Starting phenix.real_space_refine on Fri Sep 11 07:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6orv_20179/09_2026/6orv_20179.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orv_20179/09_2026/6orv_20179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6orv_20179/09_2026/6orv_20179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orv_20179/09_2026/6orv_20179.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6orv_20179/09_2026/6orv_20179.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6orv_20179/09_2026/6orv_20179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6orv_20179/09_2026/6orv_20179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orv_20179/09_2026/6orv_20179.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 5 Type Number sf(0) Gaussians S 47 5.16 5 Cl 2 4.86 5 C 5138 2.51 5 N 1390 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8041 Number of models: 1 Model: "" Number of chains: 6 Chain: "AP" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1654 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 4 Chain: "BP" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "GP" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "NP" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "RP" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2329 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain breaks: 1 Chain: "RP" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'N2V': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ALARP 209 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALARP 209 " occ=0.00 residue: pdb=" N GLNRP 210 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLNRP 210 " occ=0.00 residue: pdb=" N GLNRP 211 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLNRP 211 " occ=0.00 residue: pdb=" N HISRP 212 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HISRP 212 " occ=0.00 residue: pdb=" N ASPRP 372 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASPRP 372 " occ=0.00 residue: pdb=" N GLURP 373 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLURP 373 " occ=0.00 residue: pdb=" N HISRP 374 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HISRP 374 " occ=0.00 residue: pdb=" N ALARP 375 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALARP 375 " occ=0.00 residue: pdb=" N ARGRP 376 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARGRP 376 " occ=0.00 residue: pdb=" N GLYRP 377 " occ=0.00 ... (2 atoms not shown) pdb=" O GLYRP 377 " occ=0.00 residue: pdb=" N THRRP 378 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THRRP 378 " occ=0.00 residue: pdb=" N LEURP 379 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEURP 379 " occ=0.00 Time building chain proxies: 1.54, per 1000 atoms: 0.19 Number of scatterers: 8041 At special positions: 0 Unit cell: (84.252, 95.816, 131.334, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 47 16.00 O 1464 8.00 N 1390 7.00 C 5138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYSNP 22 " - pdb=" SG CYSNP 96 " distance=2.03 Simple disulfide: pdb=" SG CYSNP 99 " - pdb=" SG CYSNP 107 " distance=2.02 Simple disulfide: pdb=" SG CYSRP 226 " - pdb=" SG CYSRP 296 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 364.0 milliseconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 36.5% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'AP' and resid 18 through 25 Processing helix chain 'AP' and resid 28 through 38 removed outlier: 3.565A pdb=" N LYSAP 32 " --> pdb=" O LYSAP 28 " (cutoff:3.500A) Processing helix chain 'AP' and resid 234 through 240 removed outlier: 3.883A pdb=" N ASNAP 239 " --> pdb=" O GLNAP 236 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASPAP 240 " --> pdb=" O CYSAP 237 " (cutoff:3.500A) Processing helix chain 'AP' and resid 266 through 279 removed outlier: 3.513A pdb=" N SERAP 275 " --> pdb=" O LYSAP 271 " (cutoff:3.500A) Processing helix chain 'AP' and resid 312 through 316 Processing helix chain 'AP' and resid 331 through 336 removed outlier: 3.632A pdb=" N THRAP 335 " --> pdb=" O ASPAP 331 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARGAP 336 " --> pdb=" O PROAP 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP' and resid 331 through 336' Processing helix chain 'AP' and resid 337 through 350 removed outlier: 3.876A pdb=" N ILEAP 348 " --> pdb=" O GLUAP 344 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SERAP 349 " --> pdb=" O PHEAP 345 " (cutoff:3.500A) Processing helix chain 'AP' and resid 372 through 391 removed outlier: 3.518A pdb=" N ASPAP 381 " --> pdb=" O ASNAP 377 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYRAP 391 " --> pdb=" O HISAP 387 " (cutoff:3.500A) Processing helix chain 'BP' and resid 4 through 24 removed outlier: 4.014A pdb=" N GLNBP 9 " --> pdb=" O ASPBP 5 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLUBP 10 " --> pdb=" O GLNBP 6 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLNBP 17 " --> pdb=" O GLNBP 13 " (cutoff:3.500A) Processing helix chain 'BP' and resid 29 through 34 Processing helix chain 'GP' and resid 7 through 22 removed outlier: 3.971A pdb=" N ALAGP 12 " --> pdb=" O SERGP 8 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VALGP 16 " --> pdb=" O ALAGP 12 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLNGP 18 " --> pdb=" O LYSGP 14 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUGP 19 " --> pdb=" O LEUGP 15 " (cutoff:3.500A) Processing helix chain 'GP' and resid 29 through 44 removed outlier: 3.588A pdb=" N ALAGP 35 " --> pdb=" O SERGP 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASPGP 36 " --> pdb=" O LYSGP 32 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYSGP 41 " --> pdb=" O LEUGP 37 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUGP 42 " --> pdb=" O METGP 38 " (cutoff:3.500A) Processing helix chain 'GP' and resid 45 through 48 removed outlier: 3.669A pdb=" N ASPGP 48 " --> pdb=" O ALAGP 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'GP' and resid 45 through 48' Processing helix chain 'NP' and resid 28 through 32 removed outlier: 3.738A pdb=" N TYRNP 32 " --> pdb=" O PHENP 29 " (cutoff:3.500A) Processing helix chain 'NP' and resid 87 through 91 removed outlier: 3.865A pdb=" N THRNP 91 " --> pdb=" O PRONP 88 " (cutoff:3.500A) Processing helix chain 'RP' and resid 138 through 169 removed outlier: 4.530A pdb=" N PHERP 143 " --> pdb=" O GLURP 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILERP 147 " --> pdb=" O PHERP 143 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VALRP 160 " --> pdb=" O PHERP 156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILERP 161 " --> pdb=" O SERRP 157 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SERRP 163 " --> pdb=" O LEURP 159 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEURP 167 " --> pdb=" O SERRP 163 " (cutoff:3.500A) Processing helix chain 'RP' and resid 170 through 173 Processing helix chain 'RP' and resid 176 through 207 removed outlier: 3.626A pdb=" N SERRP 186 " --> pdb=" O ASNRP 182 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEURP 189 " --> pdb=" O ALARP 185 " (cutoff:3.500A) Processing helix chain 'RP' and resid 214 through 222 Processing helix chain 'RP' and resid 223 through 239 removed outlier: 3.618A pdb=" N ARGRP 227 " --> pdb=" O SERRP 223 " (cutoff:3.500A) Processing helix chain 'RP' and resid 247 through 256 removed outlier: 3.743A pdb=" N LEURP 251 " --> pdb=" O GLURP 247 " (cutoff:3.500A) Processing helix chain 'RP' and resid 263 through 273 removed outlier: 4.181A pdb=" N ARGRP 267 " --> pdb=" O GLNRP 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SERRP 271 " --> pdb=" O ARGRP 267 " (cutoff:3.500A) Processing helix chain 'RP' and resid 276 through 280 Processing helix chain 'RP' and resid 281 through 291 Processing helix chain 'RP' and resid 309 through 320 removed outlier: 3.650A pdb=" N ALARP 316 " --> pdb=" O PRORP 312 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASNRP 320 " --> pdb=" O ALARP 316 " (cutoff:3.500A) Processing helix chain 'RP' and resid 323 through 335 removed outlier: 4.118A pdb=" N CYSRP 329 " --> pdb=" O VALRP 325 " (cutoff:3.500A) Processing helix chain 'RP' and resid 348 through 361 removed outlier: 3.573A pdb=" N SERRP 352 " --> pdb=" O ARGRP 348 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEURP 354 " --> pdb=" O ALARP 350 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEURP 356 " --> pdb=" O SERRP 352 " (cutoff:3.500A) Proline residue: RP 358 - end of helix Processing helix chain 'RP' and resid 362 through 367 Processing helix chain 'RP' and resid 382 through 390 removed outlier: 3.609A pdb=" N THRRP 386 " --> pdb=" O ILERP 382 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLURP 387 " --> pdb=" O LYSRP 383 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEURP 388 " --> pdb=" O LEURP 384 " (cutoff:3.500A) Processing helix chain 'RP' and resid 393 through 401 Processing helix chain 'RP' and resid 406 through 411 Processing helix chain 'RP' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'AP' and resid 207 through 214 removed outlier: 6.106A pdb=" N HISAP 41 " --> pdb=" O HISAP 220 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHEAP 222 " --> pdb=" O HISAP 41 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEUAP 43 " --> pdb=" O PHEAP 222 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VALAP 224 " --> pdb=" O LEUAP 43 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEUAP 45 " --> pdb=" O VALAP 224 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARGAP 42 " --> pdb=" O ALAAP 243 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILEAP 245 " --> pdb=" O ARGAP 42 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEUAP 44 " --> pdb=" O ILEAP 245 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VALAP 247 " --> pdb=" O LEUAP 44 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEUAP 46 " --> pdb=" O VALAP 247 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VALAP 287 " --> pdb=" O TYRAP 360 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HISAP 362 " --> pdb=" O VALAP 287 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEUAP 289 " --> pdb=" O HISAP 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'BP' and resid 46 through 47 removed outlier: 3.756A pdb=" N ARGBP 46 " --> pdb=" O ASNBP 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'BP' and resid 46 through 47 removed outlier: 3.756A pdb=" N ARGBP 46 " --> pdb=" O ASNBP 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'BP' and