Starting phenix.real_space_refine on Sun Aug 24 02:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dr8_27674/08_2025/8dr8_27674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dr8_27674/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dr8_27674/08_2025/8dr8_27674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dr8_27674/08_2025/8dr8_27674.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dr8_27674/08_2025/8dr8_27674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dr8_27674/08_2025/8dr8_27674.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 106 5.16 5 C 10800 2.51 5 N 2525 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16270 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2667 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2519 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2653 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2651 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 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: 4.16, per 1000 atoms: 0.26 Number of scatterers: 16270 At special positions: 0 Unit cell: (95.368, 107.944, 138.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 9 15.00 O 2830 8.00 N 2525 7.00 C 10800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.04 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 794.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 76.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 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: 3.01 Time building geometry restraints manager: 1.72 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: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.320 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- 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 : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.17 % Allowed : 21.55 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.18), residues: 1842 helix: 1.13 (0.13), residues: 1290 sheet: 0.88 (0.54), residues: 104 loop : -0.86 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 118 TYR 0.036 0.001 TYR C 284 PHE 0.043 0.002 PHE E 390 TRP 0.060 0.002 TRP C 23 HIS 0.020 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00652 (16686) covalent geometry : angle 0.81718 (22448) SS BOND : bond 0.00356 ( 17) SS BOND : angle 1.32058 ( 34) hydrogen bonds : bond 0.11542 ( 1078) hydrogen bonds : angle 5.73965 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: D 27 PHE cc_start: 0.7135 (m-10) cc_final: 0.6784 (m-10) REVERT: D 33 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8541 (tp) REVERT: D 375 MET cc_start: 0.8240 (mtm) cc_final: 0.7990 (mtm) REVERT: E 241 LYS cc_start: 0.7520 (mmmt) cc_final: 0.6618 (tppt) REVERT: E 245 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6782 (mm-30) REVERT: F 243 GLU cc_start: 0.7778 (mp0) cc_final: 0.7480 (mp0) outliers start: 3 outliers final: 2 residues processed: 245 average time/residue: 0.1143 time to fit residues: 44.1459 Evaluate side-chains 229 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain E residue 52 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 400 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.184184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135157 restraints weight = 19959.300| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.41 r_work: 0.3605 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16703 Z= 0.156 Angle : 0.490 7.724 22482 Z= 0.264 Chirality : 0.039 0.155 2410 Planarity : 0.003 0.041 2682 Dihedral : 15.905 173.854 2525 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.95 % Allowed : 20.34 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.19), residues: 1842 helix: 1.86 (0.14), residues: 1311 sheet: 0.71 (0.54), residues: 98 loop : -0.92 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 118 TYR 0.016 0.001 TYR D 382 PHE 0.011 0.001 PHE A 374 TRP 0.030 0.001 TRP C 23 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00356 (16686) covalent geometry : angle 0.48936 (22448) SS BOND : bond 0.00314 ( 17) SS BOND : angle 0.98390 ( 34) hydrogen bonds : bond 0.03787 ( 1078) hydrogen bonds : angle 4.25331 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: C 46 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 284 TYR cc_start: 0.7474 (t80) cc_final: 0.7120 (t80) REVERT: D 95 THR cc_start: 0.8694 (t) cc_final: 0.8469 (p) REVERT: E 25 ASP cc_start: 0.7352 (m-30) cc_final: 0.7148 (m-30) REVERT: E 245 