Starting phenix.real_space_refine on Fri Jul 3 21:58:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dr8_27674/07_2026/8dr8_27674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dr8_27674/07_2026/8dr8_27674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dr8_27674/07_2026/8dr8_27674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dr8_27674/07_2026/8dr8_27674.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dr8_27674/07_2026/8dr8_27674.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dr8_27674/07_2026/8dr8_27674.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dr8_27674/07_2026/8dr8_27674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dr8_27674/07_2026/8dr8_27674.cif" } resolution = 3.04 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= 0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 106 5.16 5 C 10800 2.51 5 N 2525 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16270 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2667 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2519 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2653 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2651 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.75, per 1000 atoms: 0.23 Number of scatterers: 16270 At special positions: 0 Unit cell: (95.368, 107.944, 138.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 9 15.00 O 2830 8.00 N 2525 7.00 C 10800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.04 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 736.6 milliseconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 76.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.202A pdb=" N ARG A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.937A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.569A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.203A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 4.191A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 315 through 346 removed outlier: 4.141A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.100A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.053A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.559A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.917A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.226A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 343 removed outlier: 4.095A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.127A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.577A pdb=" N GLN C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.420A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.767A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 258 through 286 removed outlier: 3.577A pdb=" N PHE C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 343 removed outlier: 3.500A pdb=" N ALA C 322 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.284A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 401 Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.959A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 4.706A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 166 through 175 removed outlier: 4.019A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.644A pdb=" N GLU D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.171A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.217A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 410 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.686A pdb=" N ARG E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 19' Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.632A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 4.499A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 Processing helix chain 'E' and resid 166 through 175 removed outlier: 4.226A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 345 removed outlier: 3.542A pdb=" N ALA E 322 " --> pdb=" O PHE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 358 removed outlier: 3.596A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 383 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.198A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 409 removed outlier: 3.524A pdb=" N GLU E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 47 Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 4.236A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 167 Processing helix chain 'F' and resid 168 through 179 removed outlier: 3.949A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 Processing helix chain 'F' and resid 256 through 284 removed outlier: 3.597A pdb=" N ALA F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 312 through 344 removed outlier: 4.001A pdb=" N ARG F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 358 removed outlier: 4.191A pdb=" N GLU F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 381 removed outlier: 3.608A pdb=" N ALA F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 389 removed outlier: 4.010A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 392 No H-bonds generated for 'chain 'F' and resid 390 through 392' Processing helix chain 'F' and resid 394 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.683A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 94 " --> pdb=" O VAL A 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'F' and resid 52 through 56 1078 hydrogen bonds defined for protein. 