Starting phenix.real_space_refine on Fri Aug 22 22:02:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wa3_37390/08_2025/8wa3_37390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wa3_37390/08_2025/8wa3_37390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wa3_37390/08_2025/8wa3_37390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wa3_37390/08_2025/8wa3_37390.map" model { file = "/net/cci-nas-00/data/ceres_data/8wa3_37390/08_2025/8wa3_37390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wa3_37390/08_2025/8wa3_37390.cif" } resolution = 2.86 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= 0.019 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5156 2.51 5 N 1458 2.21 5 O 1501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8163 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2222 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1922 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Time building chain proxies: 2.07, per 1000 atoms: 0.25 Number of scatterers: 8163 At special positions: 0 Unit cell: (80.325, 100.674, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1501 8.00 N 1458 7.00 C 5156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 428.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 41.4% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 128 through 161 removed outlier: 3.607A pdb=" N LEU R 161 " --> pdb=" O LEU R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 194 Processing helix chain 'R' and resid 211 through 247 removed outlier: 3.637A pdb=" N TYR R 231 " --> pdb=" O VAL R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 265 Processing helix chain 'R' and resid 265 through 281 Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 329 removed outlier: 3.989A pdb=" N TRP R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 331 through 347 removed outlier: 3.685A pdb=" N ARG R 338 " --> pdb=" O ASP R 334 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU R 339 " --> pdb=" O TYR R 335 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU R 344 " --> pdb=" O ALA R 340 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 357 removed outlier: 4.208A pdb=" N PHE R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 394 removed outlier: 3.584A pdb=" N PHE R 371 " --> pdb=" O GLY R 367 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL R 388 " --> pdb=" O GLN R 384 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 415 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.557A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.563A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.911A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.748A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.279A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.894A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.787A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.380A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.502A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.084A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.817A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.580A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.058A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1233 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: 1.18 Time building geometry restraints manager: 0.89 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: 2703 1.34 - 1.46: 1550 1.46 - 1.58: 4002 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8321 Sorted by residual: bond pdb=" CA LEU A 46 " pdb=" C LEU A 46 " ideal model delta sigma weight residual 1.528 1.487 0.042 1.28e-02 6.10e+03 1.06e+01 bond pdb=" CA GLN R 384 " pdb=" C GLN R 384 " ideal model delta sigma weight residual 1.522 1.481 0.040 1.45e-02 4.76e+03 7.68e+00 bond pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.27e-02 6.20e+03 7.66e+00 bond pdb=" CA SER R 382 " pdb=" C SER R 382 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.24e-02 6.50e+03 4.84e+00 bond pdb=" CA PHE R 379 " pdb=" C PHE R 379 " ideal model delta sigma weight residual 1.524 1.501 0.023 1.24e-02 6.50e+03 3.38e+00 ... (remaining 8316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 11146 2.41 - 4.81: 91 4.81 - 7.22: 18 7.22 - 9.63: 2 9.63 - 12.03: 3 Bond angle restraints: 11260 Sorted by residual: angle pdb=" N