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7181 (mm-30) REVERT: F 243 GLU cc_start: 0.7734 (mp0) cc_final: 0.7530 (mp0) outliers start: 34 outliers final: 22 residues processed: 263 average time/residue: 0.1141 time to fit residues: 46.4945 Evaluate side-chains 235 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 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 153 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 158 optimal weight: 0.0470 chunk 103 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.185055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135769 restraints weight = 20065.940| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.42 r_work: 0.3600 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16703 Z= 0.126 Angle : 0.452 8.050 22482 Z= 0.244 Chirality : 0.038 0.142 2410 Planarity : 0.003 0.036 2682 Dihedral : 14.153 174.864 2518 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.23 % Allowed : 21.03 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.19), residues: 1842 helix: 2.10 (0.14), residues: 1312 sheet: 0.79 (0.55), residues: 93 loop : -1.02 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 389 TYR 0.016 0.001 TYR C 382 PHE 0.018 0.001 PHE D 244 TRP 0.019 0.001 TRP C 23 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00281 (16686) covalent geometry : angle 0.45094 (22448) SS BOND : bond 0.00284 ( 17) SS BOND : angle 0.91376 ( 34) hydrogen bonds : bond 0.03507 ( 1078) hydrogen bonds : angle 4.05370 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 275 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7623 (t80) REVERT: C 18 ARG cc_start: 0.6795 (ptp-110) cc_final: 0.6178 (ptm160) REVERT: C 46 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7770 (tm-30) REVERT: C 284 TYR cc_start: 0.7647 (t80) cc_final: 0.7178 (t80) REVERT: C 385 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6515 (tp) REVERT: D 95 THR cc_start: 0.8677 (t) cc_final: 0.8455 (p) REVERT: D 375 MET cc_start: 0.8219 (mtm) cc_final: 0.7521 (mtm) REVERT: E 25 ASP cc_start: 0.7422 (m-30) cc_final: 0.7096 (m-30) REVERT: E 154 GLU cc_start: 0.7763 (tt0) cc_final: 0.7304 (pt0) REVERT: E 245 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7120 (mm-30) REVERT: E 263 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6852 (mp) REVERT: F 243 GLU cc_start: 0.7909 (mp0) cc_final: 0.7611 (mp0) outliers start: 39 outliers final: 25 residues processed: 268 average time/residue: 0.1095 time to fit residues: 45.9126 Evaluate side-chains 252 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU 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 37 MET 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 104 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 129 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 178 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.185699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.136351 restraints weight = 19842.595| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.42 r_work: 0.3612 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16703 Z= 0.116 Angle : 0.440 7.031 22482 Z= 0.237 Chirality : 0.038 0.162 2410 Planarity : 0.003 0.035 2682 Dihedral : 12.717 160.988 2518 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 21.26 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.19), residues: 1842 helix: 2.20 (0.14), residues: 1314 sheet: 0.95 (0.55), residues: 92 loop : -0.96 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 355 TYR 0.013 0.001 TYR A 338 PHE 0.022 0.001 PHE D 244 TRP 0.020 0.001 TRP F 170 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00258 (16686) covalent geometry : angle 0.43856 (22448) SS BOND : bond 0.00274 ( 17) SS BOND : angle 0.92687 ( 34) hydrogen bonds : bond 0.03344 ( 1078) hydrogen bonds : angle 3.95035 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 275 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 51 LYS cc_start: 0.8328 (ptmt) cc_final: 0.8126 (ptmt) REVERT: C 46 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7730 (tm-30) REVERT: C 284 TYR cc_start: 0.7590 (t80) cc_final: 0.7261 (t80) REVERT: D 151 SER cc_start: 0.7825 (t) cc_final: 0.7151 (p) REVERT: D 375 MET cc_start: 0.8261 (mtm) cc_final: 0.7475 (mtm) REVERT: E 154 GLU cc_start: 0.7672 (tt0) cc_final: 0.7240 (pt0) REVERT: E 245 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7137 (mm-30) REVERT: E 263 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6859 (mp) REVERT: F 247 LYS cc_start: 0.8588 (tttt) cc_final: 0.7888 (tptt) outliers start: 35 outliers final: 22 residues processed: 270 average time/residue: 0.1039 time to fit residues: 43.3782 Evaluate side-chains 253 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 104 ASP 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 135 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 67 optimal weight: 0.0870 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.186287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137273 restraints weight = 19830.413| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.41 r_work: 0.3620 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16703 Z= 0.107 Angle : 0.432 6.304 22482 Z= 0.233 Chirality : 0.038 0.158 2410 Planarity : 0.003 0.035 2682 Dihedral : 11.736 134.826 2518 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.87 % Allowed : 20.69 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.19), residues: 1842 helix: 2.29 (0.14), residues: 1314 sheet: 1.09 (0.55), residues: 92 loop : -0.96 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 103 TYR 0.018 0.001 TYR C 382 PHE 0.022 0.001 PHE E 390 TRP 0.023 0.001 TRP F 170 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00233 (16686) covalent geometry : angle 0.43062 (22448) SS BOND : bond 0.00248 ( 17) SS BOND : angle 0.84987 ( 34) hydrogen bonds : bond 0.03245 ( 1078) hydrogen bonds : angle 3.89735 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 275 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7555 (t80) REVERT: A 309 ARG cc_start: 0.8429 (tpt170) cc_final: 0.8153 (mtp85) REVERT: B 51 LYS cc_start: 0.8337 (ptmt) cc_final: 0.8124 (ptmt) REVERT: C 46 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7842 (tm-30) REVERT: C 284 TYR cc_start: 0.7665 (t80) cc_final: 0.7409 (t80) REVERT: C 385 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6512 (tp) REVERT: D 151 SER cc_start: 0.7880 (t) cc_final: 0.7215 (p) REVERT: D 337 MET cc_start: 0.8366 (mmm) cc_final: 0.8028 (mmm) REVERT: D 375 MET cc_start: 0.8275 (mtm) cc_final: 0.7535 (mtm) REVERT: E 25 ASP cc_start: 0.7328 (m-30) cc_final: 0.7057 (m-30) REVERT: E 154 GLU cc_start: 0.7684 (tt0) cc_final: 0.7263 (pt0) REVERT: E 245 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7098 (mm-30) REVERT: E 263 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6631 (tt) REVERT: E 389 ARG cc_start: 0.7505 (ttm110) cc_final: 0.6968 (mtp85) REVERT: F 357 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7247 (pm20) outliers start: 50 outliers final: 31 residues processed: 280 average time/residue: 0.1121 time to fit residues: 48.2003 Evaluate side-chains 267 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR 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 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.185008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.136049 restraints weight = 19809.816| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.39 r_work: 0.3613 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16703 Z= 0.127 Angle : 0.453 9.190 22482 Z= 0.244 Chirality : 0.038 0.170 2410 Planarity : 0.003 0.034 2682 Dihedral : 10.890 106.038 2518 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.50 % Allowed : 20.46 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.19), residues: 1842 helix: 2.28 (0.14), residues: 1313 sheet: 1.06 (0.55), residues: 92 loop : -0.99 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 18 TYR 0.020 0.001 TYR D 382 PHE 0.023 0.001 PHE E 390 TRP 0.024 0.001 TRP F 170 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00288 (16686) covalent geometry : angle 0.45194 (22448) SS BOND : bond 0.00257 ( 17) SS BOND : angle 0.86050 ( 34) hydrogen bonds : bond 0.03336 ( 1078) hydrogen bonds : angle 3.89337 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.7999 (ptpp) cc_final: 0.7634 (ptpp) REVERT: A 265 MET cc_start: 0.7983 (tpp) cc_final: 0.7432 (tpp) REVERT: A 269 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 275 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 309 ARG cc_start: 0.8485 (tpt170) cc_final: 0.8198 (mtp-110) REVERT: B 51 LYS cc_start: 0.8299 (ptmt) cc_final: 0.8077 (ptmt) REVERT: C 46 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7671 (tm-30) REVERT: C 284 TYR cc_start: 0.7827 (t80) cc_final: 0.7615 (t80) REVERT: C 372 PHE cc_start: 0.4627 (OUTLIER) cc_final: 0.4400 (t80) REVERT: D 151 SER