3192 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: 2.84 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2697 1.33 - 1.45: 4647 1.45 - 1.57: 9172 1.57 - 1.70: 10 1.70 - 1.82: 160 Bond restraints: 16686 Sorted by residual: bond pdb=" C10 PEE F 902 " pdb=" O4 PEE F 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C10 PEE F 903 " pdb=" O4 PEE F 903 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C10 PEE D 902 " pdb=" O4 PEE D 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 16681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 22145 2.78 - 5.57: 220 5.57 - 8.35: 58 8.35 - 11.13: 10 11.13 - 13.91: 15 Bond angle restraints: 22448 Sorted by residual: angle pdb=" C ASN F 368 " pdb=" CA ASN F 368 " pdb=" CB ASN F 368 " ideal model delta sigma weight residual 116.63 109.95 6.68 1.16e+00 7.43e-01 3.32e+01 angle pdb=" C ASN E 370 " pdb=" CA ASN E 370 " pdb=" CB ASN E 370 " ideal model delta sigma weight residual 116.63 110.17 6.46 1.16e+00 7.43e-01 3.10e+01 angle pdb=" CA ASN F 368 " pdb=" C ASN F 368 " pdb=" N ASP F 369 " ideal model delta sigma weight residual 119.63 115.78 3.85 8.10e-01 1.52e+00 2.26e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.34 -13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O1P PEE D 904 " pdb=" P PEE D 904 " pdb=" O2P PEE D 904 " ideal model delta sigma weight residual 119.43 133.29 -13.86 3.00e+00 1.11e-01 2.14e+01 ... (remaining 22443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 9493 35.76 - 71.51: 361 71.51 - 107.27: 16 107.27 - 143.02: 9 143.02 - 178.78: 14 Dihedral angle restraints: 9893 sinusoidal: 4248 harmonic: 5645 Sorted by residual: dihedral pdb=" CB CYS C 57 " pdb=" SG CYS C 57 " pdb=" SG CYS C 65 " pdb=" CB CYS C 65 " ideal model delta sinusoidal sigma weight residual -86.00 -6.58 -79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS E 113 " pdb=" SG CYS E 113 " pdb=" SG CYS E 295 " pdb=" CB CYS E 295 " ideal model delta sinusoidal sigma weight residual 93.00 48.87 44.13 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 295 " pdb=" CB CYS D 295 " ideal model delta sinusoidal sigma weight residual 93.00 51.95 41.05 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 9890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2280 0.084 - 0.168: 119 0.168 - 0.252: 3 0.252 - 0.336: 1 0.336 - 0.420: 7 Chirality restraints: 2410 Sorted by residual: chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C2 PEE D 904 " pdb=" C1 PEE D 904 " pdb=" C3 PEE D 904 " pdb=" O2 PEE D 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 2407 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 23 " -0.023 2.00e-02 2.50e+03 2.21e-02 1.23e+01 pdb=" CG TRP C 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 23 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 23 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 23 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 23 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 390 " -0.012 2.00e-02 2.50e+03 1.92e-02 6.48e+00 pdb=" CG PHE E 390 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 390 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 390 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE E 390 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 390 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 390 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 170 " -0.011 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP F 170 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP F 170 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 170 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 170 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 170 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 170 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 170 " 0.001 2.00e-02 2.50e+03 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1997 2.75 - 3.29: 15693 3.29 - 3.83: 28563 3.83 - 4.36: 32184 4.36 - 4.90: 57083 Nonbonded interactions: 135520 Sorted by model distance: nonbonded pdb=" O SER F 168 " pdb=" OG1 THR F 171 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 356 " pdb=" OG SER B 360 " model vdw 2.240 3.040 nonbonded pdb=" O THR A 44 " pdb=" OG1 THR A 48 " model vdw 2.260 3.040 nonbonded pdb=" NE2 GLN B 49 " pdb=" O VAL C 47 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLN C 46 " pdb=" OH