Starting phenix.real_space_refine on Sat Jun 14 19:46:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dr8_27674/06_2025/8dr8_27674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dr8_27674/06_2025/8dr8_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_27674/06_2025/8dr8_27674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dr8_27674/06_2025/8dr8_27674.map" model { file = "/net/cci-nas-00/data/ceres_data/8dr8_27674/06_2025/8dr8_27674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dr8_27674/06_2025/8dr8_27674.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 81 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: 86 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: 46 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: 87 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: 87 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: 88 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: 10.32, per 1000 atoms: 0.63 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: 3.83 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.79 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: 5.24 Time building geometry restraints manager: 4.57 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: 9534 35.76 - 71.51: 384 71.51 - 107.27: 30 107.27 - 143.02: 19 143.02 - 178.78: 16 Dihedral angle restraints: 9983 sinusoidal: 4338 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 9980 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: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.000 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 20.916 178.780 6276 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.060 0.002 TRP C 23 HIS 0.020 0.002 HIS A 253 PHE 0.043 0.002 PHE E 390 TYR 0.036 0.001 TYR C 284 ARG 0.013 0.001 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.11542 ( 1078) hydrogen bonds : angle 5.73965 ( 3192) SS BOND : bond 0.00356 ( 17) SS BOND : angle 1.32058 ( 34) covalent geometry : bond 0.00652 (16686) covalent geometry : angle 0.81718 (22448) *********************** 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 : 2.586 Fit side-chains revert: symmetry clash REVERT: D 27 PHE cc_start: 0.7135 (m-10) cc_final: 0.6783 (m-10) REVERT: D 375 MET cc_start: 0.8240 (mtm) cc_final: 0.7989 (mtm) REVERT: E 241 LYS cc_start: 0.7520 (mmmt) cc_final: 0.6617 (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: 0.2872 time to fit residues: 110.5884 Evaluate side-chains 228 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 HIS 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 155 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 400 ASN D 253 HIS ** E 267 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 = 0.4307 r_free = 0.4307 target = 0.183528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134458 restraints weight = 19926.440| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.41 r_work: 0.3619 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16703 Z= 0.168 Angle : 0.497 7.738 22482 Z= 0.268 Chirality : 0.039 0.153 2410 Planarity : 0.003 0.040 2682 Dihedral : 15.921 175.394 2523 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.12 % Allowed : 20.46 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 1842 helix: 1.83 (0.14), residues: 1312 sheet: 0.65 (0.53), residues: 99 loop : -0.94 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 23 HIS 0.008 0.001 HIS D 253 PHE 0.011 0.001 PHE F 391 TYR 0.015 0.001 TYR D 382 ARG 0.008 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1078) hydrogen bonds : angle 4.26981 ( 3192) SS BOND : bond 0.00332 ( 17) SS BOND : angle 0.99902 ( 34) covalent geometry : bond 0.00385 (16686) covalent geometry : angle 0.49604 (22448) *********************** 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 278 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: C 46 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 284 TYR cc_start: 0.7659 (t80) cc_final: 0.7297 (t80) REVERT: D 50 ASP cc_start: 0.8474 (t0) cc_final: 0.8253 (t70) REVERT: D 95 THR cc_start: 0.8755 (t) cc_final: 0.8546 (p) REVERT: E 25 ASP cc_start: 0.7447 (m-30) cc_final: 0.7219 (m-30) REVERT: E 245 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7221 (mm-30) REVERT: F 243 GLU cc_start: 0.7733 (mp0) cc_final: 0.7520 (mp0) outliers start: 37 outliers final: 25 residues processed: 262 average time/residue: 0.2601 time to fit residues: 105.0917 Evaluate side-chains 240 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 253 HIS Chi-restraints excluded: chain D residue 265 MET 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 135 THR Chi-restraints excluded: chain F residue 161 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 163 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4313 r_free = 0.4313 target = 