Starting phenix.real_space_refine on Tue Dec 31 19:26:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dr8_27674/12_2024/8dr8_27674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dr8_27674/12_2024/8dr8_27674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dr8_27674/12_2024/8dr8_27674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dr8_27674/12_2024/8dr8_27674.map" model { file = "/net/cci-nas-00/data/ceres_data/8dr8_27674/12_2024/8dr8_27674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dr8_27674/12_2024/8dr8_27674.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 106 5.16 5 C 10800 2.51 5 N 2525 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16270 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2667 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2519 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2653 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2651 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.68, per 1000 atoms: 0.66 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: 4.47 Conformation dependent library (CDL) restraints added in 2.0 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 76.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 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: 4.90 Time building geometry restraints manager: 5.14 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: 5.740 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.080 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.610 ------------------------------------------------------------------------------- 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 16686 Z= 0.421 Angle : 0.817 13.914 22448 Z= 0.398 Chirality : 0.047 0.420 2410 Planarity : 0.005 0.062 2682 Dihedral : 20.916 178.780 6276 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.17 % Allowed : 21.55 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 1842 helix: 1.13 (0.13), residues: 1290 sheet: 0.88 (0.54), residues: 104 loop : -0.86 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 23 HIS 0.020 0.002 HIS A 253 PHE 0.043 0.002 PHE E 390 TYR 0.036 0.001 TYR C 284 ARG 0.013 0.001 ARG F 118 *********************** 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 : 1.903 Fit side-chains revert: symmetry clash REVERT: D 27 PHE cc_start: 0.7135 (m-10) cc_final: 0.6783 (m-10) REVERT: D 375 MET cc_start: 0.8240 (mtm) cc_final: 0.7989 (mtm) REVERT: E 241 LYS cc_start: 0.7520 (mmmt) cc_final: 0.6617 (tppt) REVERT: E 245 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6782 (mm-30) REVERT: F 243 GLU cc_start: 0.7778 (mp0) cc_final: 0.7480 (mp0) outliers start: 3 outliers final: 2 residues processed: 245 average time/residue: 0.2626 time to fit residues: 99.7519 Evaluate side-chains 228 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain E residue 52 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 400 ASN D 253 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16686 Z= 0.243 Angle : 0.496 7.738 22448 Z= 0.268 Chirality : 0.039 0.153 2410 Planarity : 0.003 0.040 2682 Dihedral : 15.921 175.394 2523 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.12 % Allowed : 20.46 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 1842 helix: 1.83 (0.14), residues: 1312 sheet: 0.65 (0.53), residues: 99 loop : -0.94 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 23 HIS 0.008 0.001 HIS D 253 PHE 0.011 0.001 PHE F 391 TYR 0.015 0.001 TYR D 382 ARG 0.008 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 1.857 Fit side-chains revert: symmetry clash REVERT: C 46 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7902 (tm-30) REVERT: E 245 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7038 (mm-30) REVERT: F 243 GLU cc_start: 0.7740 (mp0) cc_final: 0.7537 (mp0) outliers start: 37 outliers final: 25 residues processed: 262 average time/residue: 0.2767 time to fit residues: 111.3534 Evaluate side-chains 238 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** E 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16686 Z= 0.351 Angle : 0.535 7.538 22448 Z= 0.290 Chirality : 0.041 0.147 2410 Planarity : 0.003 0.035 2682 Dihedral : 14.597 162.786 2518 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.44 % Allowed : 20.86 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 1842 helix: 1.81 (0.14), residues: 1313 sheet: 0.42 (0.52), residues: 106 loop : -1.15 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 23 HIS 0.008 0.001 HIS D 253 PHE 0.016 0.002 PHE E 390 TYR 0.013 0.002 TYR A 338 ARG 0.005 0.000 ARG F 18 *********************** 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 288 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8409 (mp) REVERT: A 275 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 357 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7175 (ttp80) REVERT: A 404 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8078 (tp-100) REVERT: C 46 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8078 (tm-30) REVERT: C 143 TRP cc_start: 0.7144 (t60) cc_final: 0.6766 (t60) REVERT: C 372 PHE cc_start: 0.5550 (OUTLIER) cc_final: 0.5308 (t80) REVERT: C 385 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6996 (tp) REVERT: D 27 