resid 58 through 63 removed outlier: 3.749A pdb=" N ALABP 60 " --> pdb=" O ALABP 73 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYSBP 78 " --> pdb=" O SERBP 74 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEUBP 79 " --> pdb=" O ALABP 92 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ALABP 92 " --> pdb=" O LEUBP 79 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILEBP 81 " --> pdb=" O VALBP 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'BP' and resid 100 through 105 removed outlier: 6.518A pdb=" N CYSBP 121 " --> pdb=" O GLUBP 138 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLUBP 138 " --> pdb=" O CYSBP 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILEBP 123 " --> pdb=" O SERBP 136 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARGBP 134 " --> pdb=" O ASNBP 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BP' and resid 146 through 151 removed outlier: 3.906A pdb=" N ILEBP 157 " --> pdb=" O TRPBP 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'BP' and resid 187 through 192 removed outlier: 6.954A pdb=" N GLYBP 202 " --> pdb=" O METBP 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEUBP 190 " --> pdb=" O VALBP 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VALBP 200 " --> pdb=" O LEUBP 190 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEUBP 192 " --> pdb=" O LEUBP 198 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEUBP 198 " --> pdb=" O LEUBP 192 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALABP 208 " --> pdb=" O THRBP 221 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THRBP 221 " --> pdb=" O ALABP 208 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEUBP 210 " --> pdb=" O ARGBP 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'BP' and resid 229 through 234 removed outlier: 3.562A pdb=" N PHEBP 241 " --> pdb=" O PHEBP 253 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N METBP 262 " --> pdb=" O LEUBP 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'BP' and resid 273 through 278 removed outlier: 3.674A pdb=" N SERBP 275 " --> pdb=" O GLYBP 288 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYSBP 294 " --> pdb=" O VALBP 307 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VALBP 307 " --> pdb=" O CYSBP 294 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VALBP 296 " --> pdb=" O ALABP 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'NP' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'NP' and resid 10 through 11 removed outlier: 5.885A pdb=" N GLYNP 10 " --> pdb=" O THRNP 125 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N METNP 34 " --> pdb=" O ASPNP 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASPNP 50 " --> pdb=" O METNP 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRPNP 36 " --> pdb=" O VALNP 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'NP' and resid 19 through 20 299 hydrogen bonds defined for protein. 837 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: 0.90 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1294 1.31 - 1.44: 2361 1.44 - 1.56: 4499 1.56 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 8221 Sorted by residual: bond pdb=" C06 N2VRP 501 " pdb=" N05 N2VRP 501 " ideal model delta sigma weight residual 1.337 1.449 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C21 N2VRP 501 " pdb=" O42 N2VRP 501 " ideal model delta sigma weight residual 1.357 1.436 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C22 N2VRP 501 " pdb=" O23 N2VRP 501 " ideal model delta sigma weight residual 1.356 1.428 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C07 N2VRP 501 " pdb=" N08 N2VRP 501 " ideal model delta sigma weight residual 1.450 1.521 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C34 N2VRP 501 " pdb="CL35 N2VRP 501 " ideal model delta sigma weight residual 1.722 1.786 -0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 8216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10577 1.99 - 3.97: 492 3.97 - 5.96: 44 5.96 - 7.95: 15 7.95 - 9.93: 7 Bond angle restraints: 11135 Sorted by residual: angle pdb=" C CYSRP 226 " pdb=" CA CYSRP 226 " pdb=" CB CYSRP 226 " ideal model delta sigma weight residual 110.88 102.92 7.96 1.57e+00 4.06e-01 2.57e+01 angle pdb=" N SERBP 161 " pdb=" CA SERBP 161 " pdb=" C SERBP 161 " ideal model delta sigma weight residual 108.34 113.62 -5.28 1.31e+00 5.83e-01 1.62e+01 angle pdb=" CA SERRP 225 " pdb=" C SERRP 225 " pdb=" O SERRP 225 " ideal model delta sigma weight residual 120.90 117.08 3.82 1.03e+00 9.43e-01 1.37e+01 angle pdb=" N ILERP 317 " pdb=" CA ILERP 317 " pdb=" C ILERP 317 " ideal model delta sigma weight residual 112.35 107.34 5.01 1.41e+00 5.03e-01 1.26e+01 angle pdb=" CA ILERP 146 " pdb=" C ILERP 146 " pdb=" O ILERP 146 " ideal model delta sigma weight residual 120.95 117.42 3.53 1.04e+00 9.25e-01 1.15e+01 ... (remaining 11130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4314 17.54 - 35.08: 418 35.08 - 52.61: 81 52.61 - 70.15: 12 70.15 - 87.69: 5 Dihedral angle restraints: 4830 sinusoidal: 1926 harmonic: 2904 Sorted by residual: dihedral pdb=" CA TRPBP 332 " pdb=" C TRPBP 332 " pdb=" N ASPBP 333 " pdb=" CA ASPBP 333 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASNAP 292 " pdb=" C ASNAP 292 " pdb=" N LYSAP 293 " pdb=" CA LYSAP 293 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CB CYSRP 226 " pdb=" SG CYSRP 226 " pdb=" SG CYSRP 296 " pdb=" CB CYSRP 296 " ideal model delta sinusoidal sigma weight residual -86.00 -48.38 -37.62 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 4827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 930 0.064 - 0.129: 247 0.129 - 0.193: 46 0.193 - 0.258: 4 0.258 - 0.322: 2 Chirality restraints: 1229 Sorted by residual: chirality pdb=" CA CYSRP 226 " pdb=" N CYSRP 226 " pdb=" C CYSRP 226 " pdb=" CB CYSRP 226 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C09 N2VRP 501 " pdb=" C10 N2VRP 501 " pdb=" C16 N2VRP 501 " pdb=" N08 N2VRP 501 " both_signs ideal model delta sigma weight residual False 2.25 2.57 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB THRBP 47 " pdb=" CA THRBP 47 " pdb=" OG1 THRBP 47 " pdb=" CG2 THRBP 47 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1226 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEURP 224 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C LEURP 224 " -0.077 2.00e-02 2.50e+03 pdb=" O LEURP 224 " 0.029 2.00e-02 2.50e+03 pdb=" N SERRP 225 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRBP 59 " -0.029 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYRBP 59 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYRBP 59 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYRBP 59 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYRBP 59 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYRBP 59 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYRBP 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYRBP 59 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VALRP 276 " 0.043 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRORP 277 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRORP 277 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRORP 277 " 0.035 5.00e-02 4.00e+02 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 976 2.74 - 3.28: 7350 3.28 - 3.82: 13838 3.82 - 4.36: 17695 4.36 - 4.90: 29275 Nonbonded interactions: 69134 Sorted by model distance: nonbonded pdb=" OG SERBP 161 " pdb=" OD1 ASPBP 163 " model vdw 2.205 3.040 nonbonded pdb=" OG SERBP 245 " pdb=" OD1 ASPBP 247 " model vdw 2.214 3.040 nonbonded pdb=" OH TYRBP 145 " pdb=" OD2 ASPBP 186 " model vdw 2.245 3.040 nonbonded pdb=" O ILEBP 58 " pdb=" OG SERBP 316 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASPBP 228 " pdb=" OH TYRNP 117 " model vdw 2.282 3.040 ... (remaining 69129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.008 0.112 8224 Z= 0.406 Angle : 0.950 9.934 11141 Z= 0.558 Chirality : 0.061 0.322 1229 Planarity : 0.006 0.063 1410 Dihedral : 14.362 87.689 2943 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.47 % Allowed : 6.53 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.66 (0.22), residues: 977 helix: -4.08 (0.18), residues: 361 sheet: -2.48 (0.31), residues: 218 loop : -2.16 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARGNP 118 TYR 0.062 0.003 TYRBP 59 PHE 0.023 0.003 PHENP 108 TRP 0.019 0.003 TRPRP 243 HIS 0.021 0.002 HISAP 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00846 / 0.41 ( 8221) covalent geometry : angle 0.94901 / 0.56 (11135) SS BOND : bond 0.01087 / 0.54 ( 3) SS BOND : angle 2.40076 / 1.18 ( 6) hydrogen bonds : bond 0.27651 / 18.00 ( 298) hydrogen bonds : angle 10.57732 / 7.16 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 388 LEU cc_start: 0.8281 (mt) cc_final: 0.7984 (mt) outliers start: 4 outliers final: 2 residues processed: 176 average time/residue: 0.5765 time to fit residues: 106.7691 Evaluate side-chains 137 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 343 ASP Chi-restraints excluded: chain RP residue 379 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AP 29 GLN AP 41 HIS AP 218 ASN AP 227 GLN AP 267 GLN AP 278 ASN AP 292 ASN BP 32 GLN BP 88 ASN BP 132 ASN BP 176 GLN BP 259 GLN BP 340 ASN GP 59 ASN NP 31 ASN RP 240 ASN RP 320 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129310 restraints weight = 9021.667| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.49 r_work: 0.3265 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8224 Z= 0.135 Angle : 0.582 7.864 11141 Z= 0.309 Chirality : 0.043 0.204 1229 Planarity : 0.005 0.041 1410 Dihedral : 6.910 72.434 1105 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.61 % Allowed : 14.10 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.24), residues: 977 helix: -2.74 (0.23), residues: 356 sheet: -2.01 (0.32), residues: 214 loop : -1.47 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGNP 19 TYR 0.013 0.001 TYRRP 402 PHE 0.016 0.001 PHEAP 212 TRP 0.013 0.001 TRPBP 82 HIS 0.007 0.001 HISAP 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 8221) covalent geometry : angle 0.58108 / 0.31 (11135) SS BOND : bond 0.00787 / 0.39 ( 3) SS BOND : angle 1.16414 / 0.58 ( 6) hydrogen bonds : bond 0.04482 / 2.79 ( 298) hydrogen bonds : angle 5.61458 / 3.85 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: AP 314 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7153 (tp30) REVERT: AP 388 LEU cc_start: 0.8438 (mt) cc_final: 0.8203 (mt) REVERT: BP 46 ARG cc_start: 0.7660 (mmt180) cc_final: 0.7118 (mpp80) REVERT: BP 59 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: BP 205 ASP cc_start: 0.8700 (p0) cc_final: 0.8489 (p0) REVERT: BP 340 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7983 (t0) REVERT: RP 147 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7314 (mt) outliers start: 31 outliers final: 9 residues processed: 169 average time/residue: 0.5927 time to fit residues: 105.8342 Evaluate side-chains 139 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 17 GLN Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain BP residue 340 ASN Chi-restraints excluded: chain NP residue 89 GLU Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 305 TYR Chi-restraints excluded: chain RP residue 382 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AP 390 GLN ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.156196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126650 restraints weight = 9045.750| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.33 r_work: 0.3323 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8224 Z= 0.149 Angle : 0.575 7.921 11141 Z= 0.299 Chirality : 0.043 0.176 1229 Planarity : 0.004 0.036 1410 Dihedral : 6.285 69.438 1101 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.85 % Allowed : 17.02 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.26), residues: 977 helix: -1.83 (0.26), residues: 360 sheet: -1.70 (0.34), residues: 205 loop : -1.21 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGBP 134 TYR 0.012 0.001 TYRNP 60 PHE 0.014 0.001 PHEAP 212 TRP 0.013 0.001 TRPRP 243 HIS 0.014 0.001 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 8221) covalent geometry : angle 0.57515 / 0.30 (11135) SS BOND : bond 0.00181 / 0.09 ( 3) SS BOND : angle 0.88090 / 0.47 ( 6) hydrogen bonds : bond 0.03710 / 2.32 ( 298) hydrogen bonds : angle 5.08770 / 3.51 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: AP 314 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7266 (tp30) REVERT: AP 388 LEU cc_start: 0.8513 (mt) cc_final: 0.8282 (mt) REVERT: AP 392 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7990 (mm-30) REVERT: BP 46 ARG cc_start: 0.7669 (mmt180) cc_final: 0.7213 (mpp80) REVERT: BP 59 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: RP 147 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7312 (OUTLIER) REVERT: RP 247 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7828 (tp30) outliers start: 33 outliers final: 14 residues processed: 151 average time/residue: 0.5787 time to fit residues: 92.7277 Evaluate side-chains 145 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 17 GLN Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 70 LEU Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain NP residue 65 LYS Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 89 GLU Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 279 LEU Chi-restraints excluded: chain RP residue 303 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 80 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 92 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... BP 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128953 restraints weight = 9130.062| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.41 r_work: 0.3306 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8224 Z= 0.107 Angle : 0.538 7.705 11141 Z= 0.277 Chirality : 0.042 0.199 1229 Planarity : 0.003 0.035 1410 Dihedral : 5.944 67.971 1101 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.85 % Allowed : 18.88 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.27), residues: 977 helix: -1.12 (0.27), residues: 362 sheet: -1.46 (0.35), residues: 206 loop : -1.04 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGBP 134 TYR 0.015 0.001 TYRNP 60 PHE 0.014 0.001 PHEAP 212 TRP 0.012 0.001 TRPNP 47 HIS 0.014 0.001 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8221) covalent geometry : angle 0.53776 / 0.28 (11135) SS BOND : bond 0.00166 / 0.08 ( 3) SS BOND : angle 0.56938 / 0.34 ( 6) hydrogen bonds : bond 0.03093 / 1.93 ( 298) hydrogen bonds : angle 4.64167 / 3.22 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 28 LYS cc_start: 0.8216 (pptt) cc_final: 0.7951 (pttt) REVERT: AP 388 LEU cc_start: 0.8514 (mt) cc_final: 0.8295 (mt) REVERT: AP 392 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7865 (mm-30) REVERT: BP 46 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7178 (mpp80) REVERT: BP 59 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: BP 186 ASP cc_start: 0.8272 (p0) cc_final: 0.7667 (p0) REVERT: RP 189 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7876 (pt) REVERT: RP 303 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5996 (mmm) REVERT: RP 371 MET cc_start: 0.4477 (OUTLIER) cc_final: 0.4121 (mmm) outliers start: 33 outliers final: 12 residues processed: 158 average time/residue: 0.5678 time to fit residues: 95.1353 Evaluate side-chains 140 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 17 GLN Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 38 MET Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 279 LEU Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 371 