Starting phenix.real_space_refine on Wed Feb 4 23:34:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lm5_63216/02_2026/9lm5_63216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lm5_63216/02_2026/9lm5_63216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lm5_63216/02_2026/9lm5_63216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lm5_63216/02_2026/9lm5_63216.map" model { file = "/net/cci-nas-00/data/ceres_data/9lm5_63216/02_2026/9lm5_63216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lm5_63216/02_2026/9lm5_63216.cif" } resolution = 2.77 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8482 2.51 5 N 2232 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13472 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3500 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3496 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3500 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "E" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "F" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Time building chain proxies: 3.18, per 1000 atoms: 0.24 Number of scatterers: 13472 At special positions: 0 Unit cell: (141.55, 153.9, 133.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2674 8.00 N 2232 7.00 C 8482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 98 " distance=2.05 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: 1.05 Conformation dependent library (CDL) restraints added in 463.2 milliseconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3270 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 27 sheets defined 30.8% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 73 through 95 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 217 through 239 removed outlier: 4.229A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.806A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.852A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 518 removed outlier: 3.630A pdb=" N GLY A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 95 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 217 through 239 removed outlier: 4.162A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.775A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.826A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 518 removed outlier: 3.544A pdb=" N GLY B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 94 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 217 through 239 removed outlier: 4.144A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.762A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.843A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 518 removed outlier: 3.652A pdb=" N GLY C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'E' and resid 64 through 67 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 112 through 116 removed outlier: 3.531A pdb=" N PHE F 116 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 361 removed outlier: 8.025A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 361 removed outlier: 8.025A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 6.603A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.610A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 361 removed outlier: 8.053A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 361 removed outlier: 8.053A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 6.603A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.402A pdb=" N ILE B 395 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP B 489 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 434 removed outlier: 6.633A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 359 through 361 removed outlier: 7.982A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 359 through 361 removed outlier: 7.982A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 6.673A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 56 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'C' and resid 430 through 434 removed outlier: 6.554A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 5 through 10 removed outlier: 3.829A pdb=" N LEU D 81 " --> pdb=" O CYS D 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.832A pdb=" N GLY D 13 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER D 128 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL D 15 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET D 37 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.832A pdb=" N GLY D 13 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER D 128 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL D 15 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 118 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 5 through 10 removed outlier: 3.890A pdb=" N LEU E 81 " --> pdb=" O CYS E 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 13 through 16 removed outlier: 6.778A pdb=" N GLY E 13 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER E 128 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL E 15 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N MET E 37 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP E 39 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 13 through 16 removed outlier: 6.778A pdb=" N GLY E 13 