PHE cc_start: 0.6965 (m-10) cc_final: 0.6749 (m-10) REVERT: D 274 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8425 (tttp) REVERT: D 372 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6546 (t80) REVERT: E 245 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7077 (mm-30) REVERT: E 263 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7420 (mp) REVERT: F 145 TRP cc_start: 0.8159 (p-90) cc_final: 0.7956 (p-90) outliers start: 60 outliers final: 39 residues processed: 271 average time/residue: 0.2767 time to fit residues: 114.9684 Evaluate side-chains 261 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL 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 248 LYS 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 C residue 372 PHE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 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 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 165 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16686 Z= 0.222 Angle : 0.475 7.601 22448 Z= 0.256 Chirality : 0.039 0.179 2410 Planarity : 0.003 0.034 2682 Dihedral : 13.193 148.633 2518 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.87 % Allowed : 22.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 1842 helix: 1.99 (0.14), residues: 1313 sheet: 0.55 (0.52), residues: 106 loop : -1.12 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 170 HIS 0.009 0.001 HIS D 253 PHE 0.024 0.001 PHE D 244 TYR 0.014 0.001 TYR A 338 ARG 0.006 0.000 ARG F 355 *********************** 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 274 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 275 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7816 (t80) REVERT: A 404 GLN cc_start: 0.8348 (tp-100) cc_final: 0.8073 (tp-100) REVERT: C 46 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8025 (tm-30) REVERT: E 245 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7066 (mm-30) REVERT: E 263 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7411 (mp) REVERT: F 357 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7200 (pm20) outliers start: 50 outliers final: 32 residues processed: 260 average time/residue: 0.2682 time to fit residues: 107.6360 Evaluate side-chains 242 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL 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 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 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 283 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 159 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 overall best weight: 0.8122 ------------------------------------------------------------------------------- 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** E 312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16686 Z= 0.208 Angle : 0.465 8.455 22448 Z= 0.251 Chirality : 0.039 0.166 2410 Planarity : 0.003 0.034 2682 Dihedral : 12.013 140.185 2518 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.55 % Allowed : 21.60 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1842 helix: 2.08 (0.14), residues: 1314 sheet: 0.63 (0.51), residues: 105 loop : -1.07 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 170 HIS 0.015 0.001 HIS D 253 PHE 0.024 0.001 PHE D 244 TYR 0.013 0.001 TYR D 338 ARG 0.006 0.000 ARG F 355 *********************** 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 288 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 275 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7874 (t80) REVERT: A 309 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7929 (mtp180) REVERT: A 404 GLN cc_start: 0.8362 (tp-100) cc_final: 0.8057 (tp-100) REVERT: C 46 GLN cc_start: 0.8233 (tm-30) cc_final: 0.8001 (tm-30) REVERT: C 284 TYR cc_start: 0.6992 (t80) cc_final: 0.6690 (t80) REVERT: D 375 MET cc_start: 0.8247 (mtm) cc_final: 0.7757 (mtm) REVERT: E 245 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7048 (mm-30) REVERT: E 263 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7387 (mp) REVERT: F 18 ARG cc_start: 0.6779 (mpp-170) cc_final: 0.6537 (mpp-170) REVERT: F 357 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7229 (pm20) outliers start: 62 outliers final: 47 residues processed: 271 average time/residue: 0.2697 time to fit residues: 112.5592 Evaluate side-chains 263 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL 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 37 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 35 optimal weight: 0.0060 chunk 104 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 49 GLN D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16686 Z= 0.165 Angle : 0.451 8.114 22448 Z= 0.243 Chirality : 0.038 0.145 2410 Planarity : 0.003 0.033 2682 Dihedral : 11.003 132.067 2518 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.15 % Allowed : 21.60 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.19), residues: 1842 helix: 2.19 (0.14), residues: 1315 sheet: 0.84 (0.54), residues: 98 loop : -1.00 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 170 HIS 0.010 0.001 HIS D 253 PHE 0.022 0.001 PHE E 390 TYR 0.014 0.001 TYR D 338 ARG 0.005 0.000 ARG E 389 *********************** 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 