cc_start: 0.7888 (t) cc_final: 0.7227 (p) REVERT: D 334 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8624 (mm) REVERT: D 375 MET cc_start: 0.8248 (mtm) cc_final: 0.7892 (mtm) REVERT: E 25 ASP cc_start: 0.7330 (m-30) cc_final: 0.6987 (m-30) REVERT: E 154 GLU cc_start: 0.7694 (tt0) cc_final: 0.7268 (pt0) REVERT: E 245 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7237 (mm-30) REVERT: E 263 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6593 (tt) REVERT: E 389 ARG cc_start: 0.7533 (ttm110) cc_final: 0.6985 (mtp85) REVERT: E 390 PHE cc_start: 0.6964 (t80) cc_final: 0.6599 (t80) REVERT: F 96 MET cc_start: 0.8870 (mtm) cc_final: 0.8412 (mpp) REVERT: F 243 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: F 247 LYS cc_start: 0.8598 (tttt) cc_final: 0.7902 (tptt) REVERT: F 357 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7102 (pm20) outliers start: 61 outliers final: 43 residues processed: 288 average time/residue: 0.1042 time to fit residues: 46.2570 Evaluate side-chains 286 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR 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 157 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR 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 104 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 243 GLU 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 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 167 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 159 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- 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** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.181279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131931 restraints weight = 19815.820| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.39 r_work: 0.3532 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16703 Z= 0.206 Angle : 0.512 8.543 22482 Z= 0.277 Chirality : 0.041 0.186 2410 Planarity : 0.003 0.032 2682 Dihedral : 11.014 109.235 2518 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.67 % Allowed : 20.69 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.19), residues: 1842 helix: 2.10 (0.14), residues: 1313 sheet: 0.58 (0.52), residues: 106 loop : -1.14 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.019 0.001 TYR C 382 PHE 0.021 0.001 PHE E 390 TRP 0.026 0.001 TRP F 170 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00486 (16686) covalent geometry : angle 0.51082 (22448) SS BOND : bond 0.00418 ( 17) SS BOND : angle 1.01647 ( 34) hydrogen bonds : bond 0.03726 ( 1078) hydrogen bonds : angle 4.06001 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 219 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.7998 (ptpp) cc_final: 0.7568 (ptpp) REVERT: A 265 MET cc_start: 0.7893 (tpp) cc_final: 0.7388 (tpp) REVERT: A 269 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 275 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7660 (t80) REVERT: B 51 LYS cc_start: 0.8411 (ptmt) cc_final: 0.8101 (ptmt) REVERT: C 46 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 284 TYR cc_start: 0.7988 (t80) cc_final: 0.7409 (t80) REVERT: D 27 PHE cc_start: 0.6916 (m-10) cc_final: 0.6713 (m-10) REVERT: D 151 SER cc_start: 0.7900 (t) cc_final: 0.7229 (p) REVERT: D 334 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8671 (mm) REVERT: D 337 MET cc_start: 0.8318 (mmm) cc_final: 0.8055 (mmm) REVERT: D 375 MET cc_start: 0.8343 (mtm) cc_final: 0.8044 (mtm) REVERT: E 245 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7135 (mm-30) REVERT: E 263 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7036 (mp) REVERT: F 247 LYS cc_start: 0.8632 (tttt) cc_final: 0.7921 (tptt) REVERT: F 357 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7078 (pm20) outliers start: 64 outliers final: 48 residues processed: 264 average time/residue: 0.1058 time to fit residues: 42.6324 Evaluate side-chains 270 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR 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 D residue 38 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL 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 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.183453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134457 restraints weight = 19825.456| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.38 r_work: 0.3575 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16703 Z= 0.139 Angle : 0.474 9.123 22482 