Starting phenix.real_space_refine on Wed Mar 4 06:55:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5r_12048/03_2026/7b5r_12048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5r_12048/03_2026/7b5r_12048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b5r_12048/03_2026/7b5r_12048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5r_12048/03_2026/7b5r_12048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b5r_12048/03_2026/7b5r_12048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5r_12048/03_2026/7b5r_12048.map" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 53 5.16 5 C 7437 2.51 5 N 1966 2.21 5 O 2148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s 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: 11606 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2396 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2536 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "S" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2279 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TPO:plan-1': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2046 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Chain: "P" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 654 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11606 At special positions: 0 Unit cell: (149.33, 126.44, 103.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 2 15.00 O 2148 8.00 N 1966 7.00 C 7437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.94 Conformation dependent library (CDL) restraints added in 453.6 milliseconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 8 sheets defined 56.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 18 through 32 removed outlier: 3.651A pdb=" N ASP C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 Processing helix chain 'C' and resid 85 through 106 removed outlier: 3.552A pdb=" N ASP C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 137 removed outlier: 4.283A pdb=" N GLN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.539A pdb=" N HIS C 143 " --> pdb=" O TYR C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.988A pdb=" N GLY C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 253 removed outlier: 3.527A pdb=" N THR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 278 removed outlier: 3.730A pdb=" N TYR C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN C 276 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 299 through 313 Processing helix chain 'C' and resid 316 through 329 removed outlier: 3.892A pdb=" N GLY C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 340 Processing helix chain 'T' and resid 96 through 100 Processing helix chain 'T' and resid 101 through 110 Processing helix chain 'T' and resid 113 through 121 Processing helix chain 'T' and resid 124 through 131 Processing helix chain 'T' and resid 148 through 158 Processing helix chain 'T' and resid 194 through 203 Processing helix chain 'T' and resid 219 through 227 Processing helix chain 'T' and resid 244 through 255 Processing helix chain 'T' and resid 270 through 281 Processing helix chain 'T' and resid 298 through 309 Processing helix chain 'T' and resid 324 through 334 Processing helix chain 'T' and resid 350 through 359 removed outlier: 3.553A pdb=" N GLY T 357 " --> pdb=" O LEU T 354 " (cutoff:3.500A) Processing helix chain 'T' and resid 374 through 383 removed outlier: 3.763A pdb=" N LEU T 378 " --> pdb=" O GLY T 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 33 removed outlier: 3.845A pdb=" N ASP S 33 " --> pdb=" O THR S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 59 removed outlier: 3.814A pdb=" N LYS S 51 " --> pdb=" O ALA S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 93 Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 128 Processing helix chain 'S' and resid 131 through 139 Processing helix chain 'S' and resid 149 through 156 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 87 through 94 Processing helix chain 'L' and resid 100 through 121 Processing helix chain 'L' and resid 129 through 132 Processing helix chain 'L' and resid 145 through 149 removed outlier: 4.349A pdb=" N LEU L 148 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA L 149 " --> pdb=" O PHE L 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 145 through 149' Processing helix chain 'L' and resid 170 through 175 Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.688A pdb=" N TRP L 187 " --> pdb=" O ALA