TYR C 127 " model vdw 2.276 3.040 ... (remaining 135515 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 15 through 68 or resid 93 through 175 or resid 240 through \ 402 or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name O2 or name O4 )) or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 240 through \ 402 or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name O2 or name O4 )) or resid 903)) selection = (chain 'C' and (resid 15 through 402 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name O2 or name O4 ) \ ) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 175 or resid 240 through 402 or resid 902 or (r \ esid 903 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 175 or resid 240 through 402 or (resid 902 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name O2 or name O4 )) or resid 903)) } 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: 6.460 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.650 Find NCS groups from input model: 0.370 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.007 0.152 16703 Z= 0.323 Angle : 0.818 13.914 22482 Z= 0.399 Chirality : 0.047 0.420 2410 Planarity : 0.005 0.062 2682 Dihedral : 19.555 178.780 6186 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.17 % Allowed : 21.55 % Favored : 78.28 % 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: 0.91 (0.18), residues: 1842 helix: 1.13 (0.13), residues: 1290 sheet: 0.88 (0.54), residues: 104 loop : -0.86 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 118 TYR 0.036 0.001 TYR C 284 PHE 0.043 0.002 PHE E 390 TRP 0.060 0.002 TRP C 23 HIS 0.020 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.32 (16686) covalent geometry : angle 0.81718 / 0.40 (22448) SS BOND : bond 0.00356 / 0.18 ( 17) SS BOND : angle 1.32058 / 0.85 ( 34) hydrogen bonds : bond 0.11542 / 7.64 ( 1078) hydrogen bonds : angle 5.73965 / 4.03 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: D 27 PHE cc_start: 0.7135 (m-10) cc_final: 0.6784 (m-10) REVERT: D 33 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8541 (tp) REVERT: D 375 MET cc_start: 0.8240 (mtm) cc_final: 0.7990 (mtm) REVERT: E 241 LYS cc_start: 0.7520 (mmmt) cc_final: 0.6618 (tppt) REVERT: E 245 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6782 (mm-30) REVERT: F 243 GLU cc_start: 0.7778 (mp0) cc_final: 0.7480 (mp0) outliers start: 3 outliers final: 2 residues processed: 245 average time/residue: 0.1066 time to fit residues: 41.3009 Evaluate side-chains 229 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain E residue 52 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 400 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.184129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.135107 restraints weight = 19954.263| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.42 r_work: 0.3604 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16703 Z= 0.156 Angle : 0.484 7.912 22482 Z= 0.263 Chirality : 0.039 0.160 2410 Planarity : 0.003 0.041 2682 Dihedral : 15.532 176.895 2435 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.89 % Allowed : 20.40 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.19), residues: 1842 helix: 1.87 (0.14), residues: 1311 sheet: 0.71 (0.54), residues: 98 loop : -0.92 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 118 TYR 0.016 0.001 TYR D 382 PHE 0.010 0.001 PHE A 374 TRP 0.027 0.001 TRP C 23 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16686) covalent geometry : angle 0.48245 / 0.26 (22448) SS BOND : bond 0.00317 / 0.18 ( 17) SS BOND : angle 0.97608 / 0.56 ( 34) hydrogen bonds : bond 0.03763 / 2.51 ( 1078) hydrogen bonds : angle 4.24669 / 2.97 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: C 46 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7702 (tm-30) REVERT: C 284 TYR cc_start: 0.7483 (t80) cc_final: 0.7139 (t80) REVERT: D 95 THR cc_start: 0.8697 (t) cc_final: 0.8471 (p) REVERT: E 25 ASP cc_start: 0.7351 (m-30) cc_final: 0.7149 (m-30) REVERT: E 245 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7183 (mm-30) REVERT: F 243 GLU cc_start: 0.7733 (mp0) cc_final: 0.7526 (mp0) outliers start: 33 outliers final: 21 residues processed: 263 average time/residue: 0.1166 time to fit residues: 47.5985 Evaluate side-chains 234 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 153 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 158 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.185575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.136331 restraints weight = 20047.628| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.44 r_work: 0.3618 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16703 Z= 0.119 Angle : 0.443 8.094 22482 Z= 0.241 Chirality : 0.037 0.132 2410 Planarity : 0.003 0.036 2682 Dihedral : 13.321 178.473 2428 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.12 % Allowed : 20.86 