Z= 0.256 Chirality : 0.039 0.189 2410 Planarity : 0.003 0.032 2682 Dihedral : 10.490 109.828 2518 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.92 % Allowed : 21.89 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.19), residues: 1842 helix: 2.16 (0.14), residues: 1313 sheet: 0.70 (0.54), residues: 100 loop : -1.04 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 118 TYR 0.018 0.001 TYR C 382 PHE 0.026 0.001 PHE E 390 TRP 0.033 0.001 TRP E 168 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00319 (16686) covalent geometry : angle 0.47257 (22448) SS BOND : bond 0.00297 ( 17) SS BOND : angle 0.93554 ( 34) hydrogen bonds : bond 0.03410 ( 1078) hydrogen bonds : angle 3.97844 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LYS cc_start: 0.8017 (ptpp) cc_final: 0.7599 (ptpp) REVERT: A 265 MET cc_start: 0.7923 (tpp) cc_final: 0.7407 (tpp) REVERT: A 269 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 275 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7643 (t80) REVERT: A 309 ARG cc_start: 0.8527 (tpt170) cc_final: 0.8187 (mtp85) REVERT: B 51 LYS cc_start: 0.8366 (ptmt) cc_final: 0.8139 (ptmt) REVERT: C 46 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 284 TYR cc_start: 0.7962 (t80) cc_final: 0.7353 (t80) REVERT: C 375 MET cc_start: 0.6055 (mtm) cc_final: 0.5793 (mtm) REVERT: D 151 SER cc_start: 0.7897 (t) cc_final: 0.7276 (p) REVERT: D 334 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8631 (mm) REVERT: D 375 MET cc_start: 0.8290 (mtm) cc_final: 0.7966 (mtm) REVERT: E 245 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7116 (mm-30) REVERT: E 263 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7023 (mp) REVERT: E 390 PHE cc_start: 0.6961 (t80) cc_final: 0.6665 (t80) REVERT: F 247 LYS cc_start: 0.8621 (tttt) cc_final: 0.7930 (tptt) REVERT: F 357 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7111 (pm20) outliers start: 51 outliers final: 42 residues processed: 273 average time/residue: 0.1095 time to fit residues: 45.4314 Evaluate side-chains 273 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR 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 D residue 44 THR Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 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 104 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.0770 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- 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** 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 = 0.4316 r_free = 0.4316 target = 0.184451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135914 restraints weight = 19709.311| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.36 r_work: 0.3601 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16703 Z= 0.119 Angle : 0.469 10.559 22482 Z= 0.252 Chirality : 0.039 0.179 2410 Planarity : 0.003 0.032 2682 Dihedral : 10.164 112.848 2518 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.81 % Allowed : 22.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.19), residues: 1842 helix: 2.23 (0.14), residues: 1313 sheet: 0.81 (0.54), residues: 99 loop : -0.96 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 355 TYR 0.015 0.001 TYR A 338 PHE 0.027 0.001 PHE A 250 TRP 0.045 0.001 TRP E 168 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00265 (16686) covalent geometry : angle 0.46784 (22448) SS BOND : bond 0.00239 ( 17) SS BOND : angle 0.87042 ( 34) hydrogen bonds : bond 0.03295 ( 1078) hydrogen bonds : angle 3.92987 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LYS cc_start: 0.8005 (ptpp) cc_final: 0.7584 (ptpp) REVERT: A 265 MET cc_start: 0.7924 (tpp) cc_final: 0.7488 (tpp) REVERT: A 269 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 275 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7581 (t80) REVERT: A 309 ARG cc_start: 0.8465 (tpt170) cc_final: 0.8167 (mtp85) REVERT: B 350 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7651 (ptpt) REVERT: C 46 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 284 TYR cc_start: 0.7893 (t80) cc_final: 0.7309 (t80) REVERT: D 334 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8609 (mm) REVERT: D 337 MET cc_start: 0.8345 (mmm) cc_final: 0.8109 (mmm) REVERT: D 375 MET cc_start: 0.8337 (mtm) cc_final: 0.8009 (mtm) REVERT: E 245 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7104 (mm-30) REVERT: E 389 ARG cc_start: 0.7524 (ttm110) cc_final: 0.6821 (mtp85) REVERT: E 390 PHE cc_start: 