L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 220 Processing helix chain 'L' and resid 247 through 252 removed outlier: 4.039A pdb=" N VAL L 251 " --> pdb=" O ASP L 247 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 252 " --> pdb=" O PHE L 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 247 through 252' Processing helix chain 'L' and resid 256 through 265 Processing helix chain 'L' and resid 276 through 281 Processing helix chain 'L' and resid 283 through 288 Processing helix chain 'Y' and resid 178 through 190 Processing helix chain 'Y' and resid 198 through 203 removed outlier: 4.408A pdb=" N LYS Y 202 " --> pdb=" O GLY Y 198 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN Y 203 " --> pdb=" O TYR Y 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 198 through 203' Processing helix chain 'Y' and resid 207 through 225 Processing helix chain 'Y' and resid 228 through 244 removed outlier: 3.627A pdb=" N LEU Y 232 " --> pdb=" O GLN Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 249 through 251 No H-bonds generated for 'chain 'Y' and resid 249 through 251' Processing helix chain 'Y' and resid 252 through 269 Processing helix chain 'Y' and resid 274 through 282 removed outlier: 3.668A pdb=" N PHE Y 278 " --> pdb=" O GLU Y 274 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR Y 282 " --> pdb=" O PHE Y 278 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 303 removed outlier: 3.508A pdb=" N VAL Y 291 " --> pdb=" O THR Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 310 through 320 removed outlier: 3.977A pdb=" N PHE Y 314 " --> pdb=" O THR Y 310 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU Y 320 " --> pdb=" O THR Y 316 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 343 removed outlier: 3.611A pdb=" N GLU Y 330 " --> pdb=" O ASN Y 326 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP Y 343 " --> pdb=" O LEU Y 339 " (cutoff:3.500A) Processing helix chain 'Y' and resid 351 through 369 Processing helix chain 'Y' and resid 373 through 381 removed outlier: 3.718A pdb=" N ILE Y 377 " --> pdb=" O PRO Y 373 " (cutoff:3.500A) Processing helix chain 'Y' and resid 387 through 401 Processing helix chain 'Y' and resid 402 through 404 No H-bonds generated for 'chain 'Y' and resid 402 through 404' Processing helix chain 'Y' and resid 407 through 413 Processing helix chain 'Y' and resid 415 through 419 Processing helix chain 'Y' and resid 420 through 424 removed outlier: 3.771A pdb=" N LEU Y 423 " --> pdb=" O GLY Y 420 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Y 424 " --> pdb=" O VAL Y 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 420 through 424' Processing helix chain 'P' and resid 38 through 50 Processing helix chain 'P' and resid 54 through 61 Processing helix chain 'P' and resid 85 through 90 Processing sheet with id=AA1, first strand: chain 'T' and resid 139 through 141 removed outlier: 6.727A pdb=" N LEU T 140 " --> pdb=" O ARG T 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'T' and resid 260 through 262 removed outlier: 3.566A pdb=" N ASN T 289 " --> pdb=" O LEU T 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'T' and resid 339 through 341 Processing sheet with id=AA4, first strand: chain 'K' and resid 17 through 23 Processing sheet with id=AA5, first strand: chain 'S' and resid 14 through 17 removed outlier: 3.510A pdb=" N LEU S 6 " --> pdb=" O PHE S 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 31 through 36 removed outlier: 3.702A pdb=" N ALA L 31 " --> pdb=" O PHE L 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'L' and resid 123 through 124 523 hydrogen bonds defined for protein. 1509 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: 1.67 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3735 1.34 - 1.46: 1868 1.46 - 1.57: 6170 1.57 - 1.69: 6 1.69 - 1.81: 78 Bond restraints: 11857 Sorted by residual: bond pdb=" OG1 TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" OG1 TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.717 1.615 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O1P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O2P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3P TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 15783 2.41 - 4.82: 226 4.82 - 7.23: 39 7.23 - 9.64: 5 9.64 - 12.05: 3 Bond angle restraints: 16056 Sorted by residual: angle pdb=" N PRO S 2 " pdb=" CA PRO S 2 " pdb=" CB PRO S 2 " ideal model delta sigma weight residual 103.00 110.53 -7.53 1.10e+00 8.26e-01 4.68e+01 