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 1842 helix: 2.12 (0.14), residues: 1312 sheet: 0.89 (0.55), residues: 92 loop : -1.00 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 389 TYR 0.016 0.001 TYR C 382 PHE 0.018 0.001 PHE D 244 TRP 0.019 0.001 TRP C 23 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (16686) covalent geometry : angle 0.44230 / 0.24 (22448) SS BOND : bond 0.00291 / 0.14 ( 17) SS BOND : angle 0.90109 / 0.51 ( 34) hydrogen bonds : bond 0.03460 / 2.31 ( 1078) hydrogen bonds : angle 4.03993 / 2.82 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7321 (mtm180) cc_final: 0.6842 (mtp-110) REVERT: A 269 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 275 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7615 (t80) REVERT: C 18 ARG cc_start: 0.6781 (ptp-110) cc_final: 0.6196 (ptm160) REVERT: C 46 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7761 (tm-30) REVERT: C 284 TYR cc_start: 0.7624 (t80) cc_final: 0.7191 (t80) REVERT: C 385 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6541 (tp) REVERT: D 375 MET cc_start: 0.8255 (mtm) cc_final: 0.7546 (mtm) REVERT: E 25 ASP cc_start: 0.7436 (m-30) cc_final: 0.7102 (m-30) REVERT: E 154 GLU cc_start: 0.7745 (tt0) cc_final: 0.7308 (pt0) REVERT: E 245 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7124 (mm-30) REVERT: E 263 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6841 (mp) REVERT: F 243 GLU cc_start: 0.7908 (mp0) cc_final: 0.7609 (mp0) outliers start: 37 outliers final: 23 residues processed: 272 average time/residue: 0.1084 time to fit residues: 46.1152 Evaluate side-chains 252 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 129 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.183626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134501 restraints weight = 19959.148| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.40 r_work: 0.3590 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16703 Z= 0.148 Angle : 0.459 8.196 22482 Z= 0.249 Chirality : 0.039 0.167 2410 Planarity : 0.003 0.034 2682 Dihedral : 12.051 179.065 2428 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.98 % Allowed : 20.92 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 1842 helix: 2.15 (0.14), residues: 1313 sheet: 0.65 (0.53), residues: 99 loop : -1.00 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.018 0.001 TYR D 382 PHE 0.024 0.001 PHE D 244 TRP 0.019 0.001 TRP F 170 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16686) covalent geometry : angle 0.45817 / 0.25 (22448) SS BOND : bond 0.00293 / 0.16 ( 17) SS BOND : angle 0.97445 / 0.56 ( 34) hydrogen bonds : bond 0.03523 / 2.35 ( 1078) hydrogen bonds : angle 4.02463 / 2.81 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 275 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7612 (t80) REVERT: B 337 MET cc_start: 0.7922 (mtp) cc_final: 0.7392 (mtp) REVERT: C 46 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 284 TYR cc_start: 0.7620 (t80) cc_final: 0.7269 (t80) REVERT: D 151 SER cc_start: 0.7868 (t) cc_final: 0.7185 (p) REVERT: D 375 MET cc_start: 0.8275 (mtm) cc_final: 0.7921 (mtm) REVERT: E 25 ASP cc_start: 0.7516 (m-30) cc_final: 0.7098 (m-30) REVERT: E 37 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7806 (ttp) REVERT: E 154 GLU cc_start: 0.7744 (tt0) cc_final: 0.7330 (pt0) REVERT: E 245 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7143 (mm-30) REVERT: E 263 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7027 (mp) REVERT: F 18 ARG cc_start: 0.6629 (mpp-170) cc_final: 0.6389 (mpp-170) outliers start: 52 outliers final: 33 residues processed: 263 average time/residue: 0.1084 time to fit residues: 44.7775 Evaluate side-chains 257 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 135 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 chunk 27 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.186452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137507 restraints weight = 19866.481| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.40 r_work: 0.3618 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16703 Z= 0.102 Angle : 0.428 7.642 22482 Z= 0.232 Chirality : 0.037 0.164 2410 Planarity : 0.003 0.035 2682 Dihedral : 10.797 177.167 2428 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.58 % Allowed : 21.15 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 1842 helix: 2.31 (0.14), residues: 1310 sheet: 1.04 (0.55), residues: 92 loop : -0.93 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 355 TYR 0.013 0.001 TYR A 338 PHE 0.021 0.001 PHE E 390 TRP 0.023 0.001 TRP F 170 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (16686) covalent geometry : angle 0.42688 / 0.23 (22448) SS BOND : bond 0.00275 / 0.13 ( 17) SS BOND : angle 0.84498 / 0.47 ( 34) hydrogen bonds : bond 0.03224 / 2.15 ( 1078) hydrogen bonds : angle 3.89029 / 2.72 