Starting phenix.real_space_refine on Tue Mar 3 19:39:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6orv_20179/03_2026/6orv_20179.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orv_20179/03_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_20179/03_2026/6orv_20179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orv_20179/03_2026/6orv_20179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6orv_20179/03_2026/6orv_20179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orv_20179/03_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-dev-5986/lib/python3.9/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: 1.81, per 1000 atoms: 0.23 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: 0.76 Conformation dependent library (CDL) restraints added in 286.6 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: 0.40 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: 1.19 Time building geometry restraints manager: 0.95 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 - 34.49: 4749 34.49 - 68.97: 110 68.97 - 103.46: 8 103.46 - 137.95: 1 137.95 - 172.43: 2 Dihedral angle restraints: 4870 sinusoidal: 1966 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=" C17 N2VRP 501 " pdb=" C09 N2VRP 501 " pdb=" C16 N2VRP 501 " pdb=" N08 N2VRP 501 " ideal model delta sinusoidal sigma weight residual 52.78 -134.79 -172.43 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4867 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: 1.540 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.030 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:9.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 15.663 172.434 2983 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 covalent geometry : bond 0.00846 ( 8221) covalent geometry : angle 0.94901 (11135) SS BOND : bond 0.01087 ( 3) SS BOND : angle 2.40076 ( 6) hydrogen bonds : bond 0.27651 ( 298) hydrogen bonds : angle 10.57732 ( 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 : 0.295 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: 0.6860 time to fit residues: 126.6235 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 : 0.316 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 259 GLN BP 340 ASN GP 59 ASN RP 240 ASN RP 320 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.157961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129706 restraints weight = 9008.370| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.50 r_work: 0.3260 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1819 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= 0.133 Angle : 0.579 7.704 11141 Z= 0.307 Chirality : 0.043 0.218 1229 Planarity : 0.005 0.041 1410 Dihedral : 11.288 158.754 1145 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.61 % Allowed : 14.22 % Favored : 82.17 % 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: -3.18 (0.25), residues: 977 helix: -2.68 (0.23), residues: 350 sheet: -2.00 (0.32), residues: 214 loop : -1.38 (0.31), residues: 413 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 0.012 0.001 TRPBP 82 HIS 0.007 0.001 HISAP 357 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8221) covalent geometry : angle 0.57842 (11135) SS BOND : bond 0.00683 ( 3) SS BOND : angle 1.07367 ( 6) hydrogen bonds : bond 0.04198 ( 298) hydrogen bonds : angle 5.54365 ( 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 188 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: AP 314 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7164 (tp30) REVERT: AP 388 LEU cc_start: 0.8433 (mt) cc_final: 0.8196 (mt) REVERT: BP 46 ARG cc_start: 0.7653 (mmt180) cc_final: 0.7106 (mpp80) REVERT: BP 59 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: BP 176 GLN cc_start: 0.8633 (pt0) cc_final: 0.8307 (pt0) REVERT: RP 147 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7307 (mt) outliers start: 31 outliers final: 8 residues processed: 174 average time/residue: 0.6237 time to fit residues: 114.5616 Evaluate side-chains 142 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 0.0050 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3773 r_free = 0.3773 target = 0.155402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127511 restraints weight = 9048.975| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.49 r_work: 0.3278 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8224 Z= 0.163 Angle : 0.577 7.825 11141 Z= 0.301 Chirality : 0.044 0.185 1229 Planarity : 0.004 0.035 1410 Dihedral : 10.711 153.937 1141 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.85 % Allowed : 17.72 % Favored : 78.44 % 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: -2.45 (0.26), residues: 977 helix: -1.74 (0.26), residues: 361 sheet: -1.68 (0.34), residues: 203 loop : -1.24 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGBP 134 TYR 0.014 0.001 TYRNP 60 PHE 0.015 0.001 PHENP 108 TRP 0.014 0.001 TRPRP 243 HIS 0.015 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8221) covalent geometry : angle 0.57718 (11135) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.94889 ( 6) hydrogen bonds : bond 0.03690 ( 