angle pdb=" CB TPO P 187 " pdb=" OG1 TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 119.31 107.26 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N VAL L 164 " pdb=" CA VAL L 164 " pdb=" C VAL L 164 " ideal model delta sigma weight residual 109.34 116.61 -7.27 2.08e+00 2.31e-01 1.22e+01 angle pdb=" N GLY P 72 " pdb=" CA GLY P 72 " pdb=" C GLY P 72 " ideal model delta sigma weight residual 110.29 114.61 -4.32 1.28e+00 6.10e-01 1.14e+01 angle pdb=" CB TPO L 160 " pdb=" OG1 TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 119.31 109.24 10.07 3.00e+00 1.11e-01 1.13e+01 ... (remaining 16051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6410 17.91 - 35.81: 639 35.81 - 53.72: 85 53.72 - 71.63: 23 71.63 - 89.54: 10 Dihedral angle restraints: 7167 sinusoidal: 2956 harmonic: 4211 Sorted by residual: dihedral pdb=" CA LEU K 37 " pdb=" C LEU K 37 " pdb=" N MET K 38 " pdb=" CA MET K 38 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA VAL L 163 " pdb=" C VAL L 163 " pdb=" N VAL L 164 " pdb=" CA VAL L 164 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ARG P 50 " pdb=" C ARG P 50 " pdb=" N ASP P 51 " pdb=" CA ASP P 51 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 7164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1317 0.047 - 0.094: 400 0.094 - 0.141: 80 0.141 - 0.188: 9 0.188 - 0.235: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA PRO S 2 " pdb=" N PRO S 2 " pdb=" C PRO S 2 " pdb=" CB PRO S 2 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL L 163 " pdb=" N VAL L 163 " pdb=" C VAL L 163 " pdb=" CB VAL L 163 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA PRO L 238 " pdb=" N PRO L 238 " pdb=" C PRO L 238 " pdb=" CB PRO L 238 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 1804 not shown) Planarity restraints: 2034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 32 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO K 33 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO K 33 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 33 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 217 " 0.015 2.00e-02 2.50e+03 1.53e-02 5.88e+00 pdb=" CG TRP Y 217 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 217 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 217 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 217 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 217 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 217 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 217 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 217 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 217 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR S 131 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO S 132 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 132 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 132 " -0.031 5.00e-02 4.00e+02 ... (remaining 2031 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 143 2.58 - 3.16: 10701 3.16 - 3.74: 18110 3.74 - 4.32: 24069 4.32 - 4.90: 38814 Nonbonded interactions: 91837 Sorted by model distance: nonbonded pdb=" OD1 ASP Y 216 " pdb=" OG SER Y 408 " model vdw 2.001 3.040 nonbonded pdb=" O GLY Y 337 " pdb=" OG SER Y 340 " model vdw 2.109 3.040 nonbonded pdb=" OE2 GLU L 57 " pdb=" OH TYR Y 185 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR Y 350 " pdb=" OD2 ASP Y 393 " model vdw 2.171 3.040 nonbonded pdb=" NH1 ARG L 157 " pdb=" OE2 GLU Y 268 " model vdw 2.171 3.120 ... (remaining 91832 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.860 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 11857 Z= 0.272 Angle : 0.806 12.049 16056 Z= 0.440 Chirality : 0.046 0.235 1807 Planarity : 0.005 0.064 2034 Dihedral : 14.425 89.536 4427 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.41 (0.23), residues: 1392 helix: 0.48 (0.19), residues: 734 sheet: -3.59 (0.53), residues: 80 loop : -2.45 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 50 TYR 0.021 0.002 TYR Y 225 PHE 0.020 0.002 PHE S 101 TRP 0.041 0.002 TRP Y 217 HIS 0.008 0.002 HIS K 56 Details of bonding type rmsd covalent geometry : bond 0.00591 (11857) covalent geometry : angle 0.80627 (16056) hydrogen bonds : bond 0.14152 ( 523) hydrogen bonds : angle 6.41445 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: C 301 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8734 (pm20) REVERT: K 14 ASP cc_start: 0.7886 (p0) cc_final: 0.7486 (p0) REVERT: K 54 TRP cc_start: 0.8759 (m100) cc_final: 0.7721 (m100) REVERT: Y 211 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.7890 (ttp80) REVERT: Y 250 ARG cc_start: 0.6697 (tpt170) cc_final: 0.6456 (tpt170) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1028 time to fit residues: 18.4337 Evaluate side-chains 86 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 177 HIS ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 HIS Y 179 HIS Y 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.084866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065574 restraints weight = 42944.