292 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 237 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 275 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7796 (t80) REVERT: A 309 ARG cc_start: 0.8241 (tpt170) cc_final: 0.7926 (mtp85) REVERT: A 404 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8054 (tp-100) REVERT: C 46 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7905 (tm-30) REVERT: D 49 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: D 337 MET cc_start: 0.8554 (mmm) cc_final: 0.8185 (mmm) REVERT: D 375 MET cc_start: 0.8258 (mtm) cc_final: 0.7779 (mtm) REVERT: E 245 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7036 (mm-30) REVERT: E 263 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7041 (tt) REVERT: F 18 ARG cc_start: 0.6898 (mpp-170) cc_final: 0.6654 (mpp-170) REVERT: F 247 LYS cc_start: 0.8593 (tttt) cc_final: 0.7965 (tptt) REVERT: F 357 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7204 (pm20) outliers start: 55 outliers final: 39 residues processed: 273 average time/residue: 0.2705 time to fit residues: 112.6482 Evaluate side-chains 265 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 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 44 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 100 optimal weight: 0.1980 chunk 149 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16686 Z= 0.162 Angle : 0.455 8.537 22448 Z= 0.244 Chirality : 0.038 0.164 2410 Planarity : 0.003 0.032 2682 Dihedral : 10.622 126.930 2518 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.15 % Allowed : 22.12 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1842 helix: 2.27 (0.14), residues: 1313 sheet: 0.90 (0.54), residues: 98 loop : -0.99 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 170 HIS 0.014 0.001 HIS D 253 PHE 0.024 0.001 PHE E 390 TYR 0.020 0.001 TYR C 382 ARG 0.004 0.000 ARG E 389 *********************** 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 286 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7987 (tpp) cc_final: 0.7416 (tpp) REVERT: A 269 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 275 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 309 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7899 (mtp85) REVERT: A 404 GLN cc_start: 0.8356 (tp-100) cc_final: 0.8029 (tp-100) REVERT: C 46 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7945 (tm-30) REVERT: C 284 TYR cc_start: 0.7168 (t80) cc_final: 0.6749 (t80) REVERT: D 151 SER cc_start: 0.7777 (t) cc_final: 0.7181 (p) REVERT: D 375 MET cc_start: 0.8265 (mtm) cc_final: 0.7786 (mtm) REVERT: E 245 GLU cc_start: 0.7253 (mm-30) cc_final: 0.7002 (mm-30) REVERT: E 263 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7085 (tt) REVERT: F 96 MET cc_start: 0.8778 (mtm) cc_final: 0.8252 (mpp) REVERT: F 243 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: F 247 LYS cc_start: 0.8607 (tttt) cc_final: 0.7973 (tptt) REVERT: F 357 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7144 (pm20) outliers start: 55 outliers final: 41 residues processed: 270 average time/residue: 0.2699 time to fit residues: 112.3062 Evaluate side-chains 269 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 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 359 GLU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.003 0.039 16686 Z= 0.202 Angle : 0.469 8.363 22448 Z= 0.253 Chirality : 0.039 0.186 2410 Planarity : 0.003 0.032 2682 Dihedral : 10.266 110.927 2518 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.38 % Allowed : 21.95 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.19), residues: 1842 helix: 2.21 (0.14), residues: 1314 sheet: 0.71 (0.53), residues: 100 loop : -0.99 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 170 HIS 0.011 0.001 HIS D 253 PHE 0.025 0.001 PHE E 390 TYR 0.014 0.001 TYR A 338 ARG 0.004 0.000 ARG F 118 *********************** 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 284 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7862 (tpp) cc_final: 0.7283 (tpp) REVERT: A 269 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8553 (mp) REVERT: A 275 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7814 (t80) REVERT: A 309 ARG cc_start: 0.8232 (tpt170) cc_final: 0.7903 (mtp85) REVERT: A 404 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8029 (tp-100) REVERT: D 151 SER cc_start: 0.7780 (t) cc_final: 0.7173 (p) REVERT: D 337 MET cc_start: 0.8597 (mmm) cc_final: 0.8304 (mmm) REVERT: E 245 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7036 (mm-30) REVERT: E 263 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7172 (tt) REVERT: E 401 LYS cc_start: 0.4479 (pttm) cc_final: 0.4095 (tmmt) REVERT: F 247 LYS cc_start: 0.8598 (tttt) cc_final: 0.7975 (tptt) REVERT: F 357 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7132 (pm20) outliers start: 59 outliers final: 49 residues processed: 270 average time/residue: 0.2664 time to fit residues: 109.7354 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 : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 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 157 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 378 LEU 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 