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AP 220 HIS BP 176 GLN ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 5 GLN NP 31 ASN RP 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128505 restraints weight = 9032.273| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.50 r_work: 0.3258 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8224 Z= 0.156 Angle : 0.578 8.201 11141 Z= 0.298 Chirality : 0.044 0.238 1229 Planarity : 0.004 0.053 1410 Dihedral : 5.955 66.555 1101 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.61 % Allowed : 21.10 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.27), residues: 977 helix: -0.96 (0.27), residues: 372 sheet: -1.44 (0.35), residues: 206 loop : -1.13 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGBP 134 TYR 0.012 0.001 TYRNP 60 PHE 0.016 0.001 PHEAP 212 TRP 0.014 0.001 TRPRP 243 HIS 0.014 0.001 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 8221) covalent geometry : angle 0.57828 / 0.30 (11135) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 0.73644 / 0.47 ( 6) hydrogen bonds : bond 0.03254 / 2.03 ( 298) hydrogen bonds : angle 4.60424 / 3.20 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 378 ASP cc_start: 0.8066 (m-30) cc_final: 0.7620 (m-30) REVERT: AP 392 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7917 (mm-30) REVERT: BP 46 ARG cc_start: 0.7731 (mmt180) cc_final: 0.7265 (mpp80) REVERT: BP 59 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: BP 219 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8313 (mtt-85) REVERT: RP 147 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7198 (tt) REVERT: RP 189 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7936 (pt) REVERT: RP 303 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.6203 (mpm) REVERT: RP 371 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.4242 (mmm) outliers start: 31 outliers final: 13 residues processed: 136 average time/residue: 0.5781 time to fit residues: 83.3927 Evaluate side-chains 142 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 219 ARG Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 38 MET Chi-restraints excluded: chain GP residue 47 GLU Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 279 LEU Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 371 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124416 restraints weight = 9072.869| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.35 r_work: 0.3301 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8224 Z= 0.229 Angle : 0.631 8.638 11141 Z= 0.324 Chirality : 0.046 0.266 1229 Planarity : 0.004 0.056 1410 Dihedral : 6.129 65.212 1101 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.55 % Allowed : 20.16 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.27), residues: 977 helix: -0.87 (0.28), residues: 364 sheet: -1.28 (0.35), residues: 213 loop : -1.04 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGBP 134 TYR 0.015 0.002 TYRNP 60 PHE 0.019 0.002 PHENP 108 TRP 0.015 0.002 TRPRP 243 HIS 0.013 0.002 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 ( 8221) covalent geometry : angle 0.63084 / 0.32 (11135) SS BOND : bond 0.00245 / 0.12 ( 3) SS BOND : angle 1.00640 / 0.62 ( 6) hydrogen bonds : bond 0.03592 / 2.25 ( 298) hydrogen bonds : angle 4.74773 / 3.31 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 378 ASP cc_start: 0.8165 (m-30) cc_final: 0.7771 (m-30) REVERT: BP 46 ARG cc_start: 0.7820 (mmt180) cc_final: 0.7328 (mpp80) REVERT: BP 59 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8626 (m-80) REVERT: BP 219 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8308 (mtt-85) REVERT: RP 147 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7253 (tt) REVERT: RP 189 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (pt) REVERT: RP 247 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7936 (tp30) REVERT: RP 303 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6253 (mpm) REVERT: RP 371 MET cc_start: 0.4573 (OUTLIER) cc_final: 0.4339 (mmm) outliers start: 39 outliers final: 14 residues processed: 148 average time/residue: 0.5424 time to fit residues: 85.2256 Evaluate side-chains 137 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 219 ARG Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain GP residue 47 GLU Chi-restraints excluded: chain NP residue 65 LYS Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 279 LEU Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 311 LEU Chi-restraints excluded: chain RP residue 371 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 5 GLN RP 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128566 restraints weight = 9065.611| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.46 r_work: 0.3270 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8224 Z= 0.138 Angle : 0.585 8.477 11141 Z= 0.297 Chirality : 0.044 0.281 1229 Planarity : 0.003 0.036 1410 Dihedral : 5.923 65.467 1101 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.38 % Allowed : 20.75 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.27), residues: 977 helix: -0.65 (0.28), residues: 363 sheet: -1.21 (0.34), residues: 219 loop : -0.87 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGNP 19 TYR 0.015 0.001 TYRNP 