Starting phenix.real_space_refine on Sun Feb 18 13:01:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/02_2024/7x1y_32952_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/02_2024/7x1y_32952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/02_2024/7x1y_32952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/02_2024/7x1y_32952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/02_2024/7x1y_32952_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1y_32952/02_2024/7x1y_32952_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 84 5.16 5 C 13806 2.51 5 N 3852 2.21 5 O 4242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 444": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 272": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 77": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F GLU 272": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22032 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "C" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "E" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3608 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 11, 'TRANS': 446} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 11.76, per 1000 atoms: 0.53 Number of scatterers: 22032 At special positions: 0 Unit cell: (121.245, 119.875, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 36 15.00 Mg 12 11.99 O 4242 8.00 N 3852 7.00 C 13806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.94 Conformation dependent library (CDL) restraints added in 3.7 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 24 sheets defined 30.0% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 53 through 65 removed outlier: 3.557A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.957A pdb=" N SER A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.569A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 160 through 174 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 294 through 308 removed outlier: 3.966A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.512A pdb=" N ASN A 327 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'B' and resid 53 through 65 removed outlier: 3.570A pdb=" N GLY B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.957A pdb=" N SER B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.564A pdb=" N ILE B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 160 through 174 Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 321 through 331 removed outlier: 3.511A pdb=" N ASN B 327 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'B' and resid 380 through 383 No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 389 through 405 Processing helix chain 'C' and resid 53 through 65 removed outlier: 3.565A pdb=" N GLY C 63 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.960A pdb=" N SER C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 126 through 137 removed outlier: 3.536A pdb=" N ILE C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 294 through 308 removed outlier: 3.960A pdb=" N ALA C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS C 306 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 331 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 356 through 370 Processing helix chain 'C' and resid 380 through 383 No H-bonds generated for 'chain 'C' and resid 380 through 383' Processing helix chain 'C' and resid 389 through 405 Processing helix chain 'D' and resid 53 through 65 removed outlier: 3.558A pdb=" N GLY D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.961A pdb=" N SER D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 126 through 137 removed outlier: 3.576A pdb=" N ILE D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 294 through 308 removed outlier: 3.969A pdb=" N ALA D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N CYS D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 331 removed outlier: 3.508A pdb=" N ASN D 327 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 356 through 370 Processing helix chain 'D' and resid 380 through 383 No H-bonds generated for 'chain 'D' and resid 380 through 383' Processing helix chain 'D' and resid 389 through 405 Processing helix chain 'E' and resid 53 through 65 removed outlier: 3.570A pdb=" N GLY E 63 " --> pdb=" O PHE E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.959A pdb=" N SER E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 126 through 137 removed outlier: 3.564A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 160 through 174 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 305 through 308 Processing helix chain 'E' and resid 321 through 331 removed outlier: 3.511A pdb=" N ASN E 327 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 356 through 370 Processing helix chain 'E' and resid 380 through 383 No H-bonds generated for 'chain 'E' and resid 380 through 383' Processing helix chain 'E' and resid 389 through 405 Processing helix chain 'F' and resid 53 through 65 removed outlier: 3.565A pdb=" N GLY F 63 " --> pdb=" O PHE F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.959A pdb=" N SER F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 126 through 137 removed outlier: 3.533A pdb=" N ILE F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 160 through 174 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 294 through 308 removed outlier: 3.967A pdb=" N ALA F 305 " --> pdb=" O PHE F 301 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N