298) hydrogen bonds : angle 5.01200 ( 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 172 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: BP 46 ARG cc_start: 0.7904 (mmt180) cc_final: 0.7476 (mpp80) REVERT: BP 59 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: RP 147 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7496 (OUTLIER) REVERT: RP 247 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7826 (tp30) outliers start: 33 outliers final: 13 residues processed: 150 average time/residue: 0.6157 time to fit residues: 97.6199 Evaluate side-chains 144 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 65 THR 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 91 THR Chi-restraints excluded: chain RP residue 147 ILE Chi-restraints excluded: chain RP residue 279 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 80 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.0030 chunk 92 optimal weight: 0.0000 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 5 GLN NP 31 ASN NP 120 GLN RP 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133517 restraints weight = 9156.359| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.54 r_work: 0.3313 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8224 Z= 0.095 Angle : 0.531 7.751 11141 Z= 0.273 Chirality : 0.042 0.210 1229 Planarity : 0.003 0.038 1410 Dihedral : 10.239 148.412 1141 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.31 % Allowed : 18.76 % Favored : 76.92 % 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: -1.79 (0.27), residues: 977 helix: -1.03 (0.27), residues: 362 sheet: -1.39 (0.35), residues: 203 loop : -1.00 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGBP 134 TYR 0.017 0.001 TYRRP 305 PHE 0.016 0.001 PHEAP 212 TRP 0.011 0.001 TRPNP 47 HIS 0.015 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 8221) covalent geometry : angle 0.53056 (11135) SS BOND : bond 0.00169 ( 3) SS BOND : angle 0.44495 ( 6) hydrogen bonds : bond 0.02972 ( 298) hydrogen bonds : angle 4.56760 ( 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 183 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: BP 46 ARG cc_start: 0.7781 (mmt180) cc_final: 0.7398 (mpp80) REVERT: BP 59 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: BP 186 ASP cc_start: 0.8200 (p0) cc_final: 0.7675 (p0) REVERT: BP 219 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8373 (mtt-85) REVERT: NP 31 ASN cc_start: 0.8213 (m-40) cc_final: 0.7976 (m110) REVERT: RP 189 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8016 (pt) REVERT: RP 371 MET cc_start: 0.4658 (OUTLIER) cc_final: 0.4315 (mmm) outliers start: 37 outliers final: 11 residues processed: 163 average time/residue: 0.6234 time to fit residues: 107.4859 Evaluate side-chains 134 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 224 VAL 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 219 ARG Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain GP residue 19 LEU 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 189 LEU Chi-restraints excluded: chain RP residue 272 ILE Chi-restraints excluded: chain RP residue 279 LEU 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: 0.8980 chunk 69 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 0.0370 chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 0.0670 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3831 r_free = 0.3831 target = 0.161262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130645 restraints weight = 9052.475| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.44 r_work: 0.3279 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8224 Z= 0.115 Angle : 0.544 8.038 11141 Z= 0.278 Chirality : 0.042 0.240 1229 Planarity : 0.004 0.066 1410 Dihedral : 10.041 144.044 1141 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.50 % Allowed : 21.79 % 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: -1.60 (0.27), residues: 977 helix: -0.77 (0.28), residues: 367 sheet: -1.09 (0.35), residues: 212 loop : -1.12 (0.31), residues: 398 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 0.016 0.001 TRPBP 82 HIS 0.014 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8221) covalent geometry : angle 0.54414 (11135) SS BOND : bond 0.00124 ( 3) SS BOND : angle 0.48402 ( 6) hydrogen bonds : bond 0.02961 ( 298) hydrogen bonds : angle 4.43379 ( 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 160 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: BP 46 ARG cc_start: 0.7756 (mmt180) cc_final: 0.7247 (mpp80) REVERT: BP 59 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8589 (m-80) REVERT: BP 186 ASP cc_start: 0.8277 (p0) cc_final: 0.7653 (p0) REVERT: BP 219 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8281 (mtt-85) REVERT: RP 189 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7893 (pt) REVERT: RP 247 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7839 (tp30) REVERT: RP 371 MET cc_start: 0.4493 (OUTLIER) cc_final: 0.4176 (mmm) outliers start: 30 outliers final: 12 residues processed: 143 average time/residue: 0.5813 time to fit residues: 88.0747 Evaluate side-chains 139 