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER E 128 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL E 15 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 5 through 10 Processing sheet with id=AC8, first strand: chain 'F' and resid 13 through 16 removed outlier: 6.803A pdb=" N GLY F 13 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER F 128 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 15 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET F 37 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA F 53 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 13 through 16 removed outlier: 6.803A pdb=" N GLY F 13 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER F 128 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 15 " --> pdb=" O SER F 128 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1728 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: 2.43 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4367 1.34 - 1.46: 2748 1.46 - 1.58: 6459 1.58 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 13688 Sorted by residual: bond pdb=" CA SER F 24 " pdb=" CB SER F 24 " ideal model delta sigma weight residual 1.534 1.485 0.050 1.60e-02 3.91e+03 9.62e+00 bond pdb=" N LEU D 81 " pdb=" CA LEU D 81 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.65e+00 bond pdb=" CA SER F 28 " pdb=" CB SER F 28 " ideal model delta sigma weight residual 1.533 1.490 0.044 1.72e-02 3.38e+03 6.49e+00 bond pdb=" CA ALA E 104 " pdb=" CB ALA E 104 " ideal model delta sigma weight residual 1.529 1.488 0.042 1.64e-02 3.72e+03 6.41e+00 bond pdb=" CA ALA D 104 " pdb=" CB ALA D 104 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.65e-02 3.67e+03 5.38e+00 ... (remaining 13683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 18166 1.89 - 3.78: 333 3.78 - 5.66: 39 5.66 - 7.55: 6 7.55 - 9.44: 3 Bond angle restraints: 18547 Sorted by residual: angle pdb=" CA SER F 24 " pdb=" C SER F 24 " pdb=" O SER F 24 " ideal model delta sigma weight residual 121.68 117.72 3.96 1.18e+00 7.18e-01 1.13e+01 angle pdb=" N LEU D 83 " pdb=" CA LEU D 83 " pdb=" CB LEU D 83 " ideal model delta sigma weight residual 110.82 116.75 -5.93 1.85e+00 2.92e-01 1.03e+01 angle pdb=" CA TYR D 82 " pdb=" CB TYR D 82 " pdb=" CG TYR D 82 " ideal model delta sigma weight residual 113.90 119.57 -5.67 1.80e+00 3.09e-01 9.92e+00 angle pdb=" CB MET E 95 " pdb=" CG MET E 95 " pdb=" SD MET E 95 " ideal model delta sigma weight residual 112.70 122.14 -9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" CA THR E 80 " pdb=" C THR E 80 " pdb=" O THR E 80 " ideal model delta sigma weight residual 121.11 117.55 3.56 1.17e+00 7.31e-01 9.24e+00 ... (remaining 18542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7170 17.96 - 35.92: 826 35.92 - 53.89: 223 53.89 - 71.85: 76 71.85 - 89.81: 15 Dihedral angle restraints: 8310 sinusoidal: 3216 harmonic: 5094 Sorted by residual: dihedral pdb=" CB CYS B 69 " pdb=" SG CYS B 69 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -147.83 61.83 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -147.12 61.12 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -144.41 58.41 1 1.00e+01 1.00e-02 4.57e+01 ... (remaining 8307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1578 0.042 - 0.084: 446 0.084 - 0.126: 128 0.126 - 0.167: 14 0.167 - 0.209: 3 Chirality restraints: 2169 Sorted by residual: chirality pdb=" CB THR B 400 " pdb=" CA THR B 400 " pdb=" OG1 THR B 400 " pdb=" CG2 THR B 400 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA MET D 85 " pdb=" N MET D 85 " pdb=" C MET D 85 " pdb=" CB MET D 85 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA CYS D 25 " pdb=" N CYS D 25 " pdb=" C CYS D 25 " pdb=" CB CYS D 25 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 2166 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 22 " -0.015 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ARG F 22 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG F 22 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU F 23 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 505 " -0.024 2.00e-02 2.50e+03 2.20e-02 8.48e+00 pdb=" CG PHE A 505 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 505 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 505 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 505 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 505 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 505 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 319 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO B 320 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " -0.033 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1192 2.74 - 3.28: 12924 3.28 - 3.82: 22587 3.82 - 4.36: 27389 4.36 - 4.90: 48097 Nonbonded interactions: 112189 Sorted by model distance: nonbonded pdb=" O ALA F 104 " pdb=" OH TYR F 111 " model vdw 2.204 3.040 nonbonded pdb=" O ARG B 49 " pdb=" OG1 THR B 369 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP A 310 " pdb=" NH1 ARG A 364 " model vdw 2.223 3.120 nonbonded pdb=" O ARG A 49 " pdb=" OG1 THR A 369 " model vdw 2.241 3.040 nonbonded pdb=" OE2 GLU A 30 " pdb=" OG1 THR A 408 " model vdw 2.257 3.040 ... (remaining 112184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 