND : angle 0.85933 ( 28) hydrogen bonds : bond 0.04306 ( 1037) hydrogen bonds : angle 4.83083 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8342.56 seconds wall clock time: 142 minutes 41.64 seconds (8561.64 seconds total)