CYS F 306 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA F 307 " --> pdb=" O GLU F 303 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN F 308 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 331 removed outlier: 3.507A pdb=" N ASN F 327 " --> pdb=" O LEU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 356 through 370 Processing helix chain 'F' and resid 380 through 383 No H-bonds generated for 'chain 'F' and resid 380 through 383' Processing helix chain 'F' and resid 389 through 405 Processing sheet with id= A, first strand: chain 'A' and resid 216 through 225 removed outlier: 6.606A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU A 43 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 207 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 45 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ASN A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 44 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET A 180 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY A 46 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR A 182 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= C, first strand: chain 'A' and resid 448 through 457 removed outlier: 3.521A pdb=" N GLN A 441 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY A 410 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 286 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE A 412 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLY A 288 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN A 414 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 470 through 472 removed outlier: 3.710A pdb=" N MET A 471 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 215 through 225 removed outlier: 6.603A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU B 43 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 207 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER B 45 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ASN B 209 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL B 44 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 180 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY B 46 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR B 182 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= G, first strand: chain 'B' and resid 448 through 457 removed outlier: 6.453A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY B 410 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA B 286 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B 412 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N GLY B 288 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN B 414 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 470 through 472 removed outlier: 3.563A pdb=" N MET B 471 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.782A pdb=" N LYS C 224 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE C 206 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE C 222 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG C 208 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU C 220 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 210 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG C 218 " --> pdb=" O VAL C 210 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 removed outlier: 7.103A pdb=" N GLY C 71 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU C 106 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE C 73 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG C 141 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL C 74 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER C 143 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR C 177 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE C 144 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL C 179 " --> pdb=" O ILE C 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= L, first strand: chain 'C' and resid 448 through 457 removed outlier: 3.612A pdb=" N GLN C 441 " --> pdb=" O ALA C 452 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY C 410 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA C 286 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C 412 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLY C 288 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN C 414 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 470 through 472 removed outlier: 3.649A pdb=" N MET C 471 " --> pdb=" O ASP C 478 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 216 through 225 removed outlier: 6.605A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU D 43 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER D 45 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASN D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL D 44 " --> pdb=" O THR D 178 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET D 180 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY D 46 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR D 182 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= P, first strand: chain 'D' and resid 448 through 457 removed outlier: 3.518A pdb=" N GLN D 441 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY D 410 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA D 286 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE D 412 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLY D 288 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN D 414 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 216 through 225 removed outlier: 6.605A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU E 43 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU E 207 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER E 45 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ASN E 209 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL E 44 " --> pdb=" O THR E 178 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET E 180 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY E 46 " --> pdb=" O MET E 180 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR E 182 " --> pdb=" O GLY E 46 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 237 through 240 Processing sheet with id= S, first strand: chain 'E' and resid 448 through 457 removed outlier: 3.556A pdb=" N GLN E 441 " --> pdb=" O ALA E 452 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY E 410 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA E 286 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE E 412 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N GLY E 288 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN E 414 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 470 through 472 removed outlier: 3.554A pdb=" N MET E 471 " --> pdb=" O ASP E 478 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 216 through 225 removed outlier: 6.598A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU F 43 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU F 207 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER F 45 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN F 209 " --> pdb=" O SER F 45 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL F 44 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET F 180 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY F 46 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR F 182 " --> pdb=" O GLY F 46 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 237 through 240 Processing sheet with id= W, first strand: chain 'F' and resid 448 through 457 removed outlier: 3.579A pdb=" N GLN F 441 " --> pdb=" O ALA F 452 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY F 410 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA F 286 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE F 412 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY F 288 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN F 414 " --> pdb=" O GLY F 288 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 470 through 472 removed outlier: 3.663A pdb=" N MET F 471 " --> pdb=" O ASP F 478 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 1923 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: 7.47 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6820 1.34 - 1.45: 3350 1.45 - 1.57: 12016 1.57 - 1.69: 62 1.69 - 1.81: 150 Bond restraints: 22398 Sorted by residual: bond pdb=" CB PRO C 110 " pdb=" CG PRO C 110 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.77e+00 bond pdb=" CB PRO F 110 " pdb=" CG PRO F 110 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.73e+00 bond pdb=" CB PRO D 110 " pdb=" CG PRO D 110 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.86e+00 bond pdb=" CB PRO A 110 " pdb=" CG PRO A 110 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.58e+00 bond pdb=" CB PRO D 248 " pdb=" CG PRO D 248 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.55e+00 ... (remaining 22393 not shown) Histogram of bond angle deviations from ideal: 95.34 - 104.22: 317 104.22 - 113.10: 12013 113.10 - 121.98: 13254 121.98 - 130.86: 4582 130.86 - 139.74: 98 Bond angle restraints: 30264 Sorted by residual: angle pdb=" CA PRO C 110 " pdb=" N PRO C 110 " pdb=" CD PRO C 110 " ideal model delta sigma weight residual 112.00 100.11 11.89 1.40e+00 5.10e-01 7.22e+01 angle pdb=" CA PRO F 110 " pdb=" N PRO F 110 " pdb=" CD PRO F 110 " ideal model delta sigma weight residual 112.00 100.14 11.86 1.40e+00 5.10e-01 7.18e+01 angle pdb=" CA PRO B 110 " pdb=" N PRO B 110 " pdb=" CD PRO B 110 " ideal model delta sigma weight residual 112.00 100.48 11.52 1.40e+00 5.10e-01 6.78e+01 angle pdb=" CA PRO E 110 " pdb=" N PRO E 110 " pdb=" CD PRO E 110 " ideal model delta sigma weight residual 112.00 100.56 11.44 1.40e+00 5.10e-01 6.68e+01 angle pdb=" CA PRO A 248 " pdb=" N PRO A 248 " pdb=" CD PRO A 248 " ideal model delta sigma weight residual 112.00 101.20 10.80 1.40e+00 5.10e-01 5.96e+01 ... (remaining 30259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 12142 18.02 - 36.04: 1112 36.04 - 54.06: 285 54.06 - 72.08: 93 72.08 - 90.10: 36 Dihedral angle restraints: 13668 sinusoidal: 5820 harmonic: 7848 Sorted by residual: dihedral pdb=" CA GLU E 319 " pdb=" C GLU E 319 " pdb=" N SER E 320 " pdb=" CA SER E 320 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU F 319 " pdb=" C GLU F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" C ASP B 478 " pdb=" N ASP B 478 " pdb=" CA ASP B 478 " pdb=" CB ASP B 478 " ideal model delta harmonic sigma weight residual -122.60 -132.46 9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 13665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2424 0.047 - 0.093: 680 0.093 - 0.140: 235 0.140 - 0.186: 33 0.186 - 0.233: 6 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CA PRO B 110 " pdb=" N PRO B 110 " pdb=" C PRO B 110 " pdb=" CB PRO B 110 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO E 110 " pdb=" N