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 219 ARG 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 GP residue 38 MET Chi-restraints excluded: chain NP residue 11 LEU 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 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: 0.9980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127824 restraints weight = 9052.717| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.47 r_work: 0.3243 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8224 Z= 0.190 Angle : 0.598 8.409 11141 Z= 0.307 Chirality : 0.045 0.259 1229 Planarity : 0.004 0.045 1410 Dihedral : 10.108 142.319 1141 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.20 % Allowed : 21.10 % 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: -1.63 (0.27), residues: 977 helix: -0.80 (0.28), residues: 372 sheet: -1.15 (0.35), residues: 212 loop : -1.11 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGBP 134 TYR 0.015 0.002 TYRNP 60 PHE 0.017 0.001 PHENP 108 TRP 0.015 0.002 TRPBP 82 HIS 0.013 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 8221) covalent geometry : angle 0.59766 (11135) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.93742 ( 6) hydrogen bonds : bond 0.03400 ( 298) hydrogen bonds : angle 4.59841 ( 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 161 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: AP 378 ASP cc_start: 0.8114 (m-30) cc_final: 0.7708 (m-30) REVERT: BP 46 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7252 (mpp80) REVERT: BP 59 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: BP 186 ASP cc_start: 0.8332 (p0) cc_final: 0.7722 (p0) REVERT: BP 219 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8263 (mtt-85) REVERT: GP 21 MET cc_start: 0.7235 (ptm) cc_final: 0.6915 (ptm) REVERT: RP 147 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7178 (tt) REVERT: RP 189 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7922 (pt) REVERT: RP 247 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7920 (tp30) REVERT: RP 371 MET cc_start: 0.4530 (OUTLIER) cc_final: 0.4302 (mmm) outliers start: 36 outliers final: 15 residues processed: 140 average time/residue: 0.6344 time to fit residues: 93.8041 Evaluate side-chains 139 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 219 ARG Chi-restraints excluded: chain BP residue 243 THR Chi-restraints excluded: chain BP residue 270 ILE Chi-restraints excluded: chain BP residue 323 ASP Chi-restraints excluded: chain GP residue 16 VAL Chi-restraints excluded: chain GP residue 19 LEU Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 11 LEU 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 371 MET Chi-restraints excluded: chain RP residue 382 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 0.0070 chunk 54 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BP 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128820 restraints weight = 9072.887| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.38 r_work: 0.3261 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2806 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= 0.122 Angle : 0.566 8.477 11141 Z= 0.288 Chirality : 0.043 0.272 1229 Planarity : 0.004 0.051 1410 Dihedral : 9.904 139.052 1141 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.20 % Allowed : 21.68 % Favored : 74.13 % 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: -1.34 (0.27), residues: 977 helix: -0.45 (0.28), residues: 360 sheet: -1.09 (0.34), residues: 216 loop : -0.98 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGBP 134 TYR 0.015 0.001 TYRNP 60 PHE 0.014 0.001 PHEAP 212 TRP 0.014 0.001 TRPBP 82 HIS 0.012 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8221) covalent geometry : angle 0.56623 (11135) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.54098 ( 6) hydrogen bonds : bond 0.03006 ( 298) hydrogen bonds : angle 4.41235 ( 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 162 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.297 Fit side-chains REVERT: AP 358 TYR cc_start: 0.8462 (m-80) cc_final: 0.7864 (m-80) REVERT: AP 378 ASP cc_start: 0.8030 (m-30) cc_final: 0.7665 (m-30) REVERT: BP 46 ARG cc_start: 0.7800 (mmt180) cc_final: 0.7282 (mpp80) REVERT: BP 59 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: BP 186 ASP cc_start: 0.8303 (p0) cc_final: 0.7694 (p0) REVERT: BP 219 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8285 (mtt-85) REVERT: BP 266 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7414 (t-170) REVERT: GP 21 MET cc_start: 0.7149 (ptm) cc_final: 0.6864 (ptm) REVERT: RP 147 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7181 (tt) REVERT: RP 189 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7891 (pt) REVERT: RP 247 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7872 (tp30) REVERT: RP 371 MET cc_start: 0.4452 (OUTLIER) cc_final: 0.4238 (mmm) outliers start: 36 outliers final: 14 residues processed: 146 average time/residue: 0.6163 time to fit residues: 95.1198 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 : 0.290 ------------------------------------------------------------------------------- 