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067651 restraints weight = 23843.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069020 restraints weight = 16491.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069886 restraints weight = 13013.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070457 restraints weight = 11200.779| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11857 Z= 0.156 Angle : 0.649 10.199 16056 Z= 0.336 Chirality : 0.042 0.148 1807 Planarity : 0.005 0.057 2034 Dihedral : 5.271 39.308 1545 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.54 % Allowed : 8.22 % Favored : 91.23 % 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: -1.01 (0.23), residues: 1392 helix: 0.83 (0.20), residues: 730 sheet: -2.75 (0.52), residues: 96 loop : -2.35 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 50 TYR 0.023 0.001 TYR L 180 PHE 0.021 0.001 PHE T 328 TRP 0.019 0.001 TRP K 43 HIS 0.009 0.001 HIS T 177 Details of bonding type rmsd covalent geometry : bond 0.00351 (11857) covalent geometry : angle 0.64872 (16056) hydrogen bonds : bond 0.04466 ( 523) hydrogen bonds : angle 5.18597 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 37 MET cc_start: 0.7568 (mmm) cc_final: 0.6758 (mmm) REVERT: K 54 TRP cc_start: 0.8591 (m100) cc_final: 0.7921 (m100) REVERT: L 91 MET cc_start: 0.8338 (mtm) cc_final: 0.7898 (mtm) REVERT: Y 211 ARG cc_start: 0.8520 (ptm-80) cc_final: 0.8043 (ttp80) REVERT: Y 328 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8504 (ptpt) outliers start: 7 outliers final: 6 residues processed: 112 average time/residue: 0.0999 time to fit residues: 16.5574 Evaluate side-chains 95 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 158 GLN L 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.085316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065568 restraints weight = 42799.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067785 restraints weight = 22898.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069202 restraints weight = 15500.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070118 restraints weight = 12133.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.070702 restraints weight = 10375.974| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11857 Z= 0.130 Angle : 0.587 10.227 16056 Z= 0.303 Chirality : 0.041 0.137 1807 Planarity : 0.004 0.055 2034 Dihedral : 4.956 38.379 1545 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.55 % Allowed : 10.94 % Favored : 87.51 % 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: -0.69 (0.23), residues: 1392 helix: 1.09 (0.20), residues: 721 sheet: -2.42 (0.54), residues: 96 loop : -2.18 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 150 TYR 0.021 0.001 TYR L 180 PHE 0.024 0.001 PHE T 328 TRP 0.018 0.001 TRP K 43 HIS 0.004 0.001 HIS Y 395 Details of bonding type rmsd covalent geometry : bond 0.00295 (11857) covalent geometry : angle 0.58697 (16056) hydrogen bonds : bond 0.03949 ( 523) hydrogen bonds : angle 4.81578 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.7677 (tmm) cc_final: 0.7368 (tmm) REVERT: K 54 TRP cc_start: 0.8558 (m100) cc_final: 0.8231 (m100) REVERT: L 286 PHE cc_start: 0.5644 (t80) cc_final: 0.5135 (t80) REVERT: Y 211 ARG cc_start: 0.8591 (ptm-80) cc_final: 0.8029 (ttp80) REVERT: P 68 LYS cc_start: 0.8853 (tppt) cc_final: 0.8472 (ptmt) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.1048 time to fit residues: 18.1184 Evaluate side-chains 107 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 222 ILE Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain Y residue 218 LEU Chi-restraints excluded: chain Y residue 231 THR Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 99 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 229 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 = 0.3693 r_free = 0.3693 target = 0.085362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065536 restraints weight = 42580.