0.184357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.135368 restraints weight = 19732.530| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.40 r_work: 0.3602 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16703 Z= 0.134 Angle : 0.460 8.176 22482 Z= 0.248 Chirality : 0.038 0.142 2410 Planarity : 0.003 0.035 2682 Dihedral : 14.520 179.186 2518 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.29 % Allowed : 21.03 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 1842 helix: 2.06 (0.14), residues: 1310 sheet: 0.78 (0.55), residues: 93 loop : -1.06 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 23 HIS 0.010 0.001 HIS D 253 PHE 0.017 0.001 PHE D 244 TYR 0.014 0.001 TYR A 338 ARG 0.004 0.000 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 1078) hydrogen bonds : angle 4.10205 ( 3192) SS BOND : bond 0.00273 ( 17) SS BOND : angle 0.99125 ( 34) covalent geometry : bond 0.00302 (16686) covalent geometry : angle 0.45832 (22448) *********************** 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 275 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7326 (mtm180) cc_final: 0.6775 (mtp-110) REVERT: A 269 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8449 (mp) REVERT: A 275 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7620 (t80) REVERT: C 18 ARG cc_start: 0.6798 (ptp-110) cc_final: 0.6120 (ptm-80) REVERT: C 46 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7829 (tm-30) REVERT: C 284 TYR cc_start: 0.7638 (t80) cc_final: 0.7153 (t80) REVERT: C 385 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6683 (tp) REVERT: D 95 THR cc_start: 0.8702 (t) cc_final: 0.8476 (p) REVERT: D 151 SER cc_start: 0.7827 (t) cc_final: 0.7142 (p) REVERT: D 375 MET cc_start: 0.8256 (mtm) cc_final: 0.7546 (mtm) REVERT: E 25 ASP cc_start: 0.7411 (m-30) cc_final: 0.7079 (m-30) REVERT: E 154 GLU cc_start: 0.7758 (tt0) cc_final: 0.7347 (pt0) REVERT: E 245 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7129 (mm-30) REVERT: E 263 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6871 (mp) REVERT: F 243 GLU cc_start: 0.7905 (mp0) cc_final: 0.7614 (mp0) outliers start: 40 outliers final: 26 residues processed: 263 average time/residue: 0.2537 time to fit residues: 102.4061 Evaluate side-chains 246 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 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 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 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 59 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.181791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132334 restraints weight = 19870.591| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.40 r_work: 0.3569 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16703 Z= 0.180 Angle : 0.491 6.721 22482 Z= 0.265 Chirality : 0.040 0.161 2410 Planarity : 0.003 0.034 2682 Dihedral : 13.048 145.876 2518 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.21 % Allowed : 21.09 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1842 helix: 2.03 (0.14), residues: 1313 sheet: 0.59 (0.53), residues: 100 loop : -1.08 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 170 HIS 0.007 0.001 HIS D 253 PHE 0.019 0.001 PHE E 390 TYR 0.016 0.001 TYR C 382 ARG 0.006 0.000 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1078) hydrogen bonds : angle 4.11385 ( 3192) SS BOND : bond 0.00384 ( 17) SS BOND : angle 1.03861 ( 34) covalent geometry : bond 0.00420 (16686) covalent geometry : angle 0.48936 (22448) *********************** 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 284 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 3.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8398 (mp) REVERT: A 275 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7664 (t80) REVERT: C 46 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7873 (tm-30) REVERT: C 284 TYR cc_start: 0.7770 (t80) cc_final: 0.7541 (t80) REVERT: D 27 PHE cc_start: 0.6944 (m-10) cc_final: 0.6733 (m-10) REVERT: D 151 SER cc_start: 0.7884 (t) cc_final: 0.7200 (p) REVERT: D 375 MET cc_start: 0.8322 (mtm) cc_final: 0.8012 (mtm) REVERT: E 25 ASP cc_start: 0.7570 (m-30) cc_final: 0.7109 (m-30) REVERT: E 245 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7184 (mm-30) REVERT: E 263 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7064 (mp) outliers start: 56 outliers final: 37 residues processed: 270 average time/residue: 0.3444 time to fit residues: 144.7507 Evaluate side-chains 248 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 2.649 ------------------------------------------------------------------------------- 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 279 ILE Chi-restraints excluded: chain A residue 297 VAL 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 