60 PHE 0.016 0.001 PHEAP 212 TRP 0.016 0.001 TRPBP 82 HIS 0.012 0.001 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8221) covalent geometry : angle 0.58487 / 0.30 (11135) SS BOND : bond 0.00168 / 0.08 ( 3) SS BOND : angle 0.55834 / 0.37 ( 6) hydrogen bonds : bond 0.03114 / 1.94 ( 298) hydrogen bonds : angle 4.55235 / 3.17 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 28 LYS cc_start: 0.8257 (pptt) cc_final: 0.8047 (pttt) REVERT: AP 378 ASP cc_start: 0.8013 (m-30) cc_final: 0.7678 (m-30) REVERT: BP 46 ARG cc_start: 0.7807 (mmt180) cc_final: 0.7359 (mpp80) REVERT: BP 59 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8690 (m-80) REVERT: BP 219 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8391 (mtt-85) REVERT: BP 266 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7478 (t-170) REVERT: NP 43 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7982 (mtpt) REVERT: RP 147 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7215 (tt) REVERT: RP 189 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7970 (pt) REVERT: RP 247 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7836 (tp30) REVERT: RP 303 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6292 (mpm) REVERT: RP 371 MET cc_start: 0.4557 (OUTLIER) cc_final: 0.4354 (mmm) outliers start: 29 outliers final: 11 residues processed: 140 average time/residue: 0.5579 time to fit residues: 82.7706 Evaluate side-chains 139 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 219 ARG Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 266 HIS Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 371 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128617 restraints weight = 9043.559| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.47 r_work: 0.3283 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8224 Z= 0.139 Angle : 0.598 8.724 11141 Z= 0.303 Chirality : 0.044 0.295 1229 Planarity : 0.004 0.055 1410 Dihedral : 5.850 65.481 1101 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.91 % Allowed : 22.26 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.27), residues: 977 helix: -0.51 (0.28), residues: 363 sheet: -1.15 (0.34), residues: 218 loop : -0.83 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGBP 134 TYR 0.017 0.001 TYRRP 305 PHE 0.016 0.001 PHEAP 212 TRP 0.015 0.001 TRPBP 82 HIS 0.013 0.001 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8221) covalent geometry : angle 0.59797 / 0.30 (11135) SS BOND : bond 0.00154 / 0.07 ( 3) SS BOND : angle 0.56966 / 0.37 ( 6) hydrogen bonds : bond 0.03054 / 1.91 ( 298) hydrogen bonds : angle 4.48409 / 3.13 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 378 ASP cc_start: 0.7960 (m-30) cc_final: 0.7631 (m-30) REVERT: BP 13 GLN cc_start: 0.7696 (pp30) cc_final: 0.7397 (pp30) REVERT: BP 46 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7442 (mpp80) REVERT: BP 59 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8666 (m-80) REVERT: BP 186 ASP cc_start: 0.8212 (p0) cc_final: 0.7710 (p0) REVERT: BP 219 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8455 (mtt-85) REVERT: BP 266 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7512 (t-170) REVERT: GP 21 MET cc_start: 0.7361 (ptm) cc_final: 0.7094 (ptm) REVERT: RP 147 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7284 (tt) REVERT: RP 189 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8070 (pt) REVERT: RP 247 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7858 (tp30) REVERT: RP 303 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6241 (mpm) REVERT: RP 371 MET cc_start: 0.4626 (OUTLIER) cc_final: 0.4413 (mmm) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 0.5844 time to fit residues: 82.8855 Evaluate side-chains 138 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 219 ARG Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 266 HIS Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 38 MET Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 371 MET Chi-restraints excluded: chain RP residue 382 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AP 220 HIS BP 16 ASN ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126864 restraints weight = 9084.296| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.42 r_work: 0.3311 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8224 Z= 0.181 Angle : 0.624 8.962 11141 Z= 0.317 Chirality : 0.045 0.302 1229 Planarity : 0.004 0.058 1410 Dihedral : 5.955 66.586 1101 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.03 % Allowed : 22.26 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.27), residues: 977 helix: -0.48 (0.28), residues: 363 sheet: -1.19 (0.34), residues: 219 loop : -0.82 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGBP 134 TYR 0.017 0.001 TYRNP 60 PHE 0.016 0.001 PHEAP 212 TRP 0.015 0.001 TRPBP 82 HIS 0.013 0.001 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 8221) covalent geometry : angle 0.62396 / 0.32 (11135) SS BOND : bond 0.00187 / 0.09 ( 3) SS BOND : angle 0.72171 / 0.45 ( 6) hydrogen bonds : bond 0.03274 / 2.05 ( 298) hydrogen bonds : angle 4.58863 / 3.20 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 378 ASP cc_start: 0.7995 (m-30) cc_final: 0.7676 (m-30) REVERT: BP 46 