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 61 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 19 LEU Chi-restraints excluded: chain GP residue 38 MET Chi-restraints excluded: chain NP residue 11 LEU 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 213 GLN 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: 0.6980 chunk 61 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 12 optimal weight: 0.0060 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3808 r_free = 0.3808 target = 0.158656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129913 restraints weight = 8980.445| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.29 r_work: 0.3296 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8224 Z= 0.114 Angle : 0.577 8.521 11141 Z= 0.292 Chirality : 0.043 0.295 1229 Planarity : 0.003 0.057 1410 Dihedral : 9.746 135.147 1141 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.15 % Allowed : 23.43 % Favored : 73.43 % 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: -1.23 (0.27), residues: 977 helix: -0.34 (0.28), residues: 363 sheet: -1.05 (0.34), residues: 215 loop : -0.92 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGBP 134 TYR 0.016 0.001 TYRNP 60 PHE 0.016 0.001 PHEAP 212 TRP 0.015 0.001 TRPBP 82 HIS 0.012 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8221) covalent geometry : angle 0.57658 (11135) SS BOND : bond 0.00150 ( 3) SS BOND : angle 0.48784 ( 6) hydrogen bonds : bond 0.02980 ( 298) hydrogen bonds : angle 4.35026 ( 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 153 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.288 Fit side-chains REVERT: AP 378 ASP cc_start: 0.7996 (m-30) cc_final: 0.7690 (m-30) REVERT: BP 46 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7171 (mpp80) REVERT: BP 59 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8757 (m-80) REVERT: BP 186 ASP cc_start: 0.8251 (p0) cc_final: 0.7656 (p0) REVERT: BP 219 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8242 (mtt-85) REVERT: BP 266 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7364 (t-170) REVERT: GP 21 MET cc_start: 0.7063 (ptm) cc_final: 0.6834 (ptm) REVERT: RP 147 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7167 (tt) REVERT: RP 189 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7850 (pt) REVERT: RP 247 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7827 (tp30) REVERT: RP 303 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.6228 (mpm) outliers start: 27 outliers final: 14 residues processed: 139 average time/residue: 0.6020 time to fit residues: 88.3719 Evaluate side-chains 139 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain BP residue 219 ARG Chi-restraints excluded: chain BP residue 234 PHE 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 19 LEU Chi-restraints excluded: chain GP residue 38 MET Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 11 LEU 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 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: 0.2980 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 220 HIS AP 377 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 = 0.3805 r_free = 0.3805 target = 0.158505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128688 restraints weight = 9071.236| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.37 r_work: 0.3261 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2921 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= 0.145 Angle : 0.607 8.747 11141 Z= 0.306 Chirality : 0.044 0.299 1229 Planarity : 0.004 0.060 1410 Dihedral : 9.743 134.321 1141 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.80 % Allowed : 24.59 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.08 (0.27), residues: 977 helix: -0.17 (0.28), residues: 357 sheet: -1.06 (0.34), residues: 216 loop : -0.83 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGBP 134 TYR 0.015 0.001 TYRNP 60 PHE 0.016 0.001 PHEAP 212 TRP 0.014 0.001 TRPBP 82 HIS 0.012 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8221) covalent geometry : angle 0.60709 (11135) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.58672 ( 6) hydrogen bonds : bond 0.03135 ( 298) hydrogen bonds : angle 4.40359 ( 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: 24 poor density : 121 time to evaluate : 0.255 Fit side-chains REVERT: AP 24 LYS cc_start: 0.8130 (pptt) cc_final: 0.7351 (ptpp) REVERT: AP 378 ASP cc_start: 0.8069 (m-30) cc_final: 0.7811 (m-30) REVERT: BP 46 ARG cc_start: 0.7759 (mmt180) cc_final: 0.7230 (mpp80) REVERT: BP 59 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8648 (m-80) REVERT: BP 101 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8658 (mtp) REVERT: BP 186 ASP cc_start: 0.8296 (p0) cc_final: 0.7705 (p0) REVERT: BP 219 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8310 (mtt-85) REVERT: BP 266 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7432 (t-170) REVERT: GP 21 MET cc_start: 0.7094 (ptm) cc_final: 0.6885 (ptm) REVERT: RP 147 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7208 (tt) REVERT: RP 