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067758 restraints weight = 22965.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069148 restraints weight = 15564.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070069 restraints weight = 12231.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070633 restraints weight = 10460.656| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11857 Z= 0.128 Angle : 0.584 11.259 16056 Z= 0.297 Chirality : 0.040 0.138 1807 Planarity : 0.004 0.053 2034 Dihedral : 4.816 36.850 1545 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.55 % Allowed : 13.27 % Favored : 85.18 % 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: -0.52 (0.24), residues: 1392 helix: 1.22 (0.20), residues: 724 sheet: -2.36 (0.54), residues: 97 loop : -2.10 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 90 TYR 0.020 0.001 TYR L 180 PHE 0.034 0.001 PHE T 328 TRP 0.019 0.001 TRP K 43 HIS 0.007 0.001 HIS T 177 Details of bonding type rmsd covalent geometry : bond 0.00292 (11857) covalent geometry : angle 0.58405 (16056) hydrogen bonds : bond 0.03701 ( 523) hydrogen bonds : angle 4.67466 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 316 ASP cc_start: 0.7896 (m-30) cc_final: 0.7400 (m-30) REVERT: K 14 ASP cc_start: 0.7791 (p0) cc_final: 0.7346 (p0) REVERT: K 54 TRP cc_start: 0.8554 (m100) cc_final: 0.8344 (m100) REVERT: L 286 PHE cc_start: 0.5595 (t80) cc_final: 0.5151 (t80) REVERT: Y 211 ARG cc_start: 0.8460 (ptm-80) cc_final: 0.8167 (ttp80) REVERT: Y 293 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8227 (mmm160) REVERT: P 68 LYS cc_start: 0.8905 (tppt) cc_final: 0.8703 (tppt) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.0956 time to fit residues: 17.0232 Evaluate side-chains 115 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 222 ILE Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain Y residue 231 THR Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 118 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 131 optimal weight: 0.0770 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 HIS L 246 GLN Y 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.084048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.064614 restraints weight = 42865.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066647 restraints weight = 23996.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067981 restraints weight = 16692.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.068857 restraints weight = 13209.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069358 restraints weight = 11355.318| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11857 Z= 0.165 Angle : 0.613 11.368 16056 Z= 0.310 Chirality : 0.041 0.207 1807 Planarity : 0.004 0.051 2034 Dihedral : 4.849 32.142 1545 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.79 % Allowed : 14.04 % Favored : 83.17 % 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: -0.45 (0.24), residues: 1392 helix: 1.27 (0.20), residues: 723 sheet: -1.88 (0.61), residues: 82 loop : -2.15 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 90 TYR 0.018 0.001 TYR L 180 PHE 0.036 0.002 PHE T 328 TRP 0.021 0.001 TRP K 43 HIS 0.005 0.001 HIS T 177 Details of bonding type rmsd covalent geometry : bond 0.00378 (11857) covalent geometry : angle 0.61282 (16056) hydrogen bonds : bond 0.03871 ( 523) hydrogen bonds : angle 4.73192 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7967 (m-70) REVERT: C 261 MET cc_start: 0.7756 (tmm) cc_final: 0.7458 (tmm) REVERT: K 14 ASP cc_start: 0.7798 (p0) cc_final: 0.7359 (p0) REVERT: K 54 TRP cc_start: 0.8634 (m100) cc_final: 0.8423 (m100) REVERT: S 110 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8506 (tp) REVERT: L 91 MET cc_start: 0.8363 (mtm) cc_final: 0.7929 (mtm) REVERT: Y 211 ARG cc_start: 0.8509 (ptm-80) cc_final: 0.8156 (ttp80) REVERT: Y 293 ARG cc_start: 0.8726 (mmm160) cc_final: 0.8282 (mmm160) REVERT: P 59 LYS cc_start: 0.8641 (ptmm) cc_final: 0.8342 (tttp) outliers start: 36 outliers final: 23 residues processed: 129 average time/residue: 0.1059 time to fit residues: 20.0229 Evaluate side-chains 123 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 195 VAL Chi-restraints excluded: chain T residue 220 ASP Chi-restraints excluded: chain T residue 222 ILE Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Chi-restraints excluded: chain P residue 41 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 136 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.085233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065572 restraints weight = 42706.