519)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 519)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 0.050 13715 Z= 0.208 Angle : 0.650 9.441 18601 Z= 0.390 Chirality : 0.043 0.209 2169 Planarity : 0.004 0.059 2360 Dihedral : 17.202 89.809 4959 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.49 % Allowed : 24.00 % Favored : 73.51 % 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: -0.40 (0.20), residues: 1737 helix: 1.42 (0.26), residues: 429 sheet: -0.35 (0.23), residues: 459 loop : -1.08 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.018 0.001 TYR D 82 PHE 0.049 0.002 PHE A 505 TRP 0.014 0.002 TRP D 105 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00408 (13688) covalent geometry : angle 0.64682 (18547) SS BOND : bond 0.00549 ( 27) SS BOND : angle 1.31832 ( 54) hydrogen bonds : bond 0.15453 ( 672) hydrogen bonds : angle 6.59539 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8489 (m) REVERT: D 118 TYR cc_start: 0.8280 (m-80) cc_final: 0.8015 (m-80) REVERT: E 9 GLU cc_start: 0.7914 (mp0) cc_final: 0.7319 (mp0) REVERT: E 41 ARG cc_start: 0.8853 (ptt180) cc_final: 0.8337 (ptt180) REVERT: F 9 GLU cc_start: 0.8087 (mp0) cc_final: 0.7678 (mp0) REVERT: F 31 THR cc_start: 0.8619 (p) cc_final: 0.8206 (p) outliers start: 38 outliers final: 17 residues processed: 295 average time/residue: 0.6119 time to fit residues: 197.2630 Evaluate side-chains 213 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain F residue 75 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 317 HIS A 454 ASN B 27 ASN C 345 ASN D 74 GLN D 102 ASN E 79 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056579 restraints weight = 33367.085| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.25 r_work: 0.2710 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13715 Z= 0.137 Angle : 0.557 10.104 18601 Z= 0.294 Chirality : 0.041 0.175 2169 Planarity : 0.004 0.051 2360 Dihedral : 5.532 83.746 1896 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.47 % Allowed : 24.72 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1737 helix: 1.87 (0.25), residues: 435 sheet: -0.31 (0.22), residues: 489 loop : -0.85 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 22 TYR 0.016 0.001 TYR E 32 PHE 0.023 0.001 PHE A 505 TRP 0.008 0.001 TRP D 105 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00316 (13688) covalent geometry : angle 0.55691 (18547) SS BOND : bond 0.00289 ( 27) SS BOND : angle 0.58030 ( 54) hydrogen bonds : bond 0.03304 ( 672) hydrogen bonds : angle 5.07436 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.537 Fit side-chains REVERT: A 227 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8430 (t0) REVERT: B 152 VAL cc_start: 0.8797 (t) cc_final: 0.8508 (m) REVERT: B 440 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8372 (t0) REVERT: B 505 PHE cc_start: 0.9092 (t80) cc_final: 0.8890 (t80) REVERT: B 508 LYS cc_start: 0.9753 (OUTLIER) cc_final: 0.9461 (ttpp) REVERT: C 201 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9153 (mtmt) REVERT: C 440 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8343 (t0) REVERT: C 462 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8071 (tp40) REVERT: D 62 TYR cc_start: 0.8805 (m-80) cc_final: 0.8602 (m-80) REVERT: D 74 GLN cc_start: 0.8809 (tt0) cc_final: 0.7688 (tm-30) REVERT: D 75 ASP cc_start: 0.7432 (t70) cc_final: 0.6393 (t0) REVERT: D 95 MET cc_start: 0.9318 (tpp) cc_final: 0.9067 (tpp) REVERT: D 97 PHE cc_start: 0.8805 (m-80) cc_final: 0.8564 (m-10) REVERT: D 124 GLN cc_start: 0.9318 (mm-40) cc_final: 0.9082 (tp-100) REVERT: E 3 MET cc_start: 0.8186 (ppp) cc_final: 0.7816 (ppp) REVERT: E 9 GLU cc_start: 0.6823 (mp0) cc_final: 0.6222 (mp0) REVERT: E 39 TRP cc_start: 0.8719 (m100) cc_final: 0.8490 (m100) REVERT: E 62 TYR cc_start: 0.8641 (m-80) cc_final: 0.8258 (m-80) REVERT: E 95 MET cc_start: 0.9454 (tpp) cc_final: 0.9239 (tpp) REVERT: E 97 PHE cc_start: 0.8846 (m-80) cc_final: 0.8416 (m-10) REVERT: E 121 GLN cc_start: 0.8227 (pm20) cc_final: 0.7594 (pm20) REVERT: F 9 GLU cc_start: 0.6441 (mp0) cc_final: 0.6168 (mp0) REVERT: F 118 TYR cc_start: 0.8111 (m-10) cc_final: 0.7806 (m-10) REVERT: F 121 GLN cc_start: 0.8052 (pm20) cc_final: 0.7719 (pm20) outliers start: 53 outliers final: 24 residues processed: 255 average time/residue: 0.5678 time to fit residues: 159.3256 Evaluate side-chains 230 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 17 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN E 102 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054329 restraints weight = 34248.782| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.24 r_work: 0.2672 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13715 Z= 0.184 Angle : 0.551 8.976 18601 Z= 0.288 Chirality : 0.041 0.136 2169 Planarity : 0.004 0.051 2360 Dihedral : 4.736 59.902 1877 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.04 % Allowed : 24.40 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1737 helix: 2.05 (0.25), residues: 435 sheet: -0.36 (0.22), residues: 495 loop : -0.84 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 22 TYR 0.017 0.001 TYR E 118 PHE 0.019 0.001 PHE D 70 TRP 0.006 0.001 TRP B 314 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00426 (13688) covalent geometry : angle 0.55131 (18547) SS BOND : bond 0.00347 ( 27) SS BOND : angle 0.52867 ( 54) hydrogen bonds : bond 0.03086 ( 672) hydrogen bonds : angle 4.82752 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 195 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8423 (pptt) REVERT: A 227 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8550 (t0) REVERT: A 317 HIS cc_start: 0.9262 (OUTLIER) cc_final: 0.9059 (m90) REVERT: B 29 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8392 (p) REVERT: B 65 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8298 (pptt) REVERT: B 440 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8383 (t0) REVERT: B 507 ARG cc_start: 0.9128 (ttp80) cc_final: 0.8863 (ttp80) REVERT: B 508 LYS cc_start: 0.9753 (OUTLIER) cc_final: 0.9494 (ttpp) REVERT: C 365 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.8886 (p) REVERT: C 419 LYS cc_start: 0.9547 (mptm) cc_final: 0.9252 (mmmm) REVERT: C 440 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8452 (t0) REVERT: C 462 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8308 (mm-40) REVERT: D 16 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7662 (tp-100) REVERT: D 70 PHE cc_start: 0.8969 (m-80) cc_final: 0.8673 (m-80) REVERT: D 74 GLN cc_start: 0.8859 (tt0) cc_final: 0.7890 (tm-30) REVERT: D 76 ASN cc_start: 0.8968 (m-40) cc_final: 0.8228 (m-40) REVERT: D 96 TYR cc_start: 0.8686 (m-80) cc_final: 0.8447 (m-10) REVERT: D 97 PHE cc_start: 0.9010 (m-80) cc_final: 0.8667 (m-10) REVERT: E 3 MET cc_start: 0.8065 (ppp) cc_final: 0.7710 (ppp) REVERT: E 9 GLU cc_start: 0.7319 (mp0) cc_final: 0.6499 (mp0) REVERT: E 97 PHE cc_start: 0.9003 (m-80) cc_final: 0.8573 (m-10) REVERT: E 118 TYR cc_start: 0.8392 (m-10) cc_final: 0.8067 (m-80) REVERT: E 121 GLN cc_start: 0.8436 (pm20) cc_final: 0.7635 (pm20) REVERT: F 74 GLN cc_start: 0.8947 (tt0) cc_final: 0.7974 (tm-30) REVERT: F 75 ASP cc_start: 0.8435 (t0) cc_final: 0.7931 (OUTLIER) REVERT: F 78 GLU cc_start: 0.9018 (mp0) cc_final: 0.8558 (mp0) REVERT: F 96 TYR cc_start: 0.8762 (m-80) cc_final: 0.8093 (m-10) REVERT: F 118 TYR cc_start: 0.8321 (m-10) cc_final: 0.8026 (m-10) outliers start: 77 outliers final: 28 residues processed: 254 average time/residue: 0.5141 time to fit residues: 143.9491 Evaluate side-chains 225 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 26 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN D 102 ASN E 74 GLN E 102 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.055035 restraints weight = 33708.733| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.29 r_work: 0.2705 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13715 Z= 0.127 Angle : 0.515 8.173 18601 Z= 0.272 Chirality : 0.041 0.163 2169 Planarity : 0.004 0.054 2360 Dihedral : 4.351 46.542 1875 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.32 % Allowed : 25.25 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1737 helix: 2.31 (0.26), residues: 435 sheet: -0.37 (0.22), residues: 498 loop : -0.77 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 22 TYR 0.022 0.001 TYR D 32 PHE 0.013 0.001 PHE D 70 TRP 0.005 0.001 TRP C 314 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00292 (13688) covalent geometry : angle 0.51546 (18547) SS BOND : bond 0.00267 ( 27) SS BOND : angle 0.43536 ( 54) hydrogen bonds : bond 0.02681 ( 672) hydrogen bonds : angle 4.58243 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 205 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8374 (pptt) REVERT: A 227 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8545 (t0) REVERT: A 365 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8927 (p) REVERT: A 497 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8746 (mm-30) REVERT: B 152 VAL cc_start: 0.8934 (t) cc_final: 0.8624 (m) REVERT: B 419 LYS cc_start: 0.9546 (mmtm) cc_final: 0.9162 (mmpt) REVERT: B 440 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8457 (t0) REVERT: B 505 PHE cc_start: 0.9085 (t80) cc_final: 0.8619 (t80) REVERT: B 508 LYS cc_start: 0.9755 (OUTLIER) cc_final: 0.9476 (tmmt) REVERT: C 65 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8342 (pptt) REVERT: C 365 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8953 (p) REVERT: C 419 LYS cc_start: 0.9528 (mptm) cc_final: 0.9180 (mmmm) REVERT: C 440 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8470 (t0) REVERT: C 462 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8380 (mm-40) REVERT: D 3 MET cc_start: 0.7650 (ppp) cc_final: 0.7313 (ppp) REVERT: D 62 TYR cc_start: 0.8905 (m-80) cc_final: 0.8620 (m-80) REVERT: D 74 GLN cc_start: 0.8855 (tt0) cc_final: 0.7804 (tm-30) REVERT: D 75 ASP cc_start: 0.7727 (t0) cc_final: 0.7365 (t0) REVERT: D 95 MET cc_start: 0.9392 (tpp) cc_final: 0.9088 (tpp) REVERT: D 97 PHE cc_start: 0.9035 (m-80) cc_final: 0.8648 (m-10) REVERT: E 3 MET cc_start: 0.8102 (ppp) cc_final: 0.7690 (ppp) REVERT: E 9 GLU cc_start: 0.7478 (mp0) cc_final: 0.6726 (mp0) REVERT: E 95 MET cc_start: 0.9492 (tpp) cc_final: 0.9155 (tpp) REVERT: E 97 PHE cc_start: 0.8963 (m-80) cc_final: 0.8472 (m-10) REVERT: E 118 TYR cc_start: 0.8376 (m-10) cc_final: 0.8076 (m-80) REVERT: E 121 GLN cc_start: 0.8546 (pm20) cc_final: 0.7956 (pm20) REVERT: F 22 ARG cc_start: 0.9204 (tpt-90) cc_final: 0.8988 (tpt90) REVERT: F 62 TYR cc_start: 0.8714 (m-80) cc_final: 0.8255 (m-80) REVERT: F 75 ASP cc_start: 0.8409 (t0) cc_final: 0.7735 (OUTLIER) REVERT: F 78 GLU cc_start: 0.9072 (mp0) cc_final: 0.8555 (mp0) outliers start: 66 outliers final: 27 residues processed: 252 average time/residue: 0.5733 time to fit residues: 158.8278 Evaluate side-chains 228 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 121 optimal weight: 0.0970 chunk 143 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS B 227 ASN D 102 ASN E 102 ASN F 76 ASN F 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.053827 restraints weight = 34051.265| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.30 r_work: 0.2658 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13715 Z= 0.189 Angle : 0.543 10.709 18601 Z= 0.285 Chirality : 0.041 0.159 2169 Planarity : 0.004 0.053 2360 Dihedral : 4.167 46.601 1872 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.92 % Allowed : 26.16 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1737 helix: 2.35 (0.26), residues: 435 sheet: -0.28 (0.22), residues: 483 loop : -0.80 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 507 TYR 0.020 0.001 TYR F 118 PHE 0.020 0.001 PHE D 70 TRP 0.006 0.001 TRP A 314 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00439 (13688) covalent geometry : angle 0.54260 (18547) SS BOND : bond 0.00335 ( 27) SS BOND : angle 0.51962 ( 54) hydrogen bonds : bond 0.02924 ( 672) hydrogen bonds : angle 4.64343 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8325 (pptt) REVERT: A 227 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8630 (t0) REVERT: A 497 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8761 (mm-30) REVERT: B 419 LYS cc_start: 0.9564 (mmtm) cc_final: 0.9174 (mmpt) REVERT: B 440 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8394 (t0) REVERT: B 463 GLU cc_start: 0.8256 (pm20) cc_final: 0.7988 (mp0) REVERT: B 487 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: B 505 PHE cc_start: 0.9069 (t80) cc_final: 0.8658 (t80) REVERT: B 507 ARG cc_start: 0.9140 (ttp80) cc_final: 0.8932 (ttp80) REVERT: B 508 LYS cc_start: 0.9749 (OUTLIER) cc_final: 0.9459 (tmmt) REVERT: C 65 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8414 (pptt) REVERT: C 365 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8862 (p) REVERT: C 419 LYS cc_start: 0.9544 (mptm) cc_final: 0.9266 (mmmm) REVERT: C 440 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8511 (t0) REVERT: C 462 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8469 (mm-40) REVERT: D 3 MET cc_start: 0.7630 (ppp) cc_final: 0.7419 (ppp) REVERT: D 62 TYR cc_start: 0.8938 (m-80) cc_final: 0.8678 (m-80) REVERT: D 74 GLN cc_start: 0.8854 (tt0) cc_final: 0.7750 (tm-30) REVERT: D 75 ASP cc_start: 0.7821 (t0) cc_final: 0.7003 (t0) REVERT: D 78 GLU cc_start: 0.9068 (mp0) cc_final: 0.8839 (mp0) REVERT: D 95 MET cc_start: 0.9388 (tpp) cc_final: 0.9162 (tpp) REVERT: D 97 PHE cc_start: 0.9125 (m-80) cc_final: 0.8682 (m-10) REVERT: E 3 MET cc_start: 0.8139 (ppp) cc_final: 0.7935 (ppp) REVERT: E 9 GLU cc_start: 0.7530 (mp0) cc_final: 0.6785 (mp0) REVERT: E 95 MET cc_start: 0.9477 (tpp) cc_final: 0.9218 (tpp) REVERT: E 97 PHE cc_start: 0.8999 (m-80) cc_final: 0.8496 (m-10) REVERT: E 121 GLN cc_start: 0.8596 (pm20) cc_final: 0.8006 (pm20) REVERT: F 3 MET cc_start: 0.8205 (ppp) cc_final: 0.7913 (ppp) REVERT: F 51 VAL cc_start: 0.9200 (t) cc_final: 0.8969 (m) REVERT: F 62 TYR cc_start: 0.8780 (m-80) cc_final: 0.8116 (m-80) REVERT: F 75 ASP cc_start: 0.8483 (t0) cc_final: 0.8040 (t0) REVERT: F 118 TYR cc_start: 0.8089 (m-10) cc_final: 0.7879 (m-80) outliers start: 60 outliers final: 28 residues processed: 241 average time/residue: 0.5612 time to fit residues: 148.3887 Evaluate side-chains 225 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 173 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** F 61 ASN ** 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 = 0.3266 r_free = 0.3266 target = 0.074831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.054477 restraints weight = 33139.015| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.16 r_work: 0.2652 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13715 Z= 0.163 Angle : 0.546 9.500 18601 Z= 0.283 Chirality : 0.041 0.147 2169 Planarity : 0.004 0.054 2360 Dihedral : 4.117 46.852 1872 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.19 % Allowed : 26.03 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1737 helix: 2.44 (0.25), residues: 435 sheet: -0.28 (0.22), residues: 483 loop : -0.82 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 507 TYR 0.026 0.001 TYR F 32 PHE 0.021 0.001 PHE D 70 TRP 0.006 0.001 TRP A 314 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00378 (13688) covalent geometry : angle 0.54577 (18547) SS BOND : bond 0.00301 ( 27) SS BOND : angle 0.47466 ( 54) hydrogen bonds : bond 0.02819 ( 672) hydrogen bonds : angle 4.61939 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 202 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8335 (pptt) REVERT: A 227 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8699 (t0) REVERT: A 297 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9198 (tp) REVERT: A 497 