189 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7942 (pt) REVERT: RP 247 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7920 (tp30) outliers start: 24 outliers final: 15 residues processed: 133 average time/residue: 0.6200 time to fit residues: 87.1324 Evaluate side-chains 139 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP residue 221 MET 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 234 PHE 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 19 LEU Chi-restraints excluded: chain GP residue 38 MET Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 11 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 11 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.0770 chunk 90 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AP 390 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.160111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130358 restraints weight = 9052.885| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.37 r_work: 0.3294 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3013 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= 0.119 Angle : 0.601 9.614 11141 Z= 0.300 Chirality : 0.044 0.307 1229 Planarity : 0.003 0.063 1410 Dihedral : 9.646 132.801 1141 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.91 % Allowed : 24.71 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.99 (0.27), residues: 977 helix: -0.05 (0.28), residues: 357 sheet: -1.02 (0.34), residues: 216 loop : -0.82 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGBP 134 TYR 0.016 0.001 TYRNP 60 PHE 0.015 0.001 PHEAP 212 TRP 0.016 0.001 TRPRP 243 HIS 0.012 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8221) covalent geometry : angle 0.60070 (11135) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.47549 ( 6) hydrogen bonds : bond 0.02970 ( 298) hydrogen bonds : angle 4.34735 ( 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 148 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.384 Fit side-chains REVERT: AP 24 LYS cc_start: 0.8107 (pptt) cc_final: 0.7325 (ptpp) REVERT: AP 378 ASP cc_start: 0.8009 (m-30) cc_final: 0.7752 (m-30) REVERT: BP 46 ARG cc_start: 0.7742 (mmt180) cc_final: 0.7213 (mpp80) REVERT: BP 59 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8675 (m-80) REVERT: BP 101 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8655 (mtp) REVERT: BP 186 ASP cc_start: 0.8226 (p0) cc_final: 0.7683 (p0) REVERT: BP 219 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8324 (mtt-85) REVERT: BP 266 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7468 (t-170) REVERT: GP 21 MET cc_start: 0.7088 (ptm) cc_final: 0.6882 (ptm) REVERT: RP 147 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7139 (tt) REVERT: RP 189 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7895 (pt) REVERT: RP 247 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7867 (tp30) REVERT: RP 303 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6107 (mpm) outliers start: 25 outliers final: 16 residues processed: 137 average time/residue: 0.5924 time to fit residues: 86.0683 Evaluate side-chains 139 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 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 47 THR Chi-restraints excluded: chain BP residue 59 TYR Chi-restraints excluded: chain BP residue 101 MET Chi-restraints excluded: chain BP residue 114 CYS Chi-restraints excluded: chain BP residue 146 LEU Chi-restraints excluded: chain BP residue 219 ARG Chi-restraints excluded: chain BP residue 234 PHE 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 19 LEU Chi-restraints excluded: chain GP residue 38 MET Chi-restraints excluded: chain NP residue 5 GLN Chi-restraints excluded: chain NP residue 11 LEU 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 213 GLN Chi-restraints excluded: chain RP residue 303 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BP 16 ASN ** 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 = 0.3792 r_free = 0.3792 target = 0.157352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127649 restraints weight = 8991.630| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.36 r_work: 0.3262 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8224 Z= 0.149 Angle : 0.618 10.327 11141 Z= 0.309 Chirality : 0.045 0.306 1229 Planarity : 0.004 0.061 1410 Dihedral : 9.627 130.607 1141 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.03 % Allowed : 24.59 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.98 (0.27), residues: 977 helix: -0.03 (0.28), residues: 357 sheet: -1.03 (0.34), residues: 216 loop : -0.81 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGBP 134 TYR 0.016 0.001 TYRNP 60 PHE 0.015 0.001 PHEAP 212 TRP 0.018 0.001 TRPRP 243 HIS 0.012 0.001 HISRP 171 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8221) covalent geometry : angle 0.61763 (11135) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.61060 ( 6) hydrogen bonds : bond 0.03119 ( 298) hydrogen bonds : angle 4.41295 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.83 seconds wall clock time: 55 minutes 21.45 seconds (3321.45 seconds total)