286 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 362 TYR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 165 optimal weight: 0.0570 chunk 99 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16686 Z= 0.173 Angle : 0.465 9.494 22448 Z= 0.251 Chirality : 0.038 0.194 2410 Planarity : 0.003 0.033 2682 Dihedral : 9.921 111.853 2518 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.27 % Allowed : 22.18 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 1842 helix: 2.25 (0.14), residues: 1313 sheet: 0.79 (0.54), residues: 98 loop : -0.95 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 168 HIS 0.005 0.001 HIS A 104 PHE 0.026 0.001 PHE E 390 TYR 0.028 0.001 TYR C 325 ARG 0.004 0.000 ARG F 18 *********************** 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 291 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 234 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7896 (tpp) cc_final: 0.7409 (tpp) REVERT: A 269 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 275 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7800 (t80) REVERT: A 309 ARG cc_start: 0.8213 (tpt170) cc_final: 0.7906 (mtp85) REVERT: A 404 GLN cc_start: 0.8333 (tp-100) cc_final: 0.8003 (tp-100) REVERT: C 375 MET cc_start: 0.6673 (mtm) cc_final: 0.6426 (mtm) REVERT: D 337 MET cc_start: 0.8554 (mmm) cc_final: 0.8233 (mmm) REVERT: D 375 MET cc_start: 0.8060 (mtm) cc_final: 0.7578 (mtm) REVERT: E 245 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6979 (mm-30) REVERT: E 263 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7153 (tt) REVERT: F 247 LYS cc_start: 0.8622 (tttt) cc_final: 0.8000 (tptt) REVERT: F 357 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7133 (pm20) outliers start: 57 outliers final: 43 residues processed: 278 average time/residue: 0.2759 time to fit residues: 116.3106 Evaluate side-chains 274 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 320 ILE 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 275 PHE Chi-restraints excluded: chain D residue 378 LEU 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 359 GLU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 141 CYS 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 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.003 0.047 16686 Z= 0.209 Angle : 0.496 11.050 22448 Z= 0.267 Chirality : 0.039 0.197 2410 Planarity : 0.003 0.032 2682 Dihedral : 9.796 112.288 2518 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.92 % Allowed : 22.46 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 1842 helix: 2.20 (0.14), residues: 1314 sheet: 0.67 (0.53), residues: 100 loop : -1.00 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP E 168 HIS 0.005 0.001 HIS A 104 PHE 0.027 0.001 PHE E 390 TYR 0.016 0.001 TYR C 127 ARG 0.006 0.000 ARG F 355 ********************** 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 275 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LYS cc_start: 0.7883 (ptpp) cc_final: 0.7434 (ptpp) REVERT: A 265 MET cc_start: 0.7873 (tpp) cc_final: 0.7311 (tpp) REVERT: A 269 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8553 (mp) REVERT: A 275 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7817 (t80) REVERT: A 309 ARG cc_start: 0.8236 (tpt170) cc_final: 0.7893 (mtp85) REVERT: A 404 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8012 (tp-100) REVERT: D 337 MET cc_start: 0.8549 (mmm) cc_final: 0.8246 (mmm) REVERT: D 375 MET cc_start: 0.8144 (mtm) cc_final: 0.7678 (mtm) REVERT: E 245 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6976 (mm-30) REVERT: E 263 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7272 (tp) REVERT: F 247 LYS cc_start: 0.8627 (tttt) cc_final: 0.7987 (tptt) REVERT: F 357 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7186 (pm20) outliers start: 51 outliers final: 43 residues processed: 267 average time/residue: 0.2854 time to fit residues: 115.9249 Evaluate side-chains 266 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 320 ILE 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 275 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 378 LEU 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 359 GLU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 141 CYS 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 341 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.184885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135915 restraints weight = 19781.566| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.39 r_work: 0.3588 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16686 Z= 0.173 Angle : 0.485 10.489 22448 Z= 0.260 Chirality : 0.039 0.187 2410 Planarity : 0.003 0.033 2682 Dihedral : 9.519 113.671 2518 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.92 % Allowed : 22.75 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 1842 helix: 2.28 (0.14), residues: 1307 sheet: 0.71 (0.53), residues: 99 loop : -0.96 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 168 HIS 0.006 0.001 HIS A 104 PHE 0.027 0.001 PHE A 250 TYR 0.023 0.001 TYR C 284 ARG 0.004 0.000 ARG F 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.18 seconds wall clock time: 65 minutes 7.69 seconds (3907.69 seconds total)