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 275 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7571 (t80) REVERT: B 51 LYS cc_start: 0.8346 (ptmt) cc_final: 0.8106 (ptmt) REVERT: C 46 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 284 TYR cc_start: 0.7676 (t80) cc_final: 0.7407 (t80) REVERT: C 385 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6539 (tp) REVERT: D 151 SER cc_start: 0.7892 (t) cc_final: 0.7221 (p) REVERT: D 337 MET cc_start: 0.8325 (mmm) cc_final: 0.8077 (mmm) REVERT: D 375 MET cc_start: 0.8261 (mtm) cc_final: 0.7533 (mtm) REVERT: E 25 ASP cc_start: 0.7523 (m-30) cc_final: 0.7128 (m-30) REVERT: E 154 GLU cc_start: 0.7678 (tt0) cc_final: 0.7252 (pt0) REVERT: E 245 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7197 (mm-30) REVERT: E 263 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6824 (mp) REVERT: F 247 LYS cc_start: 0.8586 (tttt) cc_final: 0.7896 (tptt) REVERT: F 357 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7182 (pm20) outliers start: 45 outliers final: 27 residues processed: 283 average time/residue: 0.1130 time to fit residues: 49.3286 Evaluate side-chains 265 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.184376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.135436 restraints weight = 19873.736| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.40 r_work: 0.3583 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16703 Z= 0.137 Angle : 0.458 7.516 22482 Z= 0.248 Chirality : 0.038 0.173 2410 Planarity : 0.003 0.034 2682 Dihedral : 10.026 168.936 2428 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.92 % Allowed : 21.43 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 1842 helix: 2.26 (0.14), residues: 1313 sheet: 0.85 (0.54), residues: 98 loop : -1.04 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 355 TYR 0.019 0.001 TYR D 382 PHE 0.023 0.001 PHE E 390 TRP 0.024 0.001 TRP F 170 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16686) covalent geometry : angle 0.45638 / 0.25 (22448) SS BOND : bond 0.00455 / 0.18 ( 17) SS BOND : angle 0.99538 / 0.61 ( 34) hydrogen bonds : bond 0.03420 / 2.29 ( 1078) hydrogen bonds : angle 3.92149 / 2.74 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.7975 (ptpp) cc_final: 0.7575 (ptpp) REVERT: A 265 MET cc_start: 0.8012 (tpp) cc_final: 0.7445 (tpp) REVERT: A 269 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8468 (mp) REVERT: A 275 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7584 (t80) REVERT: A 309 ARG cc_start: 0.8500 (tpt170) cc_final: 0.8189 (mtp85) REVERT: B 51 LYS cc_start: 0.8345 (ptmt) cc_final: 0.8081 (ptmt) REVERT: C 46 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 284 TYR cc_start: 0.7790 (t80) cc_final: 0.7197 (t80) REVERT: C 385 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6582 (tp) REVERT: D 151 SER cc_start: 0.7947 (t) cc_final: 0.7229 (p) REVERT: D 375 MET cc_start: 0.8288 (mtm) cc_final: 0.7946 (mtm) REVERT: E 25 ASP cc_start: 0.7560 (m-30) cc_final: 0.7082 (m-30) REVERT: E 37 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (ttp) REVERT: E 154 GLU cc_start: 0.7705 (tt0) cc_final: 0.7275 (pt0) REVERT: E 245 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7087 (mm-30) REVERT: E 263 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6936 (mp) REVERT: E 389 ARG cc_start: 0.7543 (ttm110) cc_final: 0.7013 (mtp85) REVERT: F 247 LYS cc_start: 0.8610 (tttt) cc_final: 0.7905 (tptt) REVERT: F 357 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7154 (pm20) outliers start: 51 outliers final: 40 residues processed: 277 average time/residue: 0.1102 time to fit residues: 46.6968 Evaluate side-chains 274 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 167 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN A 400 ASN B 49 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.179716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130340 restraints weight = 19955.073| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.38 r_work: 0.3541 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16703 Z= 0.254 Angle : 0.552 8.205 22482 Z= 0.299 Chirality : 0.042 0.186 2410 Planarity : 0.003 0.033 2682 Dihedral : 9.935 142.685 2428 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.67 % Allowed : 21.20 % Favored : 75.13 % 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: 1.71 (0.19), residues: 1842 helix: 1.94 (0.14), residues: 1317 sheet: 0.41 (0.51), residues: 107 loop : -1.29 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.018 0.002 TYR C 325 PHE 0.024 0.002 PHE E 390 TRP 0.026 0.002 TRP E 168 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.25 (16686) covalent geometry : angle 0.55009 / 0.30 (22448) SS BOND : bond 0.00525 / 0.29 ( 17) SS BOND : angle 1.27412 / 0.83 ( 34) hydrogen bonds : bond 0.03995 / 2.66 ( 1078) hydrogen bonds : angle 4.17577 / 2.92 