Starting phenix.real_space_refine on Thu Mar 5 11:14:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9g_31031/03_2026/7e9g_31031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9g_31031/03_2026/7e9g_31031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e9g_31031/03_2026/7e9g_31031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9g_31031/03_2026/7e9g_31031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e9g_31031/03_2026/7e9g_31031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9g_31031/03_2026/7e9g_31031.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3577 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 121 5.16 5 Cl 1 4.86 5 C 11960 2.51 5 N 3258 2.21 5 O 3476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18816 Number of models: 1 Model: "" Number of chains: 10 Chain: "R" Number of atoms: 5686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 5686 Classifications: {'peptide': 769} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 37, 'TRANS': 731} Chain breaks: 1 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'GLN:plan1': 4, 'TYR:plan': 3, 'PHE:plan': 6, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 216 Chain: "S" Number of atoms: 5584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5584 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 36, 'TRANS': 718} Chain breaks: 2 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 12, 'ASN:plan1': 7, 'ASP:plan': 4, 'GLN:plan1': 2, 'PHE:plan': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 201 Chain: "A" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1641 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 8, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2213 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 305} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 8, 'ARG:plan': 11, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 218 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 28} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1672 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 875 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'40F': 1, 'HZR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'40F': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 4.52, per 1000 atoms: 0.24 Number of scatterers: 18816 At special positions: 0 Unit cell: (225.72, 148.39, 146.3, 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) Cl 1 17.00 S 121 16.00 O 3476 8.00 N 3258 7.00 C 11960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS R 50 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 234 " - pdb=" SG CYS R 518 " distance=2.03 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 362 " distance=2.03 Simple disulfide: pdb=" SG CYS R 400 " - pdb=" SG CYS R 407 " distance=2.03 Simple disulfide: pdb=" SG CYS R 500 " - pdb=" SG CYS R 519 " distance=2.03 Simple disulfide: pdb=" SG CYS R 504 " - pdb=" SG CYS R 522 " distance=2.03 Simple disulfide: pdb=" SG CYS R 525 " - pdb=" SG CYS R 537 " distance=2.03 Simple disulfide: pdb=" SG CYS R 540 " - pdb=" SG CYS R 553 " distance=2.03 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 721 " distance=2.03 Simple disulfide: pdb=" SG CYS S 50 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 234 " - pdb=" SG CYS S 518 " distance=2.03 Simple disulfide: pdb=" SG CYS S 355 " - pdb=" SG CYS S 362 " distance=2.03 Simple disulfide: pdb=" SG CYS S 400 " - pdb=" SG CYS S 407 " distance=2.03 Simple disulfide: pdb=" SG CYS S 500 " - pdb=" SG CYS S 519 " distance=2.03 Simple disulfide: pdb=" SG CYS S 504 " - pdb=" SG CYS S 522 " distance=2.03 Simple disulfide: pdb=" SG CYS S 525 " - pdb=" SG CYS S 537 " distance=2.03 Simple disulfide: pdb=" SG CYS S 540 " - pdb=" SG CYS S 553 " distance=2.03 Simple disulfide: pdb=" SG CYS S 632 " - pdb=" SG CYS S 721 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " 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: 1.20 Conformation dependent library (CDL) restraints added in 989.5 milliseconds 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 29 sheets defined 33.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'R' and resid 57 through 74 Processing helix chain 'R' and resid 94 through 107 Processing helix chain 'R' and resid 144 through 157 removed outlier: 3.801A pdb=" N LEU R 157 " --> pdb=" O ASN R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 174 Processing helix chain 'R' and resid 189 through 202 Processing helix chain 'R' and resid 216 through 230 removed outlier: 3.706A pdb=" N ALA R 230 " --> pdb=" O LEU R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 259 Processing helix chain 'R' and resid 271 through 285 Processing helix chain 'R' and resid 326 through 333 removed outlier: 3.509A pdb=" N SER R 333 " --> pdb=" O SER R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 353 removed outlier: 3.637A pdb=" N ARG R 346 " --> pdb=" O ASN R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 400 Processing helix chain 'R' and resid 414 through 425 removed outlier: 3.808A pdb=" N LEU R 424 " --> pdb=" O LYS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 568 through 592 removed outlier: 3.960A pdb=" N HIS R 592 " --> pdb=" O VAL R 588 " (cutoff:3.500A) Processing helix chain 'R' and resid 595 through 601 removed outlier: 4.336A pdb=" N ALA R 601 " --> pdb=" O VAL R 597 " (cutoff:3.500A) Processing helix chain 'R' and resid 602 through 624 removed outlier: 3.885A pdb=" N ILE R 624 " --> pdb=" O THR R 620 " (cutoff:3.500A) Processing helix chain 'R' and resid 628 through 664 removed outlier: 4.017A pdb=" N GLY R 640 " --> pdb=" O ARG R 636 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS R 646 " --> pdb=" O ALA R 642 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA R 664 " --> pdb=" O ILE R 660 " (cutoff:3.500A) Processing helix chain 'R' and resid 675 through 699 Processing helix chain 'R' and resid 725 through 751 Processing helix chain 'R' and resid 756 through 784 Proline residue: R 778 - end of helix Processing helix chain 'R' and resid 786 through 816 removed outlier: 3.577A pdb=" N GLN R 790 " --> pdb=" O ASP R 786 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR R 792 " --> pdb=" O ARG R 788 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N CYS R 795 " --> pdb=" O THR R 791 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL R 796 " --> pdb=" O THR R 792 " (cutoff:3.500A) Proline residue: R 812 - end of helix Processing helix chain 'S' and resid 58 through 73 removed outlier: 3.601A pdb=" N GLU S 63 " --> pdb=" O ILE S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 108 removed outlier: 4.292A pdb=" N ALA S 108 " --> pdb=" O ASP S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 158 Processing helix chain 'S' and resid 169 through 174 Processing helix chain 'S' and resid 187 through 202 removed outlier: 4.089A pdb=" N GLN S 191 " --> pdb=" O PRO S 187 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 231 removed outlier: 3.542A pdb=" N ARG S 229 " --> pdb=" O GLU S 225 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA S 230 " --> pdb=" O LEU S 226 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG S 231 " --> pdb=" O GLU S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 246 through 259 Processing helix chain 'S' and resid 271 through 284 Processing helix chain 'S' and resid 324 through 333 Processing helix chain 'S' and resid 344 through 353 removed outlier: 3.592A pdb=" N GLN S 351 " --> pdb=" O GLU S 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 377 through 400 Processing helix chain 'S' and resid 414 through 425 Processing helix chain 'S' and resid 568 through 593 removed outlier: 3.781A pdb=" N VAL S 572 " --> pdb=" O ALA S 568 " (cutoff:3.500A) Processing helix chain 'S' and resid 602 through 624 removed outlier: 4.214A pdb=" N CYS S 606 " --> pdb=" O GLY S 602 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR S 607 " --> pdb=" O ARG S 603 " (cutoff:3.500A) Processing helix chain 'S' and resid 628 through 657 removed outlier: 3.858A pdb=" N GLY S 640 " --> pdb=" O ARG S 636 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE S 657 " --> pdb=" O LYS S 653 " (cutoff:3.500A) Processing helix chain 'S' and resid 676 through 702 removed outlier: 3.516A pdb=" N GLU S 701 " --> pdb=" O TRP S 697 " (cutoff:3.500A) Processing helix chain 'S' and resid 727 through 749 removed outlier: 3.714A pdb=" N SER S 731 " --> pdb=" O SER S 727 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU S 738 " --> pdb=" O TYR S 734 " (cutoff:3.500A) Processing helix chain 'S' and resid 753 through 783 removed outlier: 5.692A pdb=" N ALA S 759 " --> pdb=" O ASN S 755 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS S 760 " --> pdb=" O PHE S 756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE S 761 " --> pdb=" O ASN S 757 " (cutoff:3.500A) Proline residue: S 778 - end of helix Processing helix chain 'S' and resid 787 through 809 Processing helix chain 'S' and resid 810 through 817 Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.226A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.899A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.846A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.837A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 35 through 38 removed outlier: 3.868A pdb=" N GLY R 36 " --> pdb=" O HIS R 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 163 through 164 Processing sheet with id=AA3, first strand: chain 'R' and resid 234 through 238 removed outlier: 7.665A pdb=" N VAL R 207 " --> pdb=" O ALA R 236 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER R 238 " --> pdb=" O VAL R 207 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR R 209 " --> pdb=" O SER R 238 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYR R 206 " --> pdb=" O VAL R 265 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N VAL R 267 " --> pdb=" O TYR R 206 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER R 208 " --> pdb=" O VAL R 267 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE R 269 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL R 210 " --> pdb=" O PHE R 269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA R 266 " --> pdb=" O THR R 290 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TRP R 291 " --> pdb=" O ILE R 315 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE R 317 " --> pdb=" O TRP R 291 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA R 293 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N LEU R 319 " --> pdb=" O ALA R 293 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR R 453 " --> pdb=" O TYR R 473 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR R 473 " --> pdb=" O TYR R 453 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE R 455 " --> pdb=" O VAL R 471 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU R 459 " --> pdb=" O ARG R 467 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG R 467 " --> pdb=" O LEU R 459 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 427 through 429 removed outlier: 3.708A pdb=" N PHE R 428 " --> pdb=" O VAL R 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 510 through 512 Processing sheet with id=AA6, first strand: chain 'S' and resid 26 through 28 removed outlier: 3.658A pdb=" N ALA S 86 " --> pdb=" O LEU S 28 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY S 36 " --> pdb=" O HIS S 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AA8, first strand: chain 'S' and resid 235 through 241 removed outlier: 7.454A pdb=" N VAL S 207 " --> pdb=" O ALA S 236 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER S 238 " --> pdb=" O VAL S 207 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR S 209 " --> pdb=" O SER S 238 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS S 240 " --> pdb=" O THR S 209 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA S 211 " --> pdb=" O LYS S 240 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER S 212 " --> pdb=" O PHE S 269 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA S 266 " --> pdb=" O VAL S 292 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA S 293 " --> pdb=" O ILE S 317 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N LEU S 319 " --> pdb=" O ALA S 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY S 472 " --> pdb=" O ILE S 455 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR S 457 " --> pdb=" O LYS S 470 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS S 470 " --> pdb=" O THR S 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 428 through 429 removed outlier: 4.193A pdb=" N PHE S 428 " --> pdb=" O VAL S 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 510 through 512 removed outlier: 3.649A pdb=" N ILE S 523 " --> pdb=" O LYS S 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.353A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.675A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.222A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.867A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.124A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 191 through 192 removed outlier: 4.087A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.621A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.751A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.629A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 81 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS D 22 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR D 69 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.741A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 12 " --> pdb=" O THR D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.598A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 97 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 146 through 148 removed outlier: 7.376A pdb=" N VAL D 147 " --> pdb=" O GLU D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 155 through 159 Processing sheet with id=AC6, first strand: chain 'D' and resid 194 through 195 removed outlier: 6.973A pdb=" N TRP D 176 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 226 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.537A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.500A pdb=" N LEU E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.916A pdb=" N THR F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP F 72 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 68 " --> pdb=" O GLN F 81 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 57 through 59 removed outlier: 5.381A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR F 33 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 57 through 59 removed outlier: 5.381A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR F 33 " --> pdb=" O ASP F 98 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2301 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: 2.71 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3044 1.31 - 1.44: 5409 1.44 - 1.56: 10631 1.56 - 1.69: 4 1.69 - 1.82: 159 Bond restraints: 19247 Sorted by residual: bond pdb=" C18 HZR R 902 " pdb=" C19 HZR R 902 " ideal model delta sigma weight residual 1.353 1.525 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C6 40F R 901 " pdb=" C7 40F R 901 " ideal model delta sigma weight residual 1.534 1.393 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C6 40F S 901 " pdb=" C7 40F S 901 " ideal model delta sigma weight residual 1.534 1.393 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C 40F S 901 " pdb=" C1 40F S 901 " ideal model delta sigma weight residual 1.554 1.414 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C 40F R 901 " pdb=" C1 40F R 901 " ideal model delta sigma weight residual 1.554 1.415 0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 19242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 26255 6.90 - 13.80: 4 13.80 - 20.70: 0 20.70 - 27.60: 0 27.60 - 34.49: 2 Bond angle restraints: 26261 Sorted by residual: angle pdb=" C3 40F S 901 " pdb=" C5 40F S 901 " pdb=" C6 40F S 901 " ideal model delta sigma weight residual 116.92 151.41 -34.49 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C3 40F R 901 " pdb=" C5 40F R 901 " pdb=" C6 40F R 901 " ideal model delta sigma weight residual 116.92 151.20 -34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C1 40F S 901 " pdb=" C2 40F S 901 " pdb=" C3 40F S 901 " ideal model delta sigma weight residual 118.97 130.70 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C1 40F R 901 " pdb=" C2 40F R 901 " pdb=" C3 40F R 901 " ideal model delta sigma weight residual 118.97 130.33 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C05 HZR R 902 " pdb=" N06 HZR R 902 " pdb=" C17 HZR R 902 " ideal model delta sigma weight residual 115.44 126.11 -10.67 3.00e+00 1.11e-01 1.26e+01 ... (remaining 26256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 10962 26.29 - 52.59: 342 52.59 - 78.88: 24 78.88 - 105.18: 7 105.18 - 131.47: 2 Dihedral angle restraints: 