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 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 38 ILE Chi-restraints excluded: chain D residue 49 GLN 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 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 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 Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 74 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 155 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.181572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132268 restraints weight = 20115.003| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.40 r_work: 0.3570 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16703 Z= 0.181 Angle : 0.491 6.712 22482 Z= 0.266 Chirality : 0.040 0.181 2410 Planarity : 0.003 0.033 2682 Dihedral : 12.296 140.021 2518 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.38 % Allowed : 21.38 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 1842 helix: 2.04 (0.14), residues: 1313 sheet: 0.52 (0.52), residues: 106 loop : -1.10 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 170 HIS 0.009 0.001 HIS A 104 PHE 0.020 0.001 PHE E 390 TYR 0.014 0.001 TYR A 338 ARG 0.011 0.000 ARG E 103 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 1078) hydrogen bonds : angle 4.10524 ( 3192) SS BOND : bond 0.00400 ( 17) SS BOND : angle 1.01509 ( 34) covalent geometry : bond 0.00424 (16686) covalent geometry : angle 0.49026 (22448) *********************** 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 285 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.8033 (tpp) cc_final: 0.7470 (tpp) REVERT: A 269 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8495 (mp) REVERT: A 275 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7686 (t80) REVERT: C 18 ARG cc_start: 0.7005 (ptp-110) cc_final: 0.6426 (ptm160) REVERT: C 46 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 284 TYR cc_start: 0.7900 (t80) cc_final: 0.7660 (t80) REVERT: C 372 PHE cc_start: 0.4671 (OUTLIER) cc_final: 0.4451 (t80) REVERT: D 151 SER cc_start: 0.7874 (t) cc_final: 0.7207 (p) REVERT: D 375 MET cc_start: 0.8324 (mtm) cc_final: 0.8025 (mtm) REVERT: E 25 ASP cc_start: 0.7591 (m-30) cc_final: 0.7136 (m-30) REVERT: E 245 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7194 (mm-30) REVERT: E 263 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7141 (mp) REVERT: F 357 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7194 (pm20) outliers start: 59 outliers final: 45 residues processed: 271 average time/residue: 0.3600 time to fit residues: 151.3576 Evaluate side-chains 263 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 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 38 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 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 60 VAL 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 372 PHE Chi-restraints excluded: chain D residue 37 MET 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 275 PHE Chi-restraints excluded: chain D residue 283 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 151 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.181074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132112 restraints weight = 19977.177| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.38 r_work: 0.3581 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16703 Z= 0.179 Angle : 0.496 8.746 22482 Z= 0.266 Chirality : 0.040 0.183 2410 Planarity : 0.003 0.033 2682 Dihedral : 11.440 137.408 2518 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.84 % Allowed : 21.15 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 1842 helix: 2.03 (0.14), residues: 1314 sheet: 0.48 (0.52), residues: 106 loop : -1.12 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 170 HIS 0.010 0.001 HIS D 253 PHE 0.021 0.001 PHE E 390 TYR 0.015 0.001 TYR A 338 ARG 0.005 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 1078) hydrogen bonds : angle 4.09006 ( 3192) SS BOND : bond 0.00364 ( 17) SS BOND : angle 0.97936 ( 34) covalent geometry : bond 0.00419 (16686) covalent geometry : angle 0.49448 (22448) *********************** 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 288 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.8102 (tpp) cc_final: 0.7395 (tpt) REVERT: A 269 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8541 (mp) REVERT: A 275 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7817 (t80) REVERT: A 309 ARG cc_start: 0.8799 (tpt170) cc_final: 0.8522 (mtp180) REVERT: C 46 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 319 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7812 (tttt) REVERT: C 372 PHE cc_start: 0.4639 (OUTLIER) cc_final: 0.4429 (t80) REVERT: D 151 SER cc_start: 0.7947 (t) cc_final: 0.7268 (p) REVERT: D 375 MET cc_start: 0.8523 (mtm) cc_final: 0.8278 (mtm) REVERT: E 25 ASP cc_start: 0.7724 (m-30) cc_final: 0.7279 (m-30) REVERT: E 245 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7234 (mm-30) REVERT: E 263 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7261 (mp) REVERT: F 18 ARG cc_start: 0.7079 (mpp-170) cc_final: 0.6797 (mpp-170) REVERT: F 96 MET cc_start: 0.8971 (mtm) cc_final: 0.8517 (mpp) REVERT: F 357 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7120 (pm20) outliers start: 67 outliers final: 52 residues processed: 270 average time/residue: 0.2747 time to fit residues: 113.6239 Evaluate side-chains 267 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 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 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 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 319 LYS 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 372 PHE Chi-restraints excluded: chain D residue 37 MET 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 51 LYS 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 44 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 161 ILE 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 148 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 154 optimal weight: 0.0070 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.183040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134204 restraints weight = 19837.495| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.38 r_work: 0.3609 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16703 Z= 0.136 Angle : 0.472 8.976 22482 Z= 0.253 Chirality : 0.039 0.189 2410 Planarity : 0.003 0.032 2682 Dihedral : 10.951 138.179 2518 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.04 % Allowed : 22.18 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 1842 helix: 2.13 (0.14), residues: 1311 sheet: 0.60 (0.53), residues: 100 loop : -1.03 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 170 HIS 0.009 0.001 HIS D 253 PHE 0.026 0.001 PHE D 244 TYR 0.019 0.001 TYR C 382 ARG 0.004 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 1078) hydrogen bonds : angle 4.02074 ( 3192) SS BOND : bond 0.00370 ( 17) SS BOND : angle 0.86454 ( 34) covalent geometry : bond 0.00311 (16686) covalent geometry : angle 0.47164 (22448) *********************** 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 274 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7875 (tpp) cc_final: 0.7319 (tpp) REVERT: A 269 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 275 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7684 (t80) REVERT: A 309 ARG cc_start: 0.8537 (tpt170) cc_final: 0.8231 (mtp180) REVERT: C 46 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7829 (tm-30) REVERT: C 284 TYR cc_start: 0.7615 (t80) cc_final: 0.7075 (t80) REVERT: C 319 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7646 (tttt) REVERT: D 151 SER cc_start: 0.7970 (t) cc_final: 0.7268 (p) REVERT: D 337 MET cc_start: 0.8369 (mmm) cc_final: 0.8085 (mmm) REVERT: D 375 MET cc_start: 0.8298 (mtm) cc_final: 0.8036 (mtm) REVERT: E 25 ASP cc_start: 0.7656 (m-30) cc_final: 0.7181 (m-30) REVERT: E 245 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7179 (mm-30) REVERT: E 263 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7130 (mp) REVERT: F 18 ARG cc_start: 0.7118 (mpp-170) cc_final: 0.6851 (mpp-170) REVERT: F 247 LYS cc_start: 0.8635 (tttt) cc_final: 0.7931 (tptt) REVERT: F 357 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7227 (pm20) outliers start: 53 outliers final: 42 residues processed: 261 average time/residue: 0.2775 time to fit residues: 110.9395 Evaluate side-chains 259 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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 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 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 60 VAL 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 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 319 LYS 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 D residue 37 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 51 LYS 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 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 161 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 88 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132867 restraints weight = 19827.180| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.38 r_work: 0.3567 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16703 Z= 0.162 Angle : 0.494 9.727 22482 Z= 0.265 Chirality : 0.040 0.178 2410 Planarity : 0.003 0.032 2682 Dihedral : 10.812 138.423 2518 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.55 % Allowed : 21.