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067769 restraints weight = 22785.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069216 restraints weight = 15411.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070110 restraints weight = 11978.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070618 restraints weight = 10272.096| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11857 Z= 0.119 Angle : 0.590 12.256 16056 Z= 0.294 Chirality : 0.040 0.174 1807 Planarity : 0.004 0.052 2034 Dihedral : 4.690 32.402 1545 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.33 % Allowed : 15.36 % Favored : 82.31 % 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: -0.28 (0.24), residues: 1392 helix: 1.40 (0.20), residues: 722 sheet: -2.20 (0.56), residues: 97 loop : -1.96 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 90 TYR 0.017 0.001 TYR L 180 PHE 0.035 0.001 PHE T 328 TRP 0.018 0.001 TRP K 43 HIS 0.005 0.001 HIS T 177 Details of bonding type rmsd covalent geometry : bond 0.00273 (11857) covalent geometry : angle 0.58963 (16056) hydrogen bonds : bond 0.03525 ( 523) hydrogen bonds : angle 4.58052 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.8900 (mmm) cc_final: 0.8690 (mmt) REVERT: C 48 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7913 (m-70) REVERT: C 261 MET cc_start: 0.7809 (tmm) cc_final: 0.7505 (tmm) REVERT: K 14 ASP cc_start: 0.7611 (p0) cc_final: 0.7206 (p0) REVERT: K 54 TRP cc_start: 0.8549 (m100) cc_final: 0.8330 (m100) REVERT: L 91 MET cc_start: 0.8415 (mtm) cc_final: 0.7929 (mtm) REVERT: L 286 PHE cc_start: 0.5707 (t80) cc_final: 0.5383 (t80) REVERT: Y 211 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.7753 (ttp80) REVERT: Y 293 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8411 (mmm160) REVERT: P 44 ASP cc_start: 0.6584 (t0) cc_final: 0.5841 (t0) outliers start: 30 outliers final: 20 residues processed: 129 average time/residue: 0.0894 time to fit residues: 17.2463 Evaluate side-chains 114 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 104 LEU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 220 ASP Chi-restraints excluded: chain T residue 222 ILE Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain Y residue 218 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 136 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 129 optimal weight: 0.6980 chunk 132 optimal weight: 0.0010 chunk 91 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 229 ASN L 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.087267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067638 restraints weight = 42337.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069934 restraints weight = 22381.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071370 restraints weight = 15002.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072323 restraints weight = 11655.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.072924 restraints weight = 9934.477| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11857 Z= 0.103 Angle : 0.579 12.016 16056 Z= 0.287 Chirality : 0.040 0.251 1807 Planarity : 0.004 0.053 2034 Dihedral : 4.478 34.595 1545 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.94 % Allowed : 16.29 % Favored : 81.77 % 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: -0.18 (0.24), residues: 1392 helix: 1.42 (0.20), residues: 724 sheet: -1.97 (0.57), residues: 97 loop : -1.87 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 58 TYR 0.016 0.001 TYR L 180 PHE 0.038 0.001 PHE T 328 TRP 0.016 0.001 TRP Y 217 HIS 0.011 0.001 HIS P 48 Details of bonding type rmsd covalent geometry : bond 0.00220 (11857) covalent geometry : angle 0.57859 (16056) hydrogen bonds : bond 0.03190 ( 523) hydrogen bonds : angle 4.44765 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7797 (m-70) REVERT: C 261 MET cc_start: 0.7873 (tmm) cc_final: 0.7589 (tmm) REVERT: T 316 ASP cc_start: 0.7478 (m-30) cc_final: 0.6916 (m-30) REVERT: K 13 ASP cc_start: 0.8296 (p0) cc_final: 0.8036 (p0) REVERT: K 14 ASP cc_start: 0.7469 (p0) cc_final: 0.7213 (p0) REVERT: S 110 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8442 (tp) REVERT: L 91 MET cc_start: 0.8421 (mtm) cc_final: 0.7972 (mtm) REVERT: L 248 PHE cc_start: 0.7539 (m-80) cc_final: 0.7289 (m-80) REVERT: Y 211 ARG cc_start: 0.8354 (ptm-80) cc_final: 0.7766 (ttp80) REVERT: Y 354 VAL cc_start: 0.7255 (t) cc_final: 0.7035 (p) REVERT: P 44 ASP cc_start: 0.6868 (t0) cc_final: 0.6566 (t0) outliers start: 25 outliers final: 16 residues processed: 137 average time/residue: 0.1053 time to fit residues: 21.0635 Evaluate side-chains 116 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 222 ILE Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 0 optimal weight: 4.9990 chunk 131 optimal weight: 0.0170 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 30 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.087367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067731 restraints weight = 42043.