11337 sinusoidal: 3969 harmonic: 7368 Sorted by residual: dihedral pdb=" CB CYS R 50 " pdb=" SG CYS R 50 " pdb=" SG CYS R 92 " pdb=" CB CYS R 92 " ideal model delta sinusoidal sigma weight residual 93.00 6.35 86.65 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS R 525 " pdb=" SG CYS R 525 " pdb=" SG CYS R 537 " pdb=" CB CYS R 537 " ideal model delta sinusoidal sigma weight residual 93.00 167.36 -74.36 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS R 400 " pdb=" SG CYS R 400 " pdb=" SG CYS R 407 " pdb=" CB CYS R 407 " ideal model delta sinusoidal sigma weight residual 93.00 166.05 -73.05 1 1.00e+01 1.00e-02 6.80e+01 ... (remaining 11334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 3016 0.988 - 1.975: 2 1.975 - 2.963: 0 2.963 - 3.951: 0 3.951 - 4.938: 1 Chirality restraints: 3019 Sorted by residual: chirality pdb=" C09 HZR R 902 " pdb=" C08 HZR R 902 " pdb=" C10 HZR R 902 " pdb=" C16 HZR R 902 " both_signs ideal model delta sigma weight residual False 2.48 -2.46 4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C5 40F S 901 " pdb=" C2 40F S 901 " pdb=" C3 40F S 901 " pdb=" C6 40F S 901 " both_signs ideal model delta sigma weight residual True 2.64 1.34 1.29 2.00e-01 2.50e+01 4.18e+01 chirality pdb=" C5 40F R 901 " pdb=" C2 40F R 901 " pdb=" C3 40F R 901 " pdb=" C6 40F R 901 " both_signs ideal model delta sigma weight residual True 2.64 1.35 1.29 2.00e-01 2.50e+01 4.14e+01 ... (remaining 3016 not shown) Planarity restraints: 3379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 570 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO R 571 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 571 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 571 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY S 570 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO S 571 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO S 571 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO S 571 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU S 741 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C LEU S 741 " -0.025 2.00e-02 2.50e+03 pdb=" O LEU S 741 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS S 742 " 0.008 2.00e-02 2.50e+03 ... (remaining 3376 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1285 2.74 - 3.28: 19219 3.28 - 3.82: 31973 3.82 - 4.36: 36666 4.36 - 4.90: 63398 Nonbonded interactions: 152541 Sorted by model distance: nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.196 3.040 nonbonded pdb=" OG SER R 262 " pdb=" O ARG R 499 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.270 3.040 nonbonded pdb=" OG SER S 356 " pdb=" OE1 GLN S 359 " model vdw 2.283 3.040 nonbonded pdb=" OE1 GLU S 308 " pdb=" OH TYR S 458 " model vdw 2.299 3.040 ... (remaining 152536 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 'E' and (resid 2 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 29 or (resid 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 through 55 or (resid 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 through 85 or (re \ sid 86 and (name N or name CA or name C or name O or name CB )) or resid 87 thro \ ugh 118)) selection = (chain 'F' and (resid 2 through 10 or (resid 11 through 12 and (name N or name C \ A or name C or name O or name CB )) or resid 13 through 45 or (resid 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 118)) } ncs_group { reference = (chain 'R' and (resid 23 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 353 or (resid 354 and (name N or n \ ame CA or name C or name O or name CB )) or resid 355 through 359 or (resid 360 \ and (name N or name CA or name C or name O or name CB )) or resid 361 through 40 \ 1 or (resid 402 and (name N or name CA or name C or name O or name CB )) or resi \ d 403 through 423 or (resid 424 through 425 and (name N or name CA or name C or \ name O or name CB )) or resid 426 or (resid 427 and (name N or name CA or name C \ or name O or name CB )) or resid 428 through 506 or (resid 507 through 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 554 or \ (resid 555 through 556 and (name N or name CA or name C or name O or name CB )) \ or resid 557 through 589 or (resid 590 through 591 and (name N or name CA or na \ me C or name O or name CB )) or resid 592 or (resid 593 through 594 and (name N \ or name CA or name C or name O or name CB )) or resid 595 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 or (re \ sid 599 through 601 and (name N or name CA or name C or name O or name CB )) or \ resid 602 through 613 or (resid 614 through 615 and (name N or name CA or name C \ or name O or name CB )) or resid 616 or (resid 617 and (name N or name CA or na \ me C or name O or name CB )) or resid 618 through 620 or (resid 621 and (name N \ or name CA or name C or name O or name CB )) or resid 622 through 635 or (resid \ 636 through 637 and (name N or name CA or name C or name O or name CB )) or resi \ d 638 through 646 or (resid 647 through 649 and (name N or name CA or name C or \ name O or name CB )) or resid 650 through 652 or (resid 653 and (name N or name \ CA or name C or name O or name CB )) or resid 654 or (resid 655 through 656 and \ (name N or name CA or name C or name O or name CB )) or resid 657 or resid 675 t \ hrough 681 or (resid 682 through 683 and (name N or name CA or name C or name O \ or name CB )) or resid 684 through 686 or (resid 687 and (name N or name CA or n \ ame C or name O or name CB )) or resid 688 through 704 or (resid 705 and (name N \ or name CA or name C or name O or name CB )) or resid 706 or (resid 707 through \ 710 and (name N or name CA or name C or name O or name CB )) or resid 711 throu \ gh 733 or (resid 734 and (name N or name CA or name C or name O or name CB )) or \ resid 735 through 780 or (resid 781 and (name N or name CA or name C or name O \ or name CB )) or resid 782 through 804 or (resid 805 and (name N or name CA or n \ ame C or name O or name CB )) or resid 806 through 816)) selection = (chain 'S' and (resid 23 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 110 or resid 136 through 300 or (r \ esid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 t \ hrough 307 or (resid 308 and (name N or name CA or name C or name O or name CB ) \ ) or resid 309 through 317 or (resid 318 and (name N or name CA or name C or nam \ e O or name CB )) or resid 319 through 334 or (resid 335 and (name N or name CA \ or name C or name O or name CB )) or resid 336 through 500 or (resid 501 through \ 502 and (name N or name CA or name C or name O or name CB )) or resid 503 throu \ gh 525 or (resid 526 and (name N or name CA or name C or name O or name CB )) or \ resid 527 through 529 or (resid 530 through 536 and (name N or name CA or name \ C or name O or name CB )) or resid 537 through 541 or (resid 542 and (name N or \ name CA or name C or name O or name CB )) or resid 543 through 555 or (resid 556 \ and (name N or name CA or name C or name O or name CB )) or resid 557 through 5 \ 59 or (resid 560 through 563 and (name N or name CA or name C or name O or name \ CB )) or resid 564 or (resid 565 through 566 and (name N or name CA or name C or \ name O or name CB )) or resid 567 through 575 or (resid 576 and (name N or name \ CA or name C or name O or name CB )) or resid 577 through 582 or (resid 583 thr \ ough 584 and (name N or name CA or name C or name O or name CB )) or resid 585 o \ r (resid 586 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 87 through 619 or (resid 620 through 621 and (name N or name CA or name C or nam \ e O or name CB )) or resid 622 through 632 or (resid 633 and (name N or name CA \ or name C or name O or name CB )) or resid 634 through 640 or (resid 641 through \ 642 and (name N or name CA or name C or name O or name CB )) or resid 643 throu \ gh 647 or (resid 648 through 649 and (name N or name CA or name C or name O or n \ ame CB )) or resid 650 through 715 or (resid 716 and (name N or name CA or name \ C or name O or name CB )) or resid 717 through 722 or (resid 723 through 726 and \ (name N or name CA or name C or name O or name CB )) or resid 727 through 751 o \ r (resid 752 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 53 through 754 or (resid 755 and (name N or name CA or name C or name O or name \ CB )) or resid 756 through 759 or (resid 760 through 762 and (name N or name CA \ or name C or name O or name CB )) or resid 763 through 765 or (resid 766 and (na \ me N or name CA or name C or name O or name CB )) or