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 1842 helix: 2.06 (0.14), residues: 1315 sheet: 0.47 (0.51), residues: 106 loop : -1.09 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 170 HIS 0.009 0.001 HIS D 253 PHE 0.025 0.001 PHE E 390 TYR 0.015 0.001 TYR A 338 ARG 0.004 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 1078) hydrogen bonds : angle 4.04471 ( 3192) SS BOND : bond 0.00317 ( 17) SS BOND : angle 0.90524 ( 34) covalent geometry : bond 0.00380 (16686) covalent geometry : angle 0.49315 (22448) *********************** 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 282 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 220 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.8119 (tpp) cc_final: 0.7659 (tpp) REVERT: A 269 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8572 (mp) REVERT: A 275 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7802 (t80) REVERT: A 309 ARG cc_start: 0.8741 (tpt170) cc_final: 0.8479 (mtp180) REVERT: C 46 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7846 (tm-30) REVERT: C 284 TYR cc_start: 0.7823 (t80) cc_final: 0.7201 (t80) REVERT: C 319 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7832 (tttt) REVERT: D 103 ARG cc_start: 0.8057 (ttt-90) cc_final: 0.7752 (tpp-160) REVERT: D 151 SER cc_start: 0.7986 (t) cc_final: 0.7291 (p) REVERT: D 375 MET cc_start: 0.8538 (mtm) cc_final: 0.8243 (mtm) REVERT: E 25 ASP cc_start: 0.7758 (m-30) cc_final: 0.7276 (m-30) REVERT: E 245 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7225 (mm-30) REVERT: E 263 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7219 (mp) REVERT: E 401 LYS cc_start: 0.4374 (pttm) cc_final: 0.4022 (tmmt) REVERT: F 18 ARG cc_start: 0.7213 (mpp-170) cc_final: 0.6883 (mpp-170) REVERT: F 247 LYS cc_start: 0.8639 (tttt) cc_final: 0.7915 (tptt) REVERT: F 357 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7047 (pm20) outliers start: 62 outliers final: 49 residues processed: 265 average time/residue: 0.2652 time to fit residues: 106.2599 Evaluate side-chains 268 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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 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 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 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 60 VAL 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 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 319 LYS 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 D residue 37 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS 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 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.183374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134342 restraints weight = 19763.266| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.38 r_work: 0.3596 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16703 Z= 0.137 Angle : 0.481 10.376 22482 Z= 0.258 Chirality : 0.039 0.198 2410 Planarity : 0.003 0.032 2682 Dihedral : 10.461 137.604 2518 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.81 % Allowed : 22.46 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 1842 helix: 2.15 (0.14), residues: 1310 sheet: 0.68 (0.53), residues: 99 loop : -1.01 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 170 HIS 0.012 0.001 HIS D 253 PHE 0.031 0.001 PHE D 244 TYR 0.019 0.001 TYR C 382 ARG 0.004 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1078) hydrogen bonds : angle 4.00053 ( 3192) SS BOND : bond 0.00289 ( 17) SS BOND : angle 0.89899 ( 34) covalent geometry : bond 0.00314 (16686) covalent geometry : angle 0.47995 (22448) *********************** 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 272 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.8181 (tpp) cc_final: 0.7717 (tpp) REVERT: A 269 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8599 (mp) REVERT: A 275 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7797 (t80) REVERT: A 309 ARG cc_start: 0.8734 (tpt170) cc_final: 0.8441 (mtp180) REVERT: C 46 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 284 TYR cc_start: 0.7923 (t80) cc_final: 0.7253 (t80) REVERT: C 319 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7856 (tttt) REVERT: D 50 ASP cc_start: 0.8414 (t70) cc_final: 0.8176 (t70) REVERT: D 151 SER cc_start: 0.8004 (t) cc_final: 0.7356 (p) REVERT: D 337 MET cc_start: 0.8492 (mmm) cc_final: 0.8254 (mmm) REVERT: D 372 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6509 (t80) REVERT: D 375 MET cc_start: 0.8453 (mtm) cc_final: 0.8203 (mtm) REVERT: E 25 ASP cc_start: 0.7789 (m-30) cc_final: 0.7301 (m-30) REVERT: E 245 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7205 (mm-30) REVERT: E 263 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7223 (mp) REVERT: F 18 ARG cc_start: 0.7252 (mpp-170) cc_final: 0.6944 (mpp-170) REVERT: F 