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070014 restraints weight = 22390.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.071454 restraints weight = 15082.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072419 restraints weight = 11743.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073023 restraints weight = 9982.884| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11857 Z= 0.104 Angle : 0.597 13.098 16056 Z= 0.294 Chirality : 0.041 0.267 1807 Planarity : 0.004 0.052 2034 Dihedral : 4.412 34.633 1545 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.86 % Allowed : 17.84 % Favored : 80.29 % 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: -0.14 (0.24), residues: 1392 helix: 1.40 (0.20), residues: 725 sheet: -1.58 (0.61), residues: 82 loop : -1.86 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 41 TYR 0.015 0.001 TYR L 180 PHE 0.043 0.001 PHE T 328 TRP 0.026 0.001 TRP K 54 HIS 0.012 0.001 HIS P 48 Details of bonding type rmsd covalent geometry : bond 0.00231 (11857) covalent geometry : angle 0.59719 (16056) hydrogen bonds : bond 0.03173 ( 523) hydrogen bonds : angle 4.44074 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.7936 (tmm) cc_final: 0.7640 (tmm) REVERT: T 316 ASP cc_start: 0.7567 (m-30) cc_final: 0.7052 (m-30) REVERT: K 13 ASP cc_start: 0.8285 (p0) cc_final: 0.8027 (p0) REVERT: K 14 ASP cc_start: 0.7494 (p0) cc_final: 0.7239 (p0) REVERT: S 110 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8455 (tp) REVERT: L 91 MET cc_start: 0.8502 (mtm) cc_final: 0.8046 (mtm) REVERT: L 248 PHE cc_start: 0.7648 (m-80) cc_final: 0.7325 (m-80) REVERT: Y 211 ARG cc_start: 0.8437 (ptm-80) cc_final: 0.7890 (ttp80) REVERT: P 68 LYS cc_start: 0.8888 (tppt) cc_final: 0.8492 (ptmt) outliers start: 24 outliers final: 16 residues processed: 124 average time/residue: 0.1011 time to fit residues: 18.4813 Evaluate side-chains 115 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 222 ILE Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.085370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065742 restraints weight = 42218.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.067932 restraints weight = 22927.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.069338 restraints weight = 15602.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070171 restraints weight = 12223.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070784 restraints weight = 10538.554| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11857 Z= 0.151 Angle : 0.642 13.149 16056 Z= 0.317 Chirality : 0.042 0.282 1807 Planarity : 0.004 0.050 2034 Dihedral : 4.608 31.327 1545 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.86 % Allowed : 18.00 % Favored : 80.14 % 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: -0.21 (0.24), residues: 1392 helix: 1.36 (0.20), residues: 723 sheet: -1.75 (0.62), residues: 82 loop : -1.89 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 41 TYR 0.015 0.001 TYR L 180 PHE 0.044 0.002 PHE T 328 TRP 0.023 0.001 TRP K 43 HIS 0.023 0.001 HIS P 48 Details of bonding type rmsd covalent geometry : bond 0.00347 (11857) covalent geometry : angle 0.64152 (16056) hydrogen bonds : bond 0.03614 ( 523) hydrogen bonds : angle 4.58838 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 MET cc_start: 0.8857 (mmm) cc_final: 0.8480 (mmt) REVERT: C 261 MET cc_start: 0.7866 (tmm) cc_final: 0.7557 (tmm) REVERT: T 316 ASP cc_start: 0.7860 (m-30) cc_final: 0.7300 (m-30) REVERT: K 13 ASP cc_start: 0.8310 (p0) cc_final: 0.8070 (p0) REVERT: L 91 MET cc_start: 0.8462 (mtm) cc_final: 0.8162 (mtm) REVERT: L 248 PHE cc_start: 0.7797 (m-80) cc_final: 0.7398 (m-80) REVERT: Y 211 ARG cc_start: 0.8631 (ptm-80) cc_final: 0.7969 (ttp80) REVERT: Y 293 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8245 (mmm160) REVERT: P 68 LYS cc_start: 0.8898 (tppt) cc_final: 0.8483 (ptmt) outliers start: 24 outliers final: 20 residues processed: 116 average time/residue: 0.0985 time to fit residues: 17.0735 Evaluate side-chains 113 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 222 ILE Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 285 PHE Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 90 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 132 optimal weight: 0.1980 chunk 79 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.087191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.067860 restraints weight = 41954.