0.6928 (t80) cc_final: 0.6436 (t80) REVERT: F 247 LYS cc_start: 0.8628 (tttt) cc_final: 0.7910 (tptt) REVERT: F 357 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7379 (pm20) outliers start: 49 outliers final: 41 residues processed: 270 average time/residue: 0.1176 time to fit residues: 47.9006 Evaluate side-chains 275 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 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 163 CYS 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 320 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE 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 334 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 140 SER 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 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 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.182337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133776 restraints weight = 19751.812| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.36 r_work: 0.3572 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16703 Z= 0.165 Angle : 0.504 10.469 22482 Z= 0.272 Chirality : 0.040 0.192 2410 Planarity : 0.003 0.030 2682 Dihedral : 10.181 115.906 2518 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.69 % Allowed : 22.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.19), residues: 1842 helix: 2.14 (0.14), residues: 1313 sheet: 0.67 (0.53), residues: 100 loop : -1.04 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.022 0.001 TYR D 382 PHE 0.027 0.001 PHE A 250 TRP 0.058 0.002 TRP E 168 HIS 0.011 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00385 (16686) covalent geometry : angle 0.50292 (22448) SS BOND : bond 0.00330 ( 17) SS BOND : angle 0.95524 ( 34) hydrogen bonds : bond 0.03503 ( 1078) hydrogen bonds : angle 4.00842 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7640 (ptpp) REVERT: A 265 MET cc_start: 0.8204 (tpp) cc_final: 0.7726 (tpp) REVERT: A 269 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8597 (mp) REVERT: A 275 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 309 ARG cc_start: 0.8759 (tpt170) cc_final: 0.8441 (mtp85) REVERT: C 46 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 284 TYR cc_start: 0.8121 (t80) cc_final: 0.7496 (t80) REVERT: D 103 ARG cc_start: 0.8115 (ttt-90) cc_final: 0.7791 (tpp-160) REVERT: D 334 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8672 (mm) REVERT: D 337 MET cc_start: 0.8449 (mmm) cc_final: 0.8204 (mmm) REVERT: D 375 MET cc_start: 0.8459 (mtm) cc_final: 0.8181 (mtm) REVERT: E 245 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7152 (mm-30) REVERT: F 247 LYS cc_start: 0.8643 (tttt) cc_final: 0.7901 (tptt) REVERT: F 357 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7047 (pm20) outliers start: 47 outliers final: 42 residues processed: 263 average time/residue: 0.1214 time to fit residues: 48.4331 Evaluate side-chains 268 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR 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 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 334 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 140 SER 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 104 ASP 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 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 90 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.183974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.135315 restraints weight = 19699.353| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.37 r_work: 0.3590 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16703 Z= 0.131 Angle : 0.490 11.943 22482 Z= 0.264 Chirality : 0.039 0.192 2410 Planarity : 0.003 0.031 2682 Dihedral : 9.923 117.049 2518 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.52 % Allowed : 22.41 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.19), residues: 1842 helix: 2.20 (0.14), residues: 1312 sheet: 0.72 (0.54), residues: 100 loop : -1.00 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.016 0.001 TYR D 284 PHE 0.030 0.001 PHE E 390 TRP 0.053 0.002 TRP E 168 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00300 (16686) covalent geometry : angle 0.48912 (22448) SS BOND : bond 0.00259 ( 17) SS BOND : angle 0.89686 ( 34) hydrogen bonds : bond 0.03355 ( 1078) hydrogen bonds : angle 3.97905 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3465.13 seconds wall clock time: 60 minutes 32.64 seconds (3632.64 seconds total)