resid 767 through 785 or (r \ esid 786 through 787 and (name N or name CA or name C or name O or name CB )) or \ resid 788 through 789 or (resid 790 and (name N or name CA or name C or name O \ or name CB )) or resid 791 through 809 or (resid 810 through 811 and (name N or \ name CA or name C or name O or name CB )) or resid 812 or (resid 813 through 814 \ and (name N or name CA or name C or name O or name CB )) or resid 815 through 8 \ 16)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.090 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 19268 Z= 0.210 Angle : 0.586 34.494 26303 Z= 0.291 Chirality : 0.104 4.938 3019 Planarity : 0.003 0.046 3379 Dihedral : 12.017 131.471 6538 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: -3.17 (0.14), residues: 2531 helix: -0.49 (0.16), residues: 820 sheet: -2.65 (0.21), residues: 443 loop : -3.07 (0.14), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 531 TYR 0.012 0.001 TYR S 386 PHE 0.016 0.001 PHE R 189 TRP 0.008 0.001 TRP R 291 HIS 0.002 0.000 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00415 (19247) covalent geometry : angle 0.58618 (26261) SS BOND : bond 0.00184 ( 21) SS BOND : angle 0.66845 ( 42) hydrogen bonds : bond 0.13658 ( 786) hydrogen bonds : angle 5.47899 ( 2301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 606 CYS cc_start: 0.6789 (p) cc_final: 0.6354 (p) REVERT: R 608 ILE cc_start: 0.8322 (pt) cc_final: 0.7960 (mt) REVERT: R 750 ARG cc_start: 0.4978 (tmt-80) cc_final: 0.4001 (mmt180) REVERT: S 198 ILE cc_start: 0.8833 (mm) cc_final: 0.8588 (mt) REVERT: D 34 MET cc_start: 0.5198 (pmm) cc_final: 0.3182 (mmt) REVERT: E 82 MET cc_start: 0.3086 (mmt) cc_final: 0.1227 (pmm) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1494 time to fit residues: 73.0094 Evaluate side-chains 236 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 73 ASN R 191 GLN R 365 HIS R 469 GLN S 73 ASN S 97 HIS S 101 GLN S 191 GLN S 365 HIS S 374 GLN S 469 GLN ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 592 HIS S 679 GLN S 690 GLN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS A 347 ASN B 62 HIS B 91 HIS B 142 HIS B 155 ASN B 156 GLN B 176 GLN B 230 ASN B 259 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN E 6 GLN E 13 GLN E 39 GLN E 76 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 113 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.118711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.104062 restraints weight = 45461.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.103929 restraints weight = 35532.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.104072 restraints weight = 30004.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.104211 restraints weight = 28534.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.104375 restraints weight = 25439.436| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19268 Z= 0.161 Angle : 0.553 8.204 26303 Z= 0.285 Chirality : 0.042 0.164 3019 Planarity : 0.004 0.049 3379 Dihedral : 5.405 110.989 2831 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.53 % Allowed : 14.11 % Favored : 84.37 % 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: -2.15 (0.16), residues: 2531 helix: 0.51 (0.17), residues: 836 sheet: -2.24 (0.21), residues: 486 loop : -2.53 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 243 TYR 0.015 0.002 TYR R 180 PHE 0.021 0.002 PHE B 199 TRP 0.014 0.001 TRP R 349 HIS 0.010 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00370 (19247) covalent geometry : angle 0.55066 (26261) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.32835 ( 42) hydrogen bonds : bond 0.03943 ( 786) hydrogen bonds : angle 4.50083 ( 2301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: R 379 MET cc_start: 0.8203 (ttp) cc_final: 0.7938 (ttp) REVERT: R 739 ILE cc_start: 0.7917 (mm) cc_final: 0.7553 (mt) REVERT: R 750 ARG cc_start: 0.4665 (tmt-80) cc_final: 0.3680 (mmt180) REVERT: S 198 ILE cc_start: 0.8637 (mm) cc_final: 0.8397 (mt) REVERT: B 88 ASN cc_start: 0.5238 (p0) cc_final: 0.4941 (p0) REVERT: D 34 MET cc_start: 0.5094 (pmm) cc_final: 0.3207 (mmt) REVERT: D 83 MET cc_start: 0.3597 (mtm) cc_final: 0.3340 (mtm) REVERT: D 93 MET cc_start: 0.5326 (tpp) cc_final: 0.4906 (ttp) REVERT: E 82 MET cc_start: 0.3346 (mmt) cc_final: 0.1332 (pmm) outliers start: 28 outliers final: 20 residues processed: 281 average time/residue: 0.1446 time to fit residues: 61.6931 Evaluate side-chains 258 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 HIS Chi-restraints excluded: chain R residue 796 VAL Chi-restraints excluded: chain R residue 815 HIS Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 694 VAL Chi-restraints excluded: chain S residue 774 LEU Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain F residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 14 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 97 HIS ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS E 73 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.115059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.099557 restraints weight = 45306.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.100118 restraints weight = 32498.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.100401 restraints weight = 28153.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.100808 restraints weight = 23781.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.100737 restraints weight = 20384.174| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19268 Z= 0.188 Angle : 0.577 8.036 26303 Z= 0.298 Chirality : 0.042 0.155 3019 Planarity : 0.004 0.051 3379 Dihedral : 5.735 112.735 2831 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.10 % Allowed : 16.01 % Favored : 80.88 % 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: -1.93 (0.16), residues: 2531 helix: 0.59 (0.18), residues: 842 sheet: -2.05 (0.22), residues: 491 loop : -2.35 (0.16), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 243 TYR 0.014 0.002 TYR D 59 PHE 0.027 0.002 PHE R 780 TRP 0.016 0.002 TRP B 339 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00437 (19247) covalent geometry : angle 0.57467 (26261) SS BOND : bond 0.00326 ( 21) SS BOND : angle 1.31045 ( 42) hydrogen bonds : bond 0.04225 ( 786) hydrogen bonds : angle 4.63609 ( 2301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: R 379 MET cc_start: 0.8304 (ttp) cc_final: 0.8014 (ttp) REVERT: R 416 ARG cc_start: 0.7211 (mtt90) cc_final: 0.6928 (mtt90) REVERT: R 519 CYS cc_start: 0.4265 (OUTLIER) cc_final: 0.2328 (m) REVERT: R 607 TYR cc_start: 0.8300 (m-80) cc_final: 0.8071 (m-80) REVERT: R 739 ILE cc_start: 0.7921 (mm) cc_final: 0.7544 (mt) REVERT: R 750 ARG cc_start: 0.5017 (tmt-80) cc_final: 0.3968 (mmt180) REVERT: S 49 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7221 (t0) REVERT: S 159 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: S 198 ILE cc_start: 0.8632 (mm) cc_final: 0.8363 (mt) REVERT: S 460 ARG cc_start: 0.5921 (mmm160) cc_final: 0.5706 (mmm160) REVERT: S 619 MET cc_start: 0.6116 (ppp) cc_final: 0.5860 (ppp) REVERT: S 779 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.7043 (mt) REVERT: A 309 ASP cc_start: 0.5795 (p0) cc_final: 0.5501 (p0) REVERT: A 349 LYS cc_start: 0.7640 (mtmm) cc_final: 0.7337 (mtpp) REVERT: B 88 ASN cc_start: 0.5263 (p0) cc_final: 0.5019 (p0) REVERT: D 34 MET cc_start: 0.5306 (pmm) cc_final: 0.3261 (mmt) REVERT: D 93 MET cc_start: 0.5421 (tpp) cc_final: 0.5066 (ttp) REVERT: E 34 MET cc_start: 0.7881 (ttt) cc_final: 0.7643 (ttt) outliers start: 57 outliers final: 41 residues processed: 290 average time/residue: 0.1395 time to fit residues: 61.9641 Evaluate side-chains 277 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 56 HIS Chi-restraints excluded: chain R residue 190 PHE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain R residue 519 CYS Chi-restraints excluded: chain R residue 588 VAL Chi-restraints excluded: chain R residue 595 THR Chi-restraints excluded: chain R residue 606 CYS Chi-restraints excluded: chain R residue 796 VAL Chi-restraints excluded: chain R residue 808 CYS Chi-restraints excluded: chain R residue 809 LEU Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 97 HIS Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 334 LEU Chi-restraints excluded: chain S residue 694 VAL Chi-restraints excluded: chain S residue 700 VAL Chi-restraints excluded: chain S residue 774 LEU Chi-restraints excluded: chain S residue 779 ILE Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 795 CYS Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 213 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 220 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 41 HIS S 338 ASN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.114814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099486 restraints weight = 45007.