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8750 (mm-30) REVERT: B 65 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8207 (pptt) REVERT: B 419 LYS cc_start: 0.9501 (mmtm) cc_final: 0.9169 (mmpt) REVERT: B 440 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8512 (t0) REVERT: B 505 PHE cc_start: 0.9048 (t80) cc_final: 0.8690 (t80) REVERT: B 507 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8896 (ttp80) REVERT: B 508 LYS cc_start: 0.9738 (OUTLIER) cc_final: 0.9469 (tmmt) REVERT: C 65 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8397 (pptt) REVERT: C 201 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9086 (mtmt) REVERT: C 365 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.9001 (p) REVERT: C 419 LYS cc_start: 0.9504 (mptm) cc_final: 0.9198 (mmmm) REVERT: C 440 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8596 (t0) REVERT: C 462 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8479 (mm-40) REVERT: D 62 TYR cc_start: 0.9032 (m-80) cc_final: 0.8631 (m-80) REVERT: D 74 GLN cc_start: 0.8858 (tt0) cc_final: 0.7802 (tm-30) REVERT: D 75 ASP cc_start: 0.8095 (t0) cc_final: 0.7563 (t0) REVERT: D 97 PHE cc_start: 0.9224 (m-80) cc_final: 0.8785 (m-10) REVERT: E 9 GLU cc_start: 0.7782 (mp0) cc_final: 0.6957 (mp0) REVERT: E 97 PHE cc_start: 0.9085 (m-80) cc_final: 0.8621 (m-10) REVERT: E 121 GLN cc_start: 0.8641 (pm20) cc_final: 0.8050 (pm20) REVERT: F 62 TYR cc_start: 0.8849 (m-80) cc_final: 0.8249 (m-80) REVERT: F 75 ASP cc_start: 0.8558 (t0) cc_final: 0.8133 (t0) outliers start: 64 outliers final: 28 residues processed: 250 average time/residue: 0.5533 time to fit residues: 151.5393 Evaluate side-chains 233 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 168 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS B 227 ASN C 371 ASN D 102 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.054603 restraints weight = 33450.165| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.32 r_work: 0.2628 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13715 Z= 0.126 Angle : 0.555 10.950 18601 Z= 0.284 Chirality : 0.041 0.143 2169 Planarity : 0.004 0.064 2360 Dihedral : 4.042 47.654 1872 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.66 % Allowed : 27.53 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1737 helix: 2.58 (0.25), residues: 435 sheet: -0.22 (0.22), residues: 492 loop : -0.79 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 22 TYR 0.019 0.001 TYR F 32 PHE 0.018 0.001 PHE D 70 TRP 0.006 0.001 TRP F 39 HIS 0.001 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00296 (13688) covalent geometry : angle 0.55506 (18547) SS BOND : bond 0.00243 ( 27) SS BOND : angle 0.39941 ( 54) hydrogen bonds : bond 0.02632 ( 672) hydrogen bonds : angle 4.50071 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8391 (pptt) REVERT: A 227 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8643 (t0) REVERT: A 289 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.7612 (tmm) REVERT: A 297 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8964 (tp) REVERT: A 419 LYS cc_start: 0.9486 (mmtp) cc_final: 0.9135 (mmmt) REVERT: A 497 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8760 (mm-30) REVERT: B 65 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8165 (pptt) REVERT: B 152 VAL cc_start: 0.9057 (t) cc_final: 0.8744 (m) REVERT: B 327 LYS cc_start: 0.7828 (mppt) cc_final: 0.7551 (mppt) REVERT: B 419 LYS cc_start: 0.9510 (mmtm) cc_final: 0.9142 (mmpt) REVERT: B 440 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8500 (t0) REVERT: B 463 GLU cc_start: 0.8288 (pm20) cc_final: 0.8024 (mp0) REVERT: B 505 PHE cc_start: 0.9102 (t80) cc_final: 0.8736 (t80) REVERT: B 507 ARG cc_start: 0.9145 (ttp80) cc_final: 0.8927 (ttp80) REVERT: B 508 LYS cc_start: 0.9750 (OUTLIER) cc_final: 0.9491 (tmmt) REVERT: C 65 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8372 (pptt) REVERT: C 365 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8964 (p) REVERT: C 419 LYS cc_start: 0.9508 (mptm) cc_final: 0.9192 (mmmm) REVERT: C 440 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8581 (t0) REVERT: C 462 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: D 62 TYR cc_start: 0.9031 (m-80) cc_final: 0.8666 (m-80) REVERT: D 74 GLN cc_start: 0.9046 (tt0) cc_final: 0.7826 (tm-30) REVERT: D 75 ASP cc_start: 0.7992 (t0) cc_final: 0.7453 (t0) REVERT: D 95 MET cc_start: 0.9345 (tpp) cc_final: 0.9076 (tpp) REVERT: D 97 PHE cc_start: 0.9229 (m-80) cc_final: 0.8801 (m-80) REVERT: E 7 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8463 (mt) REVERT: E 9 GLU cc_start: 0.7789 (mp0) cc_final: 0.6892 (mp0) REVERT: E 95 MET cc_start: 0.9463 (tpp) cc_final: 0.9058 (tpp) REVERT: E 97 PHE cc_start: 0.8974 (m-80) cc_final: 0.8473 (m-10) REVERT: E 121 GLN cc_start: 0.8700 (pm20) cc_final: 0.8149 (pm20) REVERT: F 62 TYR cc_start: 0.8815 (m-80) cc_final: 0.8298 (m-80) REVERT: F 75 ASP cc_start: 0.8514 (t0) cc_final: 0.8098 (t0) outliers start: 56 outliers final: 23 residues processed: 239 average time/residue: 0.5883 time to fit residues: 154.3437 Evaluate side-chains 231 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 151 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN D 102 ASN ** F 61 ASN ** 