144 PHE cc_start: 0.7519 (t80) cc_final: 0.7302 (t80) REVERT: F 247 LYS cc_start: 0.8668 (tttt) cc_final: 0.7957 (tptt) REVERT: F 357 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7059 (pm20) outliers start: 49 outliers final: 41 residues processed: 260 average time/residue: 0.2681 time to fit residues: 105.8656 Evaluate side-chains 265 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 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 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 330 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 319 LYS 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 D residue 37 MET 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 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS 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 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 161 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.181180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132152 restraints weight = 19894.870| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.38 r_work: 0.3579 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16703 Z= 0.187 Angle : 0.529 10.833 22482 Z= 0.283 Chirality : 0.040 0.208 2410 Planarity : 0.003 0.031 2682 Dihedral : 10.618 136.493 2518 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.27 % Allowed : 22.35 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 1842 helix: 2.01 (0.14), residues: 1315 sheet: 0.44 (0.51), residues: 106 loop : -1.14 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 168 HIS 0.008 0.001 HIS D 253 PHE 0.032 0.001 PHE D 244 TYR 0.014 0.001 TYR A 338 ARG 0.005 0.000 ARG F 355 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 1078) hydrogen bonds : angle 4.10845 ( 3192) SS BOND : bond 0.00378 ( 17) SS BOND : angle 0.97901 ( 34) covalent geometry : bond 0.00439 (16686) covalent geometry : angle 0.52806 (22448) ********************** 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 277 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.8129 (tpp) cc_final: 0.7439 (tpt) REVERT: A 269 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 275 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7825 (t80) REVERT: A 309 ARG cc_start: 0.8752 (tpt170) cc_final: 0.8481 (mtp180) REVERT: C 46 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7858 (tm-30) REVERT: C 284 TYR cc_start: 0.7924 (t80) cc_final: 0.7283 (t80) REVERT: C 319 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7872 (tttt) REVERT: D 375 MET cc_start: 0.8581 (mtm) cc_final: 0.8305 (mtm) REVERT: E 25 ASP cc_start: 0.7785 (m-30) cc_final: 0.7288 (m-30) REVERT: E 245 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7268 (mm-30) REVERT: E 263 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7213 (mp) REVERT: E 308 TYR cc_start: 0.9219 (m-80) cc_final: 0.8907 (m-80) REVERT: F 247 LYS cc_start: 0.8671 (tttt) cc_final: 0.7904 (tptt) REVERT: F 357 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7008 (pm20) outliers start: 57 outliers final: 47 residues processed: 263 average time/residue: 0.2685 time to fit residues: 107.4981 Evaluate side-chains 270 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 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 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU 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 319 LYS 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 D residue 37 MET 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 51 LYS 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 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** 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 = 0.4297 r_free = 0.4297 target = 0.183112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134366 restraints weight = 19789.987| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.37 r_work: 0.3612 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16703 Z= 0.139 Angle : 0.501 12.038 22482 Z= 0.268 Chirality : 0.039 0.199 2410 Planarity : 0.003 0.033 2682 Dihedral : 10.328 135.164 2518 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.98 % Allowed : 22.69 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 1842 helix: 2.11 (0.14), residues: 1309 sheet: 0.56 (0.53), residues: 100 loop : -1.07 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 168 HIS 0.010 0.001 HIS D 253 PHE 0.032 0.001 PHE D 244 TYR 0.016 0.001 TYR D 284 ARG 0.005 0.000 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 1078) hydrogen bonds : angle 4.04354 ( 3192) SS BOND : bond 0.00252 ( 17) SS BOND : angle 0.93558 ( 34) covalent geometry : bond 0.00320 (16686) covalent geometry : angle 0.49967 (22448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10274.35 seconds wall clock time: 181 minutes 15.45 seconds (10875.45 seconds total)