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.099618 restraints weight = 32243.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.099893 restraints weight = 29101.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100385 restraints weight = 25776.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100309 restraints weight = 20878.544| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19268 Z= 0.155 Angle : 0.545 7.721 26303 Z= 0.281 Chirality : 0.041 0.169 3019 Planarity : 0.004 0.047 3379 Dihedral : 5.648 112.346 2831 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.87 % Allowed : 18.03 % Favored : 78.10 % 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: -1.67 (0.16), residues: 2531 helix: 0.76 (0.18), residues: 843 sheet: -1.88 (0.22), residues: 487 loop : -2.18 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 243 TYR 0.011 0.001 TYR S 206 PHE 0.027 0.002 PHE R 747 TRP 0.018 0.001 TRP B 339 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00359 (19247) covalent geometry : angle 0.54337 (26261) SS BOND : bond 0.00265 ( 21) SS BOND : angle 1.05697 ( 42) hydrogen bonds : bond 0.03959 ( 786) hydrogen bonds : angle 4.52567 ( 2301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 240 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 379 MET cc_start: 0.8303 (ttp) cc_final: 0.8004 (ttp) REVERT: R 416 ARG cc_start: 0.7223 (mtt90) cc_final: 0.6951 (mtt90) REVERT: R 519 CYS cc_start: 0.4083 (OUTLIER) cc_final: 0.2277 (m) REVERT: R 607 TYR cc_start: 0.8307 (m-80) cc_final: 0.8019 (m-80) REVERT: R 739 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7492 (mt) REVERT: R 744 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6940 (tp) REVERT: R 750 ARG cc_start: 0.4710 (tmt-80) cc_final: 0.3809 (mmt180) REVERT: R 757 ASN cc_start: 0.7111 (p0) cc_final: 0.6905 (p0) REVERT: S 49 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7281 (t0) REVERT: S 198 ILE cc_start: 0.8623 (mm) cc_final: 0.8346 (mt) REVERT: S 455 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8253 (mp) REVERT: S 516 GLU cc_start: 0.3816 (OUTLIER) cc_final: 0.3516 (pt0) REVERT: S 779 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6984 (mt) REVERT: A 309 ASP cc_start: 0.5913 (p0) cc_final: 0.5645 (p0) REVERT: B 88 ASN cc_start: 0.5349 (p0) cc_final: 0.5076 (p0) REVERT: D 34 MET cc_start: 0.5348 (pmm) cc_final: 0.3340 (mmt) REVERT: D 83 MET cc_start: 0.3623 (mtm) cc_final: 0.3366 (mtm) REVERT: E 34 MET cc_start: 0.7714 (ttt) cc_final: 0.7493 (ttp) REVERT: E 112 THR cc_start: 0.6517 (p) cc_final: 0.6259 (p) outliers start: 71 outliers final: 47 residues processed: 293 average time/residue: 0.1395 time to fit residues: 62.5254 Evaluate side-chains 280 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 56 HIS Chi-restraints excluded: chain R residue 190 PHE Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain R residue 519 CYS Chi-restraints excluded: chain R residue 574 ILE Chi-restraints excluded: chain R residue 588 VAL Chi-restraints excluded: chain R residue 595 THR Chi-restraints excluded: chain R residue 606 CYS Chi-restraints excluded: chain R residue 694 VAL Chi-restraints excluded: chain R residue 739 ILE Chi-restraints excluded: chain R residue 744 LEU Chi-restraints excluded: chain R residue 796 VAL Chi-restraints excluded: chain R residue 809 LEU Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 97 HIS Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 334 LEU Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain S residue 516 GLU Chi-restraints excluded: chain S residue 572 VAL Chi-restraints excluded: chain S residue 576 CYS Chi-restraints excluded: chain S residue 583 LEU Chi-restraints excluded: chain S residue 694 VAL Chi-restraints excluded: chain S residue 729 LEU Chi-restraints excluded: chain S residue 774 LEU Chi-restraints excluded: chain S residue 779 ILE Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 795 CYS Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain F residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 182 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 250 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 199 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 338 ASN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN E 39 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.114504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.099101 restraints weight = 44892.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.098767 restraints weight = 33665.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098990 restraints weight = 27541.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.099242 restraints weight = 25311.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.099365 restraints weight = 22961.712| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19268 Z= 0.154 Angle : 0.551 10.715 26303 Z= 0.282 Chirality : 0.041 0.171 3019 Planarity : 0.004 0.063 3379 Dihedral : 5.670 111.732 2831 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.74 % Allowed : 19.44 % Favored : 75.82 % 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: -1.53 (0.16), residues: 2531 helix: 0.82 (0.18), residues: 845 sheet: -1.78 (0.22), residues: 506 loop : -2.06 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 71 TYR 0.010 0.001 TYR S 165 PHE 0.020 0.002 PHE S 189 TRP 0.019 0.001 TRP B 339 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00356 (19247) covalent geometry : angle 0.54828 (26261) SS BOND : bond 0.00238 ( 21) SS BOND : angle 1.39367 ( 42) hydrogen bonds : bond 0.03997 ( 786) hydrogen bonds : angle 4.53523 ( 2301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 236 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: R 95 ASP cc_start: 0.6391 (m-30) cc_final: 0.5944 (m-30) REVERT: R 379 MET cc_start: 0.8332 (ttp) cc_final: 0.7936 (ttp) REVERT: R 519 CYS cc_start: 0.4121 (OUTLIER) cc_final: 0.2385 (m) REVERT: R 607 TYR cc_start: 0.8295 (m-80) cc_final: 0.8069 (m-80) REVERT: R 739 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7485 (mt) REVERT: R 744 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7024 (tp) REVERT: R 750 ARG cc_start: 0.4753 (tmt-80) cc_final: 0.3820 (mmt180) REVERT: S 49 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7227 (t0) REVERT: S 198 ILE cc_start: 0.8604 (mm) cc_final: 0.8304 (mt) REVERT: S 516 GLU cc_start: 0.3908 (OUTLIER) cc_final: 0.3602 (pt0) REVERT: S 779 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6921 (mt) REVERT: A 221 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8087 (pt) REVERT: A 309 ASP cc_start: 0.5935 (p0) cc_final: 0.5705 (p0) REVERT: B 88 ASN cc_start: 0.5442 (p0) cc_final: 0.5118 (p0) REVERT: B 165 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7780 (p) REVERT: D 34 MET cc_start: 0.5396 (pmm) cc_final: 0.3366 (mmt) REVERT: E 82 MET cc_start: 0.3496 (mmt) cc_final: 0.1410 (pmm) REVERT: F 104 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.6230 (t-90) outliers start: 87 outliers final: 57 residues processed: 297 average time/residue: 0.1325 time to fit residues: 61.0101 Evaluate side-chains 294 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 228 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 56 HIS Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 190 PHE Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 404 THR Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain R residue 480 LEU Chi-restraints excluded: chain R residue 519 CYS Chi-restraints excluded: chain R residue 574 ILE Chi-restraints excluded: chain R residue 588 VAL Chi-restraints excluded: chain R residue 595 THR Chi-restraints excluded: chain R residue 606 CYS Chi-restraints excluded: chain R residue 694 VAL Chi-restraints excluded: chain R residue 739 ILE Chi-restraints excluded: chain R residue 744 LEU Chi-restraints excluded: chain R residue 773 TRP Chi-restraints excluded: chain R residue 796 VAL Chi-restraints excluded: chain R residue 808 CYS Chi-restraints excluded: chain R residue 809 LEU Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 97 HIS Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 234 CYS Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 334 LEU Chi-restraints excluded: chain S residue 376 SER Chi-restraints excluded: chain S residue 516 GLU Chi-restraints excluded: chain S residue 572 VAL Chi-restraints excluded: chain S residue 576 CYS Chi-restraints excluded: chain S residue 583 LEU Chi-restraints excluded: chain S residue 684 LEU Chi-restraints excluded: chain S residue 694 VAL Chi-restraints excluded: chain S residue 770 CYS Chi-restraints excluded: chain S residue 774 LEU Chi-restraints excluded: chain S residue 779 ILE Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 795 CYS Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 104 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 61 optimal weight: 0.9980 chunk 208 optimal weight: 9.9990 chunk 229 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 219 optimal weight: 0.4980 chunk 169 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 338 ASN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.115833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.101430 restraints weight = 43523.