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070022 restraints weight = 23192.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.071392 restraints weight = 15908.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.072270 restraints weight = 12513.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.072873 restraints weight = 10729.197| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11857 Z= 0.111 Angle : 0.619 12.233 16056 Z= 0.304 Chirality : 0.041 0.270 1807 Planarity : 0.004 0.052 2034 Dihedral : 4.476 33.314 1545 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.55 % Allowed : 18.31 % Favored : 80.14 % 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: -0.24 (0.24), residues: 1392 helix: 1.29 (0.20), residues: 733 sheet: -1.60 (0.62), residues: 82 loop : -1.92 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 41 TYR 0.015 0.001 TYR L 180 PHE 0.042 0.001 PHE T 328 TRP 0.019 0.001 TRP K 54 HIS 0.019 0.001 HIS P 48 Details of bonding type rmsd covalent geometry : bond 0.00247 (11857) covalent geometry : angle 0.61938 (16056) hydrogen bonds : bond 0.03266 ( 523) hydrogen bonds : angle 4.48023 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 MET cc_start: 0.8833 (mmm) cc_final: 0.8458 (mmt) REVERT: C 261 MET cc_start: 0.8032 (tmm) cc_final: 0.7738 (tmm) REVERT: C 338 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7871 (ptmm) REVERT: T 316 ASP cc_start: 0.7743 (m-30) cc_final: 0.7274 (m-30) REVERT: K 13 ASP cc_start: 0.8282 (p0) cc_final: 0.8060 (p0) REVERT: S 110 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8405 (tp) REVERT: L 91 MET cc_start: 0.8272 (mtm) cc_final: 0.7884 (mtm) REVERT: L 164 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7401 (p) REVERT: L 248 PHE cc_start: 0.7732 (m-80) cc_final: 0.7399 (m-80) REVERT: Y 211 ARG cc_start: 0.8661 (ptm-80) cc_final: 0.7977 (ttp80) REVERT: Y 293 ARG cc_start: 0.8533 (mmm160) cc_final: 0.8278 (mmm160) REVERT: P 68 LYS cc_start: 0.8940 (tppt) cc_final: 0.8580 (ptmt) outliers start: 20 outliers final: 17 residues processed: 113 average time/residue: 0.0973 time to fit residues: 16.4392 Evaluate side-chains 114 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 220 ASP Chi-restraints excluded: chain T residue 222 ILE Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 34 LYS Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 285 PHE Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.0010 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 100 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.086644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.067294 restraints weight = 42551.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069429 restraints weight = 23583.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070747 restraints weight = 16198.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071675 restraints weight = 12798.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.072227 restraints weight = 10958.443| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11857 Z= 0.120 Angle : 0.625 11.917 16056 Z= 0.307 Chirality : 0.041 0.264 1807 Planarity : 0.004 0.051 2034 Dihedral : 4.481 32.043 1545 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.63 % Allowed : 18.54 % Favored : 79.83 % 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: -0.22 (0.24), residues: 1392 helix: 1.29 (0.20), residues: 733 sheet: -1.71 (0.61), residues: 82 loop : -1.87 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 41 TYR 0.015 0.001 TYR L 180 PHE 0.045 0.001 PHE T 328 TRP 0.034 0.001 TRP Y 217 HIS 0.019 0.001 HIS P 48 Details of bonding type rmsd covalent geometry : bond 0.00276 (11857) covalent geometry : angle 0.62511 (16056) hydrogen bonds : bond 0.03357 ( 523) hydrogen bonds : angle 4.47786 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1840.50 seconds wall clock time: 32 minutes 53.20 seconds (1973.20 seconds total)