PRO E 110 " pdb=" C PRO E 110 " pdb=" CB PRO E 110 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP E 478 " pdb=" N ASP E 478 " pdb=" C ASP E 478 " pdb=" CB ASP E 478 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3375 not shown) Planarity restraints: 3858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 478 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" CG ASP E 478 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASP E 478 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP E 478 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 478 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" CG ASP B 478 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASP B 478 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP B 478 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 247 " 0.061 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO D 248 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 248 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 248 " 0.047 5.00e-02 4.00e+02 ... (remaining 3855 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 4 2.01 - 2.74: 1686 2.74 - 3.46: 29285 3.46 - 4.18: 49140 4.18 - 4.90: 91951 Nonbonded interactions: 172066 Sorted by model distance: nonbonded pdb=" OE2 GLU D 318 " pdb=" OG SER D 379 " model vdw 1.293 2.440 nonbonded pdb=" OE2 GLU B 318 " pdb=" OG SER B 379 " model vdw 1.608 2.440 nonbonded pdb=" OE2 GLU C 318 " pdb=" OG SER C 379 " model vdw 1.671 2.440 nonbonded pdb=" OE2 GLU A 318 " pdb=" OG SER A 379 " model vdw 1.675 2.440 nonbonded pdb=" OG1 THR B 53 " pdb="MG MG B 904 " model vdw 2.037 2.170 ... (remaining 172061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.430 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 59.040 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.006 0.156 22398 Z= 0.412 Angle : 0.854 11.894 30264 Z= 0.492 Chirality : 0.050 0.233 3378 Planarity : 0.006 0.086 3858 Dihedral : 16.187 90.104 8628 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.48 % Favored : 91.30 % Rotamer: Outliers : 0.52 % Allowed : 0.82 % Favored : 98.66 % Cbeta Deviations : 0.08 % 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: -1.68 (0.15), residues: 2724 helix: -0.39 (0.17), residues: 876 sheet: -0.68 (0.20), residues: 672 loop : -1.88 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 92 HIS 0.006 0.002 HIS B 15 PHE 0.019 0.002 PHE C 237 TYR 0.019 0.002 TYR C 442 ARG 0.011 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 2.424 Fit side-chains revert: symmetry clash REVERT: C 321 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8002 (ttt-90) REVERT: D 321 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8277 (tpt-90) REVERT: E 321 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7871 (tpt-90) REVERT: F 321 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7820 (tpt-90) outliers start: 12 outliers final: 7 residues processed: 259 average time/residue: 0.4274 time to fit residues: 159.3778 Evaluate side-chains 200 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 321 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 4.9990 chunk 204 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 HIS E 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 22398 Z= 0.329 Angle : 0.554 8.194 30264 Z= 0.296 Chirality : 0.042 0.144 3378 Planarity : 0.004 0.036 3858 Dihedral : 11.871 89.956 3469 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.98 % Favored : 92.80 % Rotamer: Outliers : 1.08 % Allowed : 7.36 % Favored : 91.56 % 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: -1.20 (0.16), residues: 2724 helix: 0.17 (0.18), residues: 900 sheet: -0.85 (0.19), residues: 750 loop : -1.48 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 92 HIS 0.003 0.001 HIS B 33 PHE 0.014 0.001 PHE E 237 TYR 0.019 0.001 TYR C 442 ARG 0.004 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 210 time to evaluate : 2.691 Fit side-chains outliers start: 25 outliers final: 25 residues processed: 218 average time/residue: 0.3734 time to fit residues: 123.3170 Evaluate side-chains 220 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 197 optimal weight: 0.0370 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 463 HIS F 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22398 Z= 0.172 Angle : 0.460 6.366 30264 Z= 0.246 Chirality : 0.040 0.141 3378 Planarity : 0.003 0.034 3858 Dihedral : 10.022 84.153 3450 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 0.99 % Allowed : 9.73 % Favored : 89.28 % 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 (0.17), residues: 2724 helix: 0.52 (0.18), residues: 906 sheet: -0.59 (0.20), residues: 738 loop : -1.50 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 92 HIS 0.001 0.000 HIS E 33 PHE 0.014 0.001 PHE E 151 TYR 0.013 0.001 TYR C 442 ARG 0.003 0.000 ARG F 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 2.618 Fit side-chains outliers start: 23 outliers final: 21 residues processed: 221 average time/residue: 0.3909 time to fit residues: 131.0384 Evaluate side-chains 219 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 260 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 22398 Z= 0.420 Angle : 0.582 7.598 30264 Z= 0.308 Chirality : 0.044 0.141 3378 Planarity : 0.004 0.037 3858 Dihedral : 10.299 89.373 3450 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.86 % Favored : 91.92 % Rotamer: Outliers : 1.77 % Allowed : 10.98 % Favored : 87.25 % 