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.101133 restraints weight = 33321.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.101335 restraints weight = 27710.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.101431 restraints weight = 26420.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.101651 restraints weight = 23472.292| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19268 Z= 0.136 Angle : 0.534 10.354 26303 Z= 0.273 Chirality : 0.040 0.177 3019 Planarity : 0.004 0.053 3379 Dihedral : 5.599 112.121 2831 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.03 % Allowed : 20.97 % Favored : 75.00 % 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: -1.40 (0.16), residues: 2531 helix: 0.92 (0.18), residues: 844 sheet: -1.70 (0.22), residues: 497 loop : -1.98 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 71 TYR 0.011 0.001 TYR S 473 PHE 0.024 0.002 PHE S 422 TRP 0.023 0.001 TRP B 339 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00314 (19247) covalent geometry : angle 0.53299 (26261) SS BOND : bond 0.00249 ( 21) SS BOND : angle 0.95934 ( 42) hydrogen bonds : bond 0.03863 ( 786) hydrogen bonds : angle 4.44079 ( 2301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: R 95 ASP cc_start: 0.6340 (m-30) cc_final: 0.5915 (m-30) REVERT: R 379 MET cc_start: 0.8269 (ttp) cc_final: 0.7929 (ttp) REVERT: R 519 CYS cc_start: 0.4054 (OUTLIER) cc_final: 0.2332 (m) REVERT: R 744 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7058 (tp) REVERT: R 750 ARG cc_start: 0.4897 (tmt-80) cc_final: 0.4033 (mmt180) REVERT: R 757 ASN cc_start: 0.7018 (p0) cc_final: 0.6669 (p0) REVERT: S 49 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7172 (t0) REVERT: S 198 ILE cc_start: 0.8605 (mm) cc_final: 0.8319 (mt) REVERT: S 516 GLU cc_start: 0.3804 (OUTLIER) cc_final: 0.3561 (pt0) REVERT: S 688 SER cc_start: 0.7047 (m) cc_final: 0.6641 (p) REVERT: A 309 ASP cc_start: 0.5940 (p0) cc_final: 0.5719 (p0) REVERT: B 88 ASN cc_start: 0.5401 (p0) cc_final: 0.5115 (p0) REVERT: D 34 MET cc_start: 0.5516 (pmm) cc_final: 0.3474 (mmt) REVERT: D 83 MET cc_start: 0.3513 (mtm) cc_final: 0.3201 (mtm) REVERT: D 230 MET cc_start: 0.6778 (tmm) cc_final: 0.6578 (tmm) REVERT: E 82 MET cc_start: 0.3559 (mmt) cc_final: 0.1499 (pmm) outliers start: 74 outliers final: 54 residues processed: 285 average time/residue: 0.1391 time to fit residues: 60.7811 Evaluate side-chains 284 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 56 HIS Chi-restraints excluded: chain R residue 190 PHE Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 404 THR Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain R residue 480 LEU Chi-restraints excluded: chain R residue 519 CYS Chi-restraints excluded: chain R residue 553 CYS Chi-restraints excluded: chain R residue 574 ILE Chi-restraints excluded: chain R residue 588 VAL Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 606 CYS Chi-restraints excluded: chain R residue 694 VAL Chi-restraints excluded: chain R residue 739 ILE Chi-restraints excluded: chain R residue 744 LEU Chi-restraints excluded: chain R residue 773 TRP Chi-restraints excluded: chain R residue 808 CYS Chi-restraints excluded: chain R residue 809 LEU Chi-restraints excluded: chain R residue 815 HIS Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 97 HIS Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 334 LEU Chi-restraints excluded: chain S residue 376 SER Chi-restraints excluded: chain S residue 516 GLU Chi-restraints excluded: chain S residue 572 VAL Chi-restraints excluded: chain S residue 576 CYS Chi-restraints excluded: chain S residue 583 LEU Chi-restraints excluded: chain S residue 684 LEU Chi-restraints excluded: chain S residue 694 VAL Chi-restraints excluded: chain S residue 729 LEU Chi-restraints excluded: chain S residue 760 LYS Chi-restraints excluded: chain S residue 770 CYS Chi-restraints excluded: chain S residue 774 LEU Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 205 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 206 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 237 optimal weight: 4.9990 chunk 150 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.115771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.101491 restraints weight = 44240.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.101015 restraints weight = 37008.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101576 restraints weight = 32974.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.101907 restraints weight = 26394.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.102065 restraints weight = 22821.904| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19268 Z= 0.141 Angle : 0.540 9.680 26303 Z= 0.275 Chirality : 0.041 0.182 3019 Planarity : 0.004 0.049 3379 Dihedral : 5.609 111.737 2831 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.08 % Allowed : 21.41 % Favored : 74.51 % 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: -1.33 (0.16), residues: 2531 helix: 0.94 (0.18), residues: 843 sheet: -1.67 (0.23), residues: 495 loop : -1.89 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 71 TYR 0.018 0.001 TYR S 473 PHE 0.027 0.002 PHE S 422 TRP 0.026 0.001 TRP B 339 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00326 (19247) covalent geometry : angle 0.53909 (26261) SS BOND : bond 0.00230 ( 21) SS BOND : angle 0.96854 ( 42) hydrogen bonds : bond 0.03908 ( 786) hydrogen bonds : angle 4.43027 ( 2301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: R 95 ASP cc_start: 0.6368 (m-30) cc_final: 0.5955 (m-30) REVERT: R 379 MET cc_start: 0.8256 (ttp) cc_final: 0.7945 (ttp) REVERT: R 519 CYS cc_start: 0.4103 (OUTLIER) cc_final: 0.2462 (m) REVERT: R 637 LEU cc_start: 0.7626 (mt) cc_final: 0.7326 (mp) REVERT: R 744 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7164 (tp) REVERT: R 750 ARG cc_start: 0.5164 (tmt-80) cc_final: 0.4089 (tpt170) REVERT: R 757 ASN cc_start: 0.7193 (p0) cc_final: 0.6967 (p0) REVERT: S 49 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7170 (t0) REVERT: S 198 ILE cc_start: 0.8635 (mm) cc_final: 0.8366 (mt) REVERT: S 516 GLU cc_start: 0.3799 (OUTLIER) cc_final: 0.3461 (pt0) REVERT: S 688 SER cc_start: 0.7038 (m) cc_final: 0.6659 (p) REVERT: A 221 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8136 (pt) REVERT: B 88 ASN cc_start: 0.5511 (p0) cc_final: 0.5209 (p0) REVERT: B 241 PHE cc_start: 0.7392 (p90) cc_final: 0.7154 (p90) REVERT: B 260 GLU cc_start: 0.3600 (mm-30) cc_final: 0.2636 (tt0) REVERT: D 34 MET cc_start: 0.5573 (pmm) cc_final: 0.3549 (mmt) REVERT: D 83 MET cc_start: 0.3483 (mtm) cc_final: 0.3202 (mtm) REVERT: D 100 ILE cc_start: 0.6639 (tp) cc_final: 0.6327 (pt) REVERT: E 82 MET cc_start: 0.3627 (mmt) cc_final: 0.1722 (pmm) REVERT: E 112 THR cc_start: 0.6914 (p) cc_final: 0.6587 (t) outliers start: 75 outliers final: 61 residues processed: 288 average time/residue: 0.1272 time to fit residues: 57.2827 Evaluate side-chains 288 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 56 HIS Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 190 PHE Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 404 THR Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain R residue 480 LEU Chi-restraints excluded: chain R residue 519 CYS Chi-restraints excluded: chain R residue 553 CYS Chi-restraints excluded: chain R residue 574 ILE Chi-restraints excluded: chain R residue 