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7495 (mpp80) REVERT: BP 59 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8591 (m-80) REVERT: BP 186 ASP cc_start: 0.8214 (p0) cc_final: 0.7754 (p0) REVERT: BP 219 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8436 (mtt-85) REVERT: BP 266 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7555 (t-170) REVERT: GP 21 MET cc_start: 0.7372 (ptm) cc_final: 0.7091 (ptm) REVERT: GP 46 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7867 (mmtt) REVERT: RP 147 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7339 (tt) REVERT: RP 189 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8141 (pt) REVERT: RP 247 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7885 (mm-30) REVERT: RP 303 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6267 (mpm) outliers start: 26 outliers final: 13 residues processed: 130 average time/residue: 0.5819 time to fit residues: 80.0198 Evaluate side-chains 133 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 219 ARG Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 266 HIS Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 65 LYS Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 303 MET Chi-restraints excluded: chain RP residue 382 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 0.0170 chunk 88 optimal weight: 0.4980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... BP 16 ASN ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127966 restraints weight = 9090.668| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.42 r_work: 0.3260 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8224 Z= 0.150 Angle : 0.618 9.044 11141 Z= 0.311 Chirality : 0.045 0.317 1229 Planarity : 0.004 0.062 1410 Dihedral : 5.880 65.561 1101 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.68 % Allowed : 23.08 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.27), residues: 977 helix: -0.39 (0.28), residues: 363 sheet: -1.17 (0.34), residues: 219 loop : -0.82 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGBP 134 TYR 0.017 0.001 TYRNP 60 PHE 0.015 0.001 PHEAP 212 TRP 0.015 0.001 TRPBP 82 HIS 0.012 0.001 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8221) covalent geometry : angle 0.61802 / 0.31 (11135) SS BOND : bond 0.00188 / 0.09 ( 3) SS BOND : angle 0.61721 / 0.40 ( 6) hydrogen bonds : bond 0.03115 / 1.95 ( 298) hydrogen bonds : angle 4.55517 / 3.18 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AP 24 LYS cc_start: 0.7985 (pptt) cc_final: 0.7252 (ptpp) REVERT: AP 378 ASP cc_start: 0.7963 (m-30) cc_final: 0.7643 (m-30) REVERT: BP 46 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7433 (mpp80) REVERT: BP 59 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8668 (m-80) REVERT: BP 186 ASP cc_start: 0.8173 (p0) cc_final: 0.7699 (p0) REVERT: BP 219 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8426 (mtt-85) REVERT: BP 266 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7524 (t-170) REVERT: GP 21 MET cc_start: 0.7259 (ptm) cc_final: 0.6984 (ptm) REVERT: GP 46 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7878 (mmtt) REVERT: RP 147 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7309 (tt) REVERT: RP 189 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8098 (pt) REVERT: RP 247 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7866 (mm-30) outliers start: 23 outliers final: 13 residues processed: 130 average time/residue: 0.5400 time to fit residues: 74.5786 Evaluate side-chains 131 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL Chi-restraints excluded: chain AP residue 266 LEU Chi-restraints excluded: chain BP residue 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 219 ARG Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 266 HIS Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain NP residue 65 LYS Chi-restraints excluded: chain NP residue 78 THR Chi-restraints excluded: chain NP residue 91 THR Chi-restraints excluded: chain NP residue 120 GLN Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 189 LEU Chi-restraints excluded: chain RP residue 382 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123252 restraints weight = 9006.401| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.35 r_work: 0.3309 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8224 Z= 0.189 Angle : 0.639 9.130 11141 Z= 0.322 Chirality : 0.046 0.325 1229 Planarity : 0.004 0.060 1410 Dihedral : 5.986 66.534 1101 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.68 % Allowed : 23.08 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.27), residues: 977 helix: -0.44 (0.28), residues: 364 sheet: -1.18 (0.34), residues: 219 loop : -0.84 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGBP 134 TYR 0.017 0.002 TYRRP 305 PHE 0.016 0.001 PHEAP 212 TRP 0.016 0.002 TRPRP 243 HIS 0.012 0.001 HISRP 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 8221) covalent geometry : angle 0.63885 / 0.32 (11135) SS BOND : bond 0.00213 / 0.10 ( 3) SS BOND : angle 0.84079 / 0.51 ( 6) hydrogen bonds : bond 0.03325 / 2.08 ( 298) hydrogen bonds : angle 4.64474 / 3.24 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.92 seconds wall clock time: 50 minutes 1.32 seconds (3001.32 seconds total)