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: -0.96 (0.17), residues: 2724 helix: 0.61 (0.18), residues: 906 sheet: -0.86 (0.19), residues: 750 loop : -1.47 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 92 HIS 0.005 0.001 HIS D 33 PHE 0.017 0.002 PHE B 237 TYR 0.014 0.001 TYR C 442 ARG 0.004 0.000 ARG D 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 2.604 Fit side-chains REVERT: D 338 MET cc_start: 0.7410 (mmt) cc_final: 0.7186 (mmt) outliers start: 41 outliers final: 33 residues processed: 219 average time/residue: 0.3650 time to fit residues: 121.5052 Evaluate side-chains 221 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22398 Z= 0.339 Angle : 0.539 7.020 30264 Z= 0.286 Chirality : 0.043 0.144 3378 Planarity : 0.003 0.032 3858 Dihedral : 10.012 89.919 3450 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.60 % Favored : 92.18 % Rotamer: Outliers : 1.89 % Allowed : 13.05 % Favored : 85.06 % 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: -0.73 (0.17), residues: 2724 helix: 1.07 (0.19), residues: 858 sheet: -0.90 (0.19), residues: 750 loop : -1.34 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 92 HIS 0.004 0.001 HIS D 33 PHE 0.016 0.002 PHE B 237 TYR 0.012 0.001 TYR C 442 ARG 0.003 0.000 ARG D 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 194 time to evaluate : 2.677 Fit side-chains outliers start: 44 outliers final: 36 residues processed: 222 average time/residue: 0.3678 time to fit residues: 124.4683 Evaluate side-chains 220 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 137 optimal weight: 30.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22398 Z= 0.289 Angle : 0.513 6.829 30264 Z= 0.272 Chirality : 0.042 0.145 3378 Planarity : 0.003 0.032 3858 Dihedral : 9.739 87.632 3450 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.67 % Favored : 92.11 % Rotamer: Outliers : 2.02 % Allowed : 13.52 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.61 (0.17), residues: 2724 helix: 1.07 (0.19), residues: 870 sheet: -0.84 (0.19), residues: 750 loop : -1.21 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 92 HIS 0.003 0.001 HIS C 33 PHE 0.014 0.001 PHE B 237 TYR 0.012 0.001 TYR C 442 ARG 0.004 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 199 time to evaluate : 2.784 Fit side-chains REVERT: A 474 ASP cc_start: 0.7921 (t0) cc_final: 0.7565 (t0) REVERT: B 319 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: C 15 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.7293 (m170) REVERT: D 474 ASP cc_start: 0.7909 (t0) cc_final: 0.7564 (t0) REVERT: E 474 ASP cc_start: 0.7778 (t0) cc_final: 0.7479 (t0) REVERT: F 15 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7304 (m170) outliers start: 47 outliers final: 35 residues processed: 229 average time/residue: 0.3897 time to fit residues: 135.9037 Evaluate side-chains 229 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 219 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 260 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22398 Z= 0.211 Angle : 0.479 6.506 30264 Z= 0.253 Chirality : 0.041 0.144 3378 Planarity : 0.003 0.031 3858 Dihedral : 9.317 85.789 3447 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.16 % Favored : 92.69 % Rotamer: Outliers : 1.89 % Allowed : 13.57 % Favored : 84.54 % 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: -0.47 (0.17), residues: 2724 helix: 1.20 (0.19), residues: 870 sheet: -0.75 (0.19), residues: 750 loop : -1.15 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 92 HIS 0.005 0.001 HIS B 15 PHE 0.012 0.001 PHE F 237 TYR 0.011 0.001 TYR C 442 ARG 0.004 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 2.454 Fit side-chains REVERT: A 15 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.7073 (m170) REVERT: A 474 ASP cc_start: 0.7882 (t0) cc_final: 0.7538 (t0) REVERT: B 319 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: B 474 ASP cc_start: 0.7758 (t0) cc_final: 0.7470 (t0) REVERT: C 15 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7250 (m170) REVERT: C 344 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9236 (tp) REVERT: D 15 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7072 (m170) REVERT: D 474 ASP cc_start: 0.7866 (t0) cc_final: 0.7569 (t0) REVERT: E 474 ASP cc_start: 0.7751 (t0) cc_final: 0.7422 (t0) REVERT: F 15 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7266 (m170) REVERT: F 344 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9243 (tp) outliers start: 44 outliers final: 35 residues processed: 231 average time/residue: 0.3804 time to fit residues: 132.8750 Evaluate side-chains 239 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22398 Z= 0.236 Angle : 0.495 6.638 30264 Z= 0.261 Chirality : 0.041 0.144 3378 Planarity : 0.003 0.044 3858 Dihedral : 9.322 86.497 3447 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.53 % Favored : 92.36 % Rotamer: Outliers : 2.41 % Allowed : 13.91 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2724 helix: 1.21 (0.19), residues: 870 sheet: -0.71 (0.19), residues: 750 loop : -1.10 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 92 HIS 0.005 0.001 HIS B 15 PHE 0.012 0.001 PHE C 237 TYR 0.010 0.001 TYR C 442 ARG 0.009 0.000 ARG D 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 192 time to evaluate : 2.535 Fit side-chains REVERT: A 15 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7081 (m170) REVERT: A 474 ASP cc_start: 0.7893 (t0) cc_final: 0.7559 (t0) REVERT: B 474 ASP cc_start: 0.7744 (t0) cc_final: 0.7479 (t0) REVERT: C 15 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7275 (m170) REVERT: C 344 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9262 (tp) REVERT: D 15 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7087 (m170) REVERT: D 474 ASP cc_start: 0.7846 (t0) cc_final: 0.7552 (t0) REVERT: E 474 ASP cc_start: 0.7744 (t0) cc_final: 0.7468 (t0) REVERT: F 15 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.7283 (m170) REVERT: F 344 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9262 (tp) outliers start: 56 outliers final: 43 residues processed: 230 average time/residue: 0.3867 time to fit residues: 133.3520 Evaluate side-chains 238 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 9.9990 chunk 249 optimal weight: 20.0000 chunk 227 optimal weight: 0.0770 chunk 242 optimal weight: 4.9990 chunk 145 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 190 optimal weight: 0.0870 chunk 74 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22398 Z= 0.138 Angle : 0.450 8.210 30264 Z= 0.236 Chirality : 0.040 0.145 3378 Planarity : 0.003 0.031 3858 Dihedral : 8.681 87.967 3441 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 1.51 % Allowed : 15.03 % Favored : 83.46 % 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: -0.31 (0.17), residues: 2724 helix: 1.24 (0.19), residues: 870 sheet: -0.45 (0.19), residues: 738 loop : -1.12 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 462 HIS 0.004 0.001 HIS E 15 PHE 0.013 0.001 PHE A 151 TYR 0.009 0.001 TYR C 442 ARG 0.007 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 2.517 Fit side-chains REVERT: A 15 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.7028 (m170) REVERT: A 474 ASP cc_start: 0.7813 (t0) cc_final: 0.7498 (t0) REVERT: B 474 ASP cc_start: 0.7683 (t0) cc_final: 0.7422 (t0) REVERT: C 15 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7187 (m170) REVERT: C 344 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9211 (tp) REVERT: D 15 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7034 (m170) REVERT: D 474 ASP cc_start: 0.7789 (t0) cc_final: 0.7534 (t0) REVERT: E 474 ASP cc_start: 0.7663 (t0) cc_final: 0.7391 (t0) REVERT: F 15 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.7196 (m170) REVERT: F 344 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9193 (tp) REVERT: F 474 ASP cc_start: 0.7783 (t0) cc_final: 0.7460 (t0) outliers start: 35 outliers final: 23 residues processed: 240 average time/residue: 0.3621 time to fit residues: 132.6223 Evaluate side-chains 227 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 121 optimal weight: 0.3980 chunk 178 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 0.0020 chunk 165 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22398 Z= 0.177 Angle : 0.473 7.677 30264 Z= 0.248 Chirality : 0.040 0.144 3378 Planarity : 0.003 0.037 3858 Dihedral : 8.591 88.154 3435 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % 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: -0.23 (0.17), residues: 2724 helix: 1.35 (0.19), residues: 858 sheet: -0.45 (0.19), residues: 750 loop : -1.07 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 92 HIS 0.004 0.001 HIS E 15 PHE 0.013 0.001 PHE A 151 TYR 0.009 0.001 TYR C 442 ARG 0.008 0.000 ARG A 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 2.704 Fit side-chains REVERT: A 15 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.7034 (m170) REVERT: A 474 ASP cc_start: 0.7838 (t0) cc_final: 0.7553 (t0) REVERT: B 474 ASP cc_start: 0.7710 (t0) cc_final: 0.7448 (t0) REVERT: C 15 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7198 (m170) REVERT: C 344 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9237 (tp) REVERT: C 474 ASP cc_start: 0.7738 (t0) cc_final: 0.7518 (t0) REVERT: D 15 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.7027 (m170) REVERT: D 474 ASP cc_start: 0.7805 (t0) cc_final: 0.7554 (t0) REVERT: E 474 ASP cc_start: 0.7688 (t0) cc_final: 0.7417 (t0) REVERT: F 15 HIS cc_start: 0.7532 (OUTLIER) cc_final: 0.7208 (m170) REVERT: F 344 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9236 (tp) REVERT: F 474 ASP cc_start: 0.7812 (t0) cc_final: 0.7507 (t0) outliers start: 31 outliers final: 23 residues processed: 221 average time/residue: 0.3676 time to fit residues: 123.5722 Evaluate side-chains 225 residues out of total 2322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 15 HIS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 15 HIS Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.080768 restraints weight = 36173.576| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.69 r_work: 0.2776 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22398 Z= 0.370 Angle : 0.573 7.919 30264 Z= 0.299 Chirality : 0.043 0.147 3378 Planarity : 0.003 0.041 3858 Dihedral : 9.334 88.470 3432 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.19 % Favored : 91.70 % Rotamer: Outliers : 1.59 % Allowed : 15.46 % Favored : 82.95 % 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: -0.38 (0.17), residues: 2724 helix: 1.31 (0.19), residues: 858 sheet: -0.62 (0.19), residues: 750 loop : -1.15 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 92 HIS 0.005 0.001 HIS B 15 PHE 0.015 0.002 PHE C 237 TYR 0.012 0.001 TYR C 442 ARG 0.007 0.000 ARG A 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3996.78 seconds wall clock time: 73 minutes 59.55 seconds (4439.55 seconds total)