588 VAL Chi-restraints excluded: chain R residue 595 THR Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 606 CYS Chi-restraints excluded: chain R residue 739 ILE Chi-restraints excluded: chain R residue 744 LEU Chi-restraints excluded: chain R residue 773 TRP Chi-restraints excluded: chain R residue 808 CYS Chi-restraints excluded: chain R residue 809 LEU Chi-restraints excluded: chain R residue 815 HIS Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 97 HIS Chi-restraints excluded: chain S residue 188 ASP Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 334 LEU Chi-restraints excluded: chain S residue 376 SER Chi-restraints excluded: chain S residue 460 ARG Chi-restraints excluded: chain S residue 516 GLU Chi-restraints excluded: chain S residue 572 VAL Chi-restraints excluded: chain S residue 576 CYS Chi-restraints excluded: chain S residue 583 LEU Chi-restraints excluded: chain S residue 684 LEU Chi-restraints excluded: chain S residue 694 VAL Chi-restraints excluded: chain S residue 729 LEU Chi-restraints excluded: chain S residue 760 LYS Chi-restraints excluded: chain S residue 770 CYS Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 104 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 112 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 206 optimal weight: 0.0060 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 91 optimal weight: 0.0170 chunk 237 optimal weight: 0.8980 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 259 GLN ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.116086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101574 restraints weight = 43764.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.101481 restraints weight = 32289.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101765 restraints weight = 26719.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.101845 restraints weight = 23808.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.102069 restraints weight = 22150.727| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19268 Z= 0.125 Angle : 0.530 9.688 26303 Z= 0.271 Chirality : 0.040 0.183 3019 Planarity : 0.004 0.046 3379 Dihedral : 5.503 110.445 2831 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.98 % Allowed : 21.79 % Favored : 74.24 % 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: -1.21 (0.17), residues: 2531 helix: 1.05 (0.18), residues: 841 sheet: -1.66 (0.22), residues: 499 loop : -1.79 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 71 TYR 0.016 0.001 TYR S 473 PHE 0.022 0.002 PHE A 191 TRP 0.025 0.001 TRP R 697 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00286 (19247) covalent geometry : angle 0.52896 (26261) SS BOND : bond 0.00203 ( 21) SS BOND : angle 0.84763 ( 42) hydrogen bonds : bond 0.03758 ( 786) hydrogen bonds : angle 4.33765 ( 2301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 233 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 95 ASP cc_start: 0.6316 (m-30) cc_final: 0.5898 (m-30) REVERT: R 379 MET cc_start: 0.8245 (ttp) cc_final: 0.7936 (ttp) REVERT: R 519 CYS cc_start: 0.4104 (OUTLIER) cc_final: 0.2448 (m) REVERT: R 574 ILE cc_start: 0.6044 (OUTLIER) cc_final: 0.5633 (mt) REVERT: R 637 LEU cc_start: 0.7658 (mt) cc_final: 0.7345 (mp) REVERT: R 750 ARG cc_start: 0.4925 (tmt-80) cc_final: 0.4048 (tpt170) REVERT: R 757 ASN cc_start: 0.7101 (p0) cc_final: 0.6830 (p0) REVERT: S 49 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7086 (t0) REVERT: S 198 ILE cc_start: 0.8618 (mm) cc_final: 0.8347 (mt) REVERT: S 516 GLU cc_start: 0.3689 (OUTLIER) cc_final: 0.3408 (pt0) REVERT: S 688 SER cc_start: 0.7012 (m) cc_final: 0.6621 (p) REVERT: A 221 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8113 (pt) REVERT: B 88 ASN cc_start: 0.5601 (p0) cc_final: 0.5188 (p0) REVERT: B 241 PHE cc_start: 0.7378 (p90) cc_final: 0.7166 (p90) REVERT: D 34 MET cc_start: 0.5490 (pmm) cc_final: 0.3471 (mmt) REVERT: D 83 MET cc_start: 0.3502 (mtm) cc_final: 0.3225 (mtm) REVERT: D 100 ILE cc_start: 0.6568 (tp) cc_final: 0.6319 (tt) REVERT: E 82 MET cc_start: 0.3592 (mmt) cc_final: 0.1555 (pmm) REVERT: E 112 THR cc_start: 0.6979 (p) cc_final: 0.6608 (t) REVERT: F 105 ASN cc_start: 0.6808 (t0) cc_final: 0.6523 (t0) outliers start: 73 outliers final: 59 residues processed: 289 average time/residue: 0.1293 time to fit residues: 58.4608 Evaluate side-chains 293 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 229 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 190 PHE Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 229 ARG Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain R residue 480 LEU Chi-restraints excluded: chain R residue 519 CYS Chi-restraints excluded: chain R residue 553 CYS Chi-restraints excluded: chain R residue 574 ILE Chi-restraints excluded: chain R residue 595 THR Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 606 CYS Chi-restraints excluded: chain R residue 644 SER Chi-restraints excluded: chain R residue 739 ILE Chi-restraints excluded: chain R residue 773 TRP Chi-restraints excluded: chain R residue 808 CYS Chi-restraints excluded: chain R residue 809 LEU Chi-restraints excluded: chain R residue 815 HIS Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 97 HIS Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 334 LEU Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 376 SER Chi-restraints excluded: chain S residue 516 GLU Chi-restraints excluded: chain S residue 572 VAL Chi-restraints excluded: chain S residue 576 CYS Chi-restraints excluded: chain S residue 583 LEU Chi-restraints excluded: chain S residue 684 LEU Chi-restraints excluded: chain S residue 729 LEU Chi-restraints excluded: chain S residue 760 LYS Chi-restraints excluded: chain S residue 770 CYS Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 68 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 128 optimal weight: 0.0370 chunk 245 optimal weight: 0.9990 chunk 202 optimal weight: 0.3980 chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 340 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.115677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.101374 restraints weight = 43623.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100989 restraints weight = 34670.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.101223 restraints weight = 28812.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.101391 restraints weight = 24932.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.101532 restraints weight = 23330.694| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19268 Z= 0.132 Angle : 0.546 9.557 26303 Z= 0.279 Chirality : 0.040 0.189 3019 Planarity : 0.004 0.046 3379 Dihedral : 5.510 109.852 2831 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.14 % Allowed : 21.84 % Favored : 74.02 % 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: -1.20 (0.17), residues: 2531 helix: 1.04 (0.18), residues: 842 sheet: -1.71 (0.22), residues: 505 loop : -1.73 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 71 TYR 0.017 0.001 TYR S 473 PHE 0.024 0.002 PHE A 191 TRP 0.024 0.001 TRP B 339 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00305 (19247) covalent geometry : angle 0.54562 (26261) SS BOND : bond 0.00215 ( 21) SS BOND : angle 0.91568 ( 42) hydrogen bonds : bond 0.03816 ( 786) hydrogen bonds : angle 4.35261 ( 2301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 233 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ASP cc_start: 0.6299 (m-30) cc_final: 0.5893 (m-30) REVERT: R 379 MET cc_start: 0.8267 (ttp) cc_final: 0.7943 (ttp) REVERT: R 519 CYS cc_start: 0.4047 (OUTLIER) cc_final: 0.2401 (m) REVERT: R 574 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5655 (mt) REVERT: R 637 LEU cc_start: 0.7655 (mt) cc_final: 0.7340 (mp) REVERT: R 739 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7672 (mt) REVERT: R 750 ARG cc_start: 0.4889 (tmt-80) cc_final: 0.3930 (tpt170) REVERT: R 757 ASN cc_start: 0.7043 (p0) cc_final: 0.6787 (p0) REVERT: S 49 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7140 (t0) REVERT: S 198 ILE cc_start: 0.8624 (mm) cc_final: 0.8348 (mt) REVERT: S 516 GLU cc_start: 0.3669 (OUTLIER) cc_final: 0.3381 (pt0) REVERT: S 688 SER cc_start: 0.6987 (m) cc_final: 0.6585 (p) REVERT: A 37 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7440 (pp) REVERT: A 221 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8105 (pt) REVERT: B 88 ASN cc_start: 0.5892 (p0) cc_final: 0.5409 (p0) REVERT: B 241 PHE cc_start: 0.7371 (p90) cc_final: 0.7169 (p90) REVERT: B 260 GLU cc_start: 0.3688 (mm-30) cc_final: 0.2786 (tt0) REVERT: D 34 MET cc_start: 0.5520 (pmm) cc_final: 0.3485 (mmt) REVERT: D 83 MET cc_start: 0.3555 (mtm) cc_final: 0.3307 (mtm) REVERT: D 100 ILE cc_start: 0.6766 (tp) cc_final: 0.6552 (tt) REVERT: E 112 THR cc_start: 0.7073 (p) cc_final: 0.6700 (t) outliers start: 76 outliers final: 62 residues processed: 292 average time/residue: 0.1311 time to fit residues: 59.6099 Evaluate side-chains 297 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 228 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 190 PHE Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 404 THR Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain R residue 480 LEU Chi-restraints excluded: chain R residue 519 CYS Chi-restraints excluded: chain R residue 553 CYS Chi-restraints excluded: chain R residue 574 ILE Chi-restraints excluded: chain R residue 588 VAL Chi-restraints excluded: chain R residue 595 THR Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 606 CYS Chi-restraints excluded: chain R residue 644 SER Chi-restraints excluded: chain R residue 739 ILE Chi-restraints excluded: chain R residue 743 THR Chi-restraints excluded: chain R residue 773 TRP Chi-restraints excluded: chain R residue 808 CYS Chi-restraints excluded: chain R residue 809 LEU Chi-restraints excluded: chain R residue 815 HIS Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 97 HIS Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 334 LEU Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 376 SER Chi-restraints excluded: chain S residue 516 GLU Chi-restraints excluded: chain S residue 572 VAL Chi-restraints excluded: chain S residue 576 CYS Chi-restraints excluded: chain S residue 583 LEU Chi-restraints excluded: chain S residue 684 LEU Chi-restraints excluded: chain S residue 729 LEU Chi-restraints excluded: chain S residue 760 LYS Chi-restraints excluded: chain S residue 770 CYS Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 181 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 247 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.116671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.102264 restraints weight = 43702.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.102328 restraints weight = 43057.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.102641 restraints weight = 35050.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.103175 restraints weight = 30915.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.103281 restraints weight = 26920.879| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19268 Z= 0.161 Angle : 0.568 9.905 26303 Z= 0.291 Chirality : 0.041 0.198 3019 Planarity : 0.004 0.046 3379 Dihedral : 5.649 109.847 2831 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.14 % Allowed : 21.68 % Favored : 74.18 % 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: -1.23 (0.17), residues: 2531 helix: 0.92 (0.18), residues: 846 sheet: -1.69 (0.22), residues: 513 loop : -1.70 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 71 TYR 0.019 0.001 TYR S 473 PHE 0.027 0.002 PHE R 747 TRP 0.037 0.002 TRP A 211 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00373 (19247) covalent geometry : angle 0.56661 (26261) SS BOND : bond 0.00264 ( 21) SS BOND : angle 1.07237 ( 42) hydrogen bonds : bond 0.04038 ( 786) hydrogen bonds : angle 4.47820 ( 2301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5062 Ramachandran restraints generated. 2531 Oldfield, 0 Emsley, 2531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 234 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ASP cc_start: 0.6372 (m-30) cc_final: 0.5972 (m-30) REVERT: R 379 MET cc_start: 0.8267 (ttp) cc_final: 0.7968 (ttp) REVERT: R 519 CYS cc_start: 0.4116 (OUTLIER) cc_final: 0.2603 (m) REVERT: R 637 LEU cc_start: 0.7528 (mt) cc_final: 0.7216 (mp) REVERT: R 739 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7721 (mt) REVERT: R 750 ARG cc_start: 0.4760 (tmt-80) cc_final: 0.4049 (tpt170) REVERT: R 757 ASN cc_start: 0.7090 (p0) cc_final: 0.6847 (p0) REVERT: S 49 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7130 (t0) REVERT: S 198 ILE cc_start: 0.8680 (mm) cc_final: 0.8402 (mt) REVERT: S 516 GLU cc_start: 0.3677 (OUTLIER) cc_final: 0.3318 (pt0) REVERT: S 688 SER cc_start: 0.7004 (m) cc_final: 0.6651 (p) REVERT: A 37 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7531 (pp) REVERT: A 221 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8161 (pt) REVERT: B 88 ASN cc_start: 0.5892 (p0) cc_final: 0.5387 (p0) REVERT: B 241 PHE cc_start: 0.7382 (p90) cc_final: 0.7174 (p90) REVERT: B 260 GLU cc_start: 0.3748 (mm-30) cc_final: 0.2854 (tt0) REVERT: D 34 MET cc_start: 0.5654 (pmm) cc_final: 0.3701 (mmt) REVERT: D 83 MET cc_start: 0.3517 (mtm) cc_final: 0.3269 (mtm) REVERT: D 100 ILE cc_start: 0.6696 (tp) cc_final: 0.6471 (tt) REVERT: E 112 THR cc_start: 0.7069 (p) cc_final: 0.6808 (t) outliers start: 76 outliers final: 68 residues processed: 291 average time/residue: 0.1298 time to fit residues: 59.2980 Evaluate side-chains 306 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 232 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 190 PHE Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 404 THR Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain R residue 480 LEU Chi-restraints excluded: chain R residue 519 CYS Chi-restraints excluded: chain R residue 553 CYS Chi-restraints excluded: chain R residue 574 ILE Chi-restraints excluded: chain R residue 588 VAL Chi-restraints excluded: chain R residue 595 THR Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 606 CYS Chi-restraints excluded: chain R residue 644 SER Chi-restraints excluded: chain R residue 739 ILE Chi-restraints excluded: chain R residue 743 THR Chi-restraints excluded: chain R residue 773 TRP Chi-restraints excluded: chain R residue 808 CYS Chi-restraints excluded: chain R residue 809 LEU Chi-restraints excluded: chain R residue 815 HIS Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 97 HIS Chi-restraints excluded: chain S residue 188 ASP Chi-restraints excluded: chain S residue 221 ILE Chi-restraints excluded: chain S residue 290 THR Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 334 LEU Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 376 SER Chi-restraints excluded: chain S residue 460 ARG Chi-restraints excluded: chain S residue 516 GLU Chi-restraints excluded: chain S residue 572 VAL Chi-restraints excluded: chain S residue 576 CYS Chi-restraints excluded: chain S residue 583 LEU Chi-restraints excluded: chain S residue 684 LEU Chi-restraints excluded: chain S residue 729 LEU Chi-restraints excluded: chain S residue 760 LYS Chi-restraints excluded: chain S residue 770 CYS Chi-restraints excluded: chain S residue 792 THR Chi-restraints excluded: chain S residue 804 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 104 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 43 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 172 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.116484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.102165 restraints weight = 43804.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.102300 restraints weight = 42364.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.102635 restraints weight = 39005.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.103030 restraints weight = 33424.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.103137 restraints weight = 27274.134| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19268 Z= 0.161 Angle : 0.570 10.188 26303 Z= 0.292 Chirality : 0.041 0.195 3019 Planarity : 0.004 0.122 3379 Dihedral : 5.727 109.660 2831 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.14 % Allowed : 21.62 % Favored : 74.24 % 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: -1.22 (0.17), residues: 2531 helix: 0.92 (0.18), residues: 846 sheet: -1.64 (0.22), residues: 503 loop : -1.71 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 71 TYR 0.019 0.001 TYR S 473 PHE 0.022 0.002 PHE A 191 TRP 0.038 0.002 TRP A 211 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00375 (19247) covalent geometry : angle 0.56845 (26261) SS BOND : bond 0.00261 ( 21) SS BOND : angle 1.05386 ( 42) hydrogen bonds : bond 0.04045 ( 786) hydrogen bonds : angle 4.49226 ( 2301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.32 seconds wall clock time: 53 minutes 31.30 seconds (3211.30 seconds total)