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 = 0.3285 r_free = 0.3285 target = 0.075065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.053663 restraints weight = 33201.937| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.29 r_work: 0.2608 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13715 Z= 0.158 Angle : 0.568 11.017 18601 Z= 0.291 Chirality : 0.041 0.146 2169 Planarity : 0.004 0.061 2360 Dihedral : 3.810 16.419 1869 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.60 % Allowed : 27.47 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1737 helix: 2.60 (0.25), residues: 435 sheet: -0.11 (0.22), residues: 477 loop : -0.83 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 22 TYR 0.017 0.001 TYR F 32 PHE 0.015 0.001 PHE D 70 TRP 0.006 0.001 TRP A 314 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00373 (13688) covalent geometry : angle 0.56799 (18547) SS BOND : bond 0.00286 ( 27) SS BOND : angle 0.45367 ( 54) hydrogen bonds : bond 0.02765 ( 672) hydrogen bonds : angle 4.56345 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8400 (pptt) REVERT: A 227 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8687 (t0) REVERT: A 297 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9159 (tp) REVERT: A 429 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8476 (mtm-85) REVERT: A 497 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8789 (mm-30) REVERT: B 327 LYS cc_start: 0.7829 (mppt) cc_final: 0.7553 (mppt) REVERT: B 419 LYS cc_start: 0.9535 (mmtm) cc_final: 0.9153 (mmpt) REVERT: B 440 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8487 (t0) REVERT: B 463 GLU cc_start: 0.8348 (pm20) cc_final: 0.8073 (mp0) REVERT: B 505 PHE cc_start: 0.9136 (t80) cc_final: 0.8718 (t80) REVERT: B 507 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8938 (ttp80) REVERT: B 508 LYS cc_start: 0.9742 (OUTLIER) cc_final: 0.9472 (tmmt) REVERT: C 65 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8328 (pptt) REVERT: C 201 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9102 (mtmt) REVERT: C 365 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.8952 (p) REVERT: C 419 LYS cc_start: 0.9524 (mptm) cc_final: 0.9205 (mmmm) REVERT: C 462 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: D 62 TYR cc_start: 0.9053 (m-80) cc_final: 0.8814 (m-80) REVERT: D 74 GLN cc_start: 0.9053 (tt0) cc_final: 0.7749 (tm-30) REVERT: D 75 ASP cc_start: 0.7968 (t0) cc_final: 0.7063 (t0) REVERT: D 78 GLU cc_start: 0.9028 (mp0) cc_final: 0.8751 (mp0) REVERT: D 92 ASP cc_start: 0.8930 (m-30) cc_final: 0.8663 (m-30) REVERT: D 95 MET cc_start: 0.9364 (tpp) cc_final: 0.9069 (tpp) REVERT: D 97 PHE cc_start: 0.9202 (m-80) cc_final: 0.8618 (m-10) REVERT: E 9 GLU cc_start: 0.7803 (mp0) cc_final: 0.6902 (mp0) REVERT: E 121 GLN cc_start: 0.8728 (pm20) cc_final: 0.8339 (pm20) REVERT: F 6 GLN cc_start: 0.8522 (mp10) cc_final: 0.8232 (pm20) REVERT: F 62 TYR cc_start: 0.8863 (m-80) cc_final: 0.8583 (m-80) REVERT: F 75 ASP cc_start: 0.8465 (t0) cc_final: 0.8030 (t0) outliers start: 55 outliers final: 27 residues processed: 233 average time/residue: 0.5539 time to fit residues: 141.4063 Evaluate side-chains 227 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 61 optimal weight: 3.9990 chunk 76 optimal weight: 0.0170 chunk 134 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 170 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN C 227 ASN D 102 ASN E 76 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052146 restraints weight = 33924.256| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.32 r_work: 0.2571 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13715 Z= 0.222 Angle : 0.610 11.394 18601 Z= 0.312 Chirality : 0.042 0.158 2169 Planarity : 0.004 0.083 2360 Dihedral : 3.945 16.425 1869 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.94 % Allowed : 27.73 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1737 helix: 2.52 (0.25), residues: 435 sheet: -0.17 (0.22), residues: 477 loop : -0.85 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 22 TYR 0.018 0.002 TYR F 118 PHE 0.019 0.001 PHE D 70 TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00516 (13688) covalent geometry : angle 0.61039 (18547) SS BOND : bond 0.00369 ( 27) SS BOND : angle 0.57409 ( 54) hydrogen bonds : bond 0.03030 ( 672) hydrogen bonds : angle 4.73555 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8399 (pptt) REVERT: A 227 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8750 (t0) REVERT: A 297 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9113 (tp) REVERT: A 429 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8409 (mtm180) REVERT: A 497 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8789 (mm-30) REVERT: B 327 LYS cc_start: 0.7810 (mppt) cc_final: 0.7529 (mppt) REVERT: B 419 LYS cc_start: 0.9573 (mmtm) cc_final: 0.9152 (mmpt) REVERT: B 463 GLU cc_start: 0.8351 (pm20) cc_final: 0.8072 (mp0) REVERT: B 505 PHE cc_start: 0.9140 (t80) cc_final: 0.8711 (t80) REVERT: B 507 ARG cc_start: 0.9161 (ttp80) cc_final: 0.8948 (ttp80) REVERT: B 508 LYS cc_start: 0.9747 (OUTLIER) cc_final: 0.9470 (tmmt) REVERT: C 65 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8364 (pptt) REVERT: C 201 LYS cc_start: 0.9550 (OUTLIER) cc_final: 0.9338 (mmmm) REVERT: C 365 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8837 (p) REVERT: C 419 LYS cc_start: 0.9544 (mptm) cc_final: 0.9243 (mmmm) REVERT: C 462 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8376 (mm-40) REVERT: D 74 GLN cc_start: 0.9049 (tt0) cc_final: 0.7681 (tm-30) REVERT: D 75 ASP cc_start: 0.7939 (t0) cc_final: 0.7050 (t0) REVERT: D 78 GLU cc_start: 0.9030 (mp0) cc_final: 0.8674 (mp0) REVERT: D 92 ASP cc_start: 0.8913 (m-30) cc_final: 0.8509 (m-30) REVERT: D 95 MET cc_start: 0.9378 (tpp) cc_final: 0.9103 (tpp) REVERT: D 97 PHE cc_start: 0.9179 (m-80) cc_final: 0.8670 (m-10) REVERT: E 9 GLU cc_start: 0.7779 (mp0) cc_final: 0.7037 (mp0) REVERT: E 62 TYR cc_start: 0.8832 (m-80) cc_final: 0.8405 (m-80) REVERT: E 121 GLN cc_start: 0.8701 (pm20) cc_final: 0.8277 (pm20) REVERT: F 6 GLN cc_start: 0.8491 (mp10) cc_final: 0.8198 (pm20) REVERT: F 75 ASP cc_start: 0.8487 (t0) cc_final: 0.8041 (t0) outliers start: 45 outliers final: 23 residues processed: 228 average time/residue: 0.5856 time to fit residues: 145.9001 Evaluate side-chains 221 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.054924 restraints weight = 33107.284| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.18 r_work: 0.2643 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13715 Z= 0.125 Angle : 0.600 12.645 18601 Z= 0.303 Chirality : 0.041 0.182 2169 Planarity : 0.004 0.055 2360 Dihedral : 3.834 17.777 1869 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.03 % Allowed : 28.84 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1737 helix: 2.67 (0.25), residues: 435 sheet: -0.29 (0.22), residues: 495 loop : -0.78 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 22 TYR 0.013 0.001 TYR E 82 PHE 0.016 0.001 PHE E 70 TRP 0.006 0.001 TRP C 314 HIS 0.001 0.000 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00300 (13688) covalent geometry : angle 0.60076 (18547) SS BOND : bond 0.00228 ( 27) SS BOND : angle 0.38985 ( 54) hydrogen bonds : bond 0.02583 ( 672) hydrogen bonds : angle 4.56197 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8373 (pptt) REVERT: A 227 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8657 (t0) REVERT: A 297 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9162 (tp) REVERT: A 429 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8578 (mtm-85) REVERT: A 497 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 505 PHE cc_start: 0.9129 (t80) cc_final: 0.8465 (t80) REVERT: B 152 VAL cc_start: 0.9065 (t) cc_final: 0.8747 (m) REVERT: B 419 LYS cc_start: 0.9513 (mmtm) cc_final: 0.9151 (mmpt) REVERT: B 463 GLU cc_start: 0.8275 (pm20) cc_final: 0.7993 (mp0) REVERT: B 505 PHE cc_start: 0.9178 (t80) cc_final: 0.8679 (t80) REVERT: B 507 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8923 (ttp80) REVERT: B 508 LYS cc_start: 0.9740 (OUTLIER) cc_final: 0.9475 (tmmt) REVERT: C 365 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8967 (p) REVERT: C 419 LYS cc_start: 0.9515 (mptm) cc_final: 0.9096 (mmmm) REVERT: C 462 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8296 (tp40) REVERT: C 505 PHE cc_start: 0.8983 (t80) cc_final: 0.8610 (t80) REVERT: D 3 MET cc_start: 0.7890 (ppp) cc_final: 0.7627 (tmm) REVERT: D 75 ASP cc_start: 0.8036 (t0) cc_final: 0.6965 (t0) REVERT: D 78 GLU cc_start: 0.9009 (mp0) cc_final: 0.8669 (mp0) REVERT: D 89 LYS cc_start: 0.8650 (mttp) cc_final: 0.8369 (mttm) REVERT: D 92 ASP cc_start: 0.8962 (m-30) cc_final: 0.8725 (m-30) REVERT: D 95 MET cc_start: 0.9357 (tpp) cc_final: 0.9138 (tpp) REVERT: D 97 PHE cc_start: 0.9173 (m-80) cc_final: 0.8696 (m-10) REVERT: E 9 GLU cc_start: 0.7762 (mp0) cc_final: 0.6873 (mp0) REVERT: E 95 MET cc_start: 0.9185 (tpp) cc_final: 0.8855 (tpp) REVERT: E 121 GLN cc_start: 0.8630 (pm20) cc_final: 0.8225 (pm20) REVERT: F 6 GLN cc_start: 0.8554 (mp10) cc_final: 0.8255 (pm20) REVERT: F 62 TYR cc_start: 0.9077 (m-80) cc_final: 0.8770 (m-80) REVERT: F 73 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8752 (p) REVERT: F 75 ASP cc_start: 0.8463 (t0) cc_final: 0.8065 (t0) outliers start: 31 outliers final: 19 residues processed: 227 average time/residue: 0.5812 time to fit residues: 144.3202 Evaluate side-chains 220 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.053076 restraints weight = 33736.387| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.30 r_work: 0.2601 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13715 Z= 0.173 Angle : 0.608 12.380 18601 Z= 0.308 Chirality : 0.041 0.170 2169 Planarity : 0.004 0.055 2360 Dihedral : 3.885 17.943 1869 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.42 % Allowed : 28.19 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1737 helix: 2.63 (0.25), residues: 435 sheet: -0.22 (0.22), residues: 477 loop : -0.82 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 22 TYR 0.017 0.001 TYR D 118 PHE 0.014 0.001 PHE E 70 TRP 0.006 0.001 TRP A 314 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00407 (13688) covalent geometry : angle 0.60814 (18547) SS BOND : bond 0.00311 ( 27) SS BOND : angle 0.48973 ( 54) hydrogen bonds : bond 0.02804 ( 672) hydrogen bonds : angle 4.64012 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4939.64 seconds wall clock time: 85 minutes 5.94 seconds (5105.94 seconds total)