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.8109 (ptpp) cc_final: 0.7701 (ptpp) REVERT: A 265 MET cc_start: 0.8193 (tpp) cc_final: 0.7427 (tpt) REVERT: A 269 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 275 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7787 (t80) REVERT: C 46 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7822 (tm-30) REVERT: C 284 TYR cc_start: 0.8189 (t80) cc_final: 0.7603 (t80) REVERT: C 308 TYR cc_start: 0.9106 (m-80) cc_final: 0.8739 (m-80) REVERT: C 385 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6594 (tp) REVERT: D 49 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: D 151 SER cc_start: 0.7896 (t) cc_final: 0.7208 (p) REVERT: D 375 MET cc_start: 0.8593 (mtm) cc_final: 0.8347 (mtm) REVERT: E 25 ASP cc_start: 0.7733 (m-30) cc_final: 0.7253 (m-30) REVERT: E 245 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7223 (mm-30) REVERT: E 263 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7299 (mp) REVERT: F 144 PHE cc_start: 0.7688 (t80) cc_final: 0.7422 (t80) REVERT: F 243 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7741 (mm-30) REVERT: F 357 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7069 (pm20) outliers start: 64 outliers final: 44 residues processed: 268 average time/residue: 0.1195 time to fit residues: 49.8065 Evaluate side-chains 263 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.183511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134559 restraints weight = 19896.398| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.38 r_work: 0.3577 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16703 Z= 0.132 Angle : 0.479 10.062 22482 Z= 0.259 Chirality : 0.039 0.192 2410 Planarity : 0.003 0.057 2682 Dihedral : 9.204 143.763 2428 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.12 % Allowed : 23.27 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 1842 helix: 2.08 (0.14), residues: 1314 sheet: 0.59 (0.53), residues: 100 loop : -1.09 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 251 TYR 0.020 0.001 TYR C 382 PHE 0.026 0.001 PHE E 390 TRP 0.034 0.002 TRP E 168 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16686) covalent geometry : angle 0.47733 / 0.26 (22448) SS BOND : bond 0.00241 / 0.15 ( 17) SS BOND : angle 1.02226 / 0.60 ( 34) hydrogen bonds : bond 0.03473 / 2.33 ( 1078) hydrogen bonds : angle 4.03336 / 2.83 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7954 (tpp) cc_final: 0.7493 (tpp) REVERT: A 269 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 275 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 309 ARG cc_start: 0.8544 (tpt170) cc_final: 0.8214 (mtp85) REVERT: C 46 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 284 TYR cc_start: 0.7943 (t80) cc_final: 0.7387 (t80) REVERT: C 375 MET cc_start: 0.6116 (mtm) cc_final: 0.5857 (mtm) REVERT: C 385 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6495 (tp) REVERT: D 49 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: D 151 SER cc_start: 0.7857 (t) cc_final: 0.7179 (p) REVERT: D 375 MET cc_start: 0.8353 (mtm) cc_final: 0.8015 (mtm) REVERT: E 25 ASP cc_start: 0.7617 (m-30) cc_final: 0.7134 (m-30) REVERT: E 245 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7175 (mm-30) REVERT: E 263 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7035 (mp) REVERT: F 243 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: F 247 LYS cc_start: 0.8635 (tttt) cc_final: 0.7936 (tptt) REVERT: F 357 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7169 (pm20) outliers start: 37 outliers final: 26 residues processed: 258 average time/residue: 0.1281 time to fit residues: 49.9948 Evaluate side-chains 254 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 1.9990 chunk 4 optimal weight: 0.0030 chunk 97 optimal weight: 0.0000 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.185024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136358 restraints weight = 19743.983| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.38 r_work: 0.3604 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16703 Z= 0.113 Angle : 0.472 10.549 22482 Z= 0.254 Chirality : 0.038 0.177 2410 Planarity : 0.003 0.033 2682 Dihedral : 8.802 149.806 2428 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.12 % Allowed : 22.98 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.19), residues: 1842 helix: 2.19 (0.14), residues: 1313 sheet: 0.71 (0.53), residues: 99 loop : -1.02 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 355 TYR 0.015 0.001 TYR A 338 PHE 0.028 0.001 PHE E 390 TRP 0.047 0.002 TRP E 168 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16686) covalent geometry : angle 0.47046 / 0.25 (22448) SS BOND : bond 0.00209 / 0.13 ( 17) SS BOND : angle 0.94147 / 0.55 ( 34) hydrogen bonds : bond 0.03320 / 2.22 ( 1078) hydrogen bonds : angle 3.96741 / 2.78 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7898 (tpp) cc_final: 0.7480 (tpp) REVERT: A 269 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 275 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 309 ARG cc_start: 0.8467 (tpt170) cc_final: 0.8181 (mtp85) REVERT: B 350 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7634 (ptpt) REVERT: C 46 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7637 (tm-30) REVERT: C 284 TYR cc_start: 0.7922 (t80) cc_final: 0.7333 (t80) REVERT: C 375 MET cc_start: 0.6098 (mtm) cc_final: 0.5839 (mtm) REVERT: C 385 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6498 (tp) REVERT: D 49 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: D 134 LEU cc_start: 0.8024 (mt) cc_final: 0.7791 (mm) REVERT: D 151 SER cc_start: 0.7967 (t) cc_final: 0.7278 (p) REVERT: D 375 MET cc_start: 0.8279 (mtm) cc_final: 0.7942 (mtm) REVERT: E 25 ASP cc_start: 0.7612 (m-30) cc_final: 0.7128 (m-30) REVERT: E 245 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7126 (mm-30) REVERT: E 389 ARG cc_start: 0.7521 (ttm110) cc_final: 0.6794 (mtp85) REVERT: F 243 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: F 247 LYS cc_start: 0.8631 (tttt) cc_final: 0.7911 (tptt) REVERT: F 357 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7367 (pm20) outliers start: 37 outliers final: 27 residues processed: 266 average time/residue: 0.1119 time to fit residues: 45.7263 Evaluate side-chains 267 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.183876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135450 restraints weight = 19769.815| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.36 r_work: 0.3591 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16703 Z= 0.133 Angle : 0.495 11.151 22482 Z= 0.267 Chirality : 0.039 0.176 2410 Planarity : 0.003 0.032 2682 Dihedral : 8.673 151.997 2428 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.35 % Allowed : 23.15 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 1842 helix: 2.17 (0.14), residues: 1313 sheet: 0.70 (0.53), residues: 99 loop : -1.02 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.022 0.001 TYR C 382 PHE 0.029 0.001 PHE E 390 TRP 0.052 0.002 TRP E 168 HIS 0.011 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (16686) covalent geometry : angle 0.49385 / 0.27 (22448) SS BOND : bond 0.00225 / 0.13 ( 17) SS BOND : angle 0.96361 / 0.57 ( 34) hydrogen bonds : bond 0.03372 / 2.26 ( 1078) hydrogen bonds : angle 3.99210 / 2.81 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 265 MET cc_start: 0.7944 (tpp) cc_final: 0.7496 (tpp) REVERT: A 269 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8512 (mp) REVERT: A 275 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 309 ARG cc_start: 0.8493 (tpt170) cc_final: 0.8205 (mtp85) REVERT: C 46 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 284 TYR cc_start: 0.7931 (t80) cc_final: 0.7340 (t80) REVERT: C 385 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6654 (tp) REVERT: D 134 LEU cc_start: 0.8062 (mt) cc_final: 0.7834 (mm) REVERT: D 151 SER cc_start: 0.7987 (t) cc_final: 0.7326 (p) REVERT: D 334 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8579 (mm) REVERT: D 375 MET cc_start: 0.8278 (mtm) cc_final: 0.7921 (mtm) REVERT: E 25 ASP cc_start: 0.7625 (m-30) cc_final: 0.7144 (m-30) REVERT: E 245 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7158 (mm-30) REVERT: F 247 LYS cc_start: 0.8627 (tttt) cc_final: 0.7900 (tptt) REVERT: F 357 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7158 (pm20) outliers start: 41 outliers final: 30 residues processed: 267 average time/residue: 0.1239 time to fit residues: 50.7320 Evaluate side-chains 267 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 90 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.184497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135802 restraints weight = 19783.166| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.38 r_work: 0.3644 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16703 Z= 0.130 Angle : 0.493 12.205 22482 Z= 0.265 Chirality : 0.039 0.187 2410 Planarity : 0.003 0.033 2682 Dihedral : 8.495 151.017 2428 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.18 % Allowed : 22.92 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.19), residues: 1842 helix: 2.19 (0.14), residues: 1313 sheet: 0.72 (0.53), residues: 99 loop : -1.04 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.016 0.001 TYR D 284 PHE 0.030 0.001 PHE E 390 TRP 0.047 0.002 TRP E 168 HIS 0.011 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (16686) covalent geometry : angle 0.49168 / 0.27 (22448) SS BOND : bond 0.00227 / 0.14 ( 17) SS BOND : angle 0.95964 / 0.56 ( 34) hydrogen bonds : bond 0.03349 / 2.25 ( 1078) hydrogen bonds : angle 3.97274 / 2.79 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.58 seconds wall clock time: 68 minutes 16.78 seconds (4096.78 seconds total)