GLN R 384 " pdb=" CA GLN R 384 " pdb=" C GLN R 384 " ideal model delta sigma weight residual 112.34 102.20 10.14 1.30e+00 5.92e-01 6.09e+01 angle pdb=" N LYS A 307 " pdb=" CA LYS A 307 " pdb=" C LYS A 307 " ideal model delta sigma weight residual 113.89 101.86 12.03 1.58e+00 4.01e-01 5.80e+01 angle pdb=" N LEU A 46 " pdb=" CA LEU A 46 " pdb=" C LEU A 46 " ideal model delta sigma weight residual 109.86 103.86 6.00 1.55e+00 4.16e-01 1.50e+01 angle pdb=" N SER A 51 " pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 114.64 109.14 5.50 1.52e+00 4.33e-01 1.31e+01 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 113.12 108.90 4.22 1.25e+00 6.40e-01 1.14e+01 ... (remaining 11255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4471 17.29 - 34.59: 404 34.59 - 51.88: 81 51.88 - 69.18: 8 69.18 - 86.47: 12 Dihedral angle restraints: 4976 sinusoidal: 1984 harmonic: 2992 Sorted by residual: dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual 180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -160.41 -19.59 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 4973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 944 0.044 - 0.088: 242 0.088 - 0.132: 73 0.132 - 0.177: 6 0.177 - 0.221: 1 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA LYS A 307 " pdb=" N LYS A 307 " pdb=" C LYS A 307 " pdb=" CB LYS A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU R 387 " pdb=" CB LEU R 387 " pdb=" CD1 LEU R 387 " pdb=" CD2 LEU R 387 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA GLU A 15 " pdb=" N GLU A 15 " pdb=" C GLU A 15 " pdb=" CB GLU A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1263 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 44 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C LEU A 44 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 44 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 45 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 11 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C ASP A 11 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP A 11 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 12 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO G 55 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.024 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 112 2.65 - 3.21: 7635 3.21 - 3.78: 12854 3.78 - 4.34: 17503 4.34 - 4.90: 28618 Nonbonded interactions: 66722 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.090 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.165 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.167 3.040 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.180 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.207 3.040 ... (remaining 66717 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.990 Find NCS groups from input model: 0.030 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.003 0.042 8324 Z= 0.171 Angle : 0.649 12.032 11266 Z= 0.379 Chirality : 0.043 0.221 1266 Planarity : 0.003 0.043 1440 Dihedral : 14.056 86.470 3033 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.03 % Allowed : 0.91 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.27), residues: 1015 helix: 1.95 (0.27), residues: 410 sheet: 0.37 (0.35), residues: 219 loop : -1.11 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.027 0.001 TYR B 59 PHE 0.014 0.001 PHE R 371 TRP 0.017 0.001 TRP R 296 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8321) covalent geometry : angle 0.64634 (11260) SS BOND : bond 0.00306 ( 3) SS BOND : angle 2.81019 ( 6) hydrogen bonds : bond 0.11881 ( 423) hydrogen bonds : angle 5.09090 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.395 Fit side-chains REVERT: R 408 HIS cc_start: 0.8077 (m170) cc_final: 0.7755 (m-70) REVERT: A 300 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7142 (ttpt) REVERT: A 356 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7361 (mtp-110) REVERT: B 7 LEU cc_start: 0.9270 (mm) cc_final: 0.8922 (mm) REVERT: B 8 ARG cc_start: 0.9019 (mpt-90) cc_final: 0.8743 (mpt-90) REVERT: G 16 VAL cc_start: 0.9371 (p) cc_final: 0.9089 (p) REVERT: G 18 GLN cc_start: 0.9232 (tp40) cc_final: 0.8708 (tp40) REVERT: G 20 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8654 (pttp) REVERT: N 5 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8107 (tp40) REVERT: N 43 LYS cc_start: 0.7882 (mmpt) cc_final: 0.7664 (mmmm) REVERT: N 73 ASP cc_start: 0.7819 (t0) cc_final: 0.7354 (t0) REVERT: N 87 LYS cc_start: 0.9319 (mttp) cc_final: 0.8853 (mttm) outliers start: 9 outliers final: 4 residues processed: 180 average time/residue: 0.6114 time to fit residues: 116.0377 Evaluate side-chains 146 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 381 SER Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN R 384 GLN A 387 HIS B 266 HIS B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.075238 restraints weight = 16154.527| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.63 r_work: 0.2895 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8324 Z= 0.152 Angle : 0.640 10.134 11266 Z= 0.328 Chirality : 0.042 0.146 1266 Planarity : 0.004 0.052 1440 Dihedral : 4.808 44.743 1147 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.17 % Allowed : 12.56 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.27), residues: 1015 helix: 2.19 (0.27), residues: 411 sheet: 0.32 (0.35), residues: 219 loop : -1.32 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.015 0.001 TYR R 141 PHE 0.019 0.001 PHE R 371 TRP 0.020 0.002 TRP R 287 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8321) covalent geometry : angle 0.63605 (11260) SS BOND : bond 0.00679 ( 3) SS BOND : angle 3.22323 ( 6) hydrogen bonds : bond 0.03989 ( 423) hydrogen bonds : angle 4.10640 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8414 (m110) cc_final: 0.8181 (m-40) REVERT: R 181 MET cc_start: 0.8517 (mmm) cc_final: 0.8164 (mmt) REVERT: R 282 GLU cc_start: 0.7422 (pp20) cc_final: 0.7211 (pp20) REVERT: R 408 HIS cc_start: 0.8306 (m170) cc_final: 0.7957 (m-70) REVERT: A 311 TYR cc_start: 0.7391 (m-10) cc_final: 0.7044 (m-10) REVERT: A 356 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7554 (mtp-110) REVERT: B 7 LEU cc_start: 0.8992 (mm) cc_final: 0.8205 (mm) REVERT: B 8 ARG cc_start: 0.8995 (mpt-90) cc_final: 0.8645 (mpt-90) REVERT: B 15 LYS cc_start: 0.9204 (mtmm) cc_final: 0.8735 (tmtm) REVERT: B 23 LYS cc_start: 0.9477 (tmmm) cc_final: 0.9257 (tptp) REVERT: G 13 ARG cc_start: 0.9353 (ptp-110) cc_final: 0.8944 (ptp-110) REVERT: G 18 GLN cc_start: 0.9046 (tp40) cc_final: 0.8514 (tp40) REVERT: N 5 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8047 (tp40) REVERT: N 46 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: N 53 GLN cc_start: 0.7857 (mp10) cc_final: 0.7518 (mp10) REVERT: N 73 ASP cc_start: 0.7732 (t0) cc_final: 0.7342 (t0) REVERT: N 87 LYS cc_start: 0.9128 (mttp) cc_final: 0.8762 (mttm) outliers start: 19 outliers final: 7 residues processed: 163 average time/residue: 0.5968 time to fit residues: 102.5290 Evaluate side-chains 157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 384 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073508 restraints weight = 15557.308| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.58 r_work: 0.2879 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8324 Z= 0.158 Angle : 0.614 10.082 11266 Z= 0.316 Chirality : 0.042 0.153 1266 Planarity : 0.004 0.056 1440 Dihedral : 4.545 45.129 1141 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.05 % Allowed : 17.12 % Favored : 80.82 % 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 aren not related in a simple way. whole: 0.73 (0.27), residues: 1015 helix: 2.16 (0.26), residues: 410 sheet: 0.41 (0.36), residues: 205 loop : -1.32 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.014 0.001 TYR R 141 PHE 0.018 0.001 PHE R 371 TRP 0.022 0.002 TRP R 287 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8321) covalent geometry : angle 0.60989 (11260) SS BOND : bond 0.00350 ( 3) SS BOND : angle 3.21658 ( 6) hydrogen bonds : bond 0.03917 ( 423) hydrogen bonds : angle 4.05226 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8463 (m110) cc_final: 0.8205 (m-40) REVERT: R 293 LYS cc_start: 0.6474 (pptt) cc_final: 0.6227 (pptt) REVERT: R 408 HIS cc_start: 0.8311 (m170) cc_final: 0.7962 (m-70) REVERT: A 311 TYR cc_start: 0.7568 (m-10) cc_final: 0.7188 (m-10) REVERT: A 356 ARG cc_start: 0.8151 (mtp-110) cc_final: 0.7738 (mtp-110) REVERT: B 8 ARG cc_start: 0.9012 (mpt-90) cc_final: 0.8600 (mpt-90) REVERT: B 15 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8762 (tmmt) REVERT: B 23 LYS cc_start: 0.9504 (tmmm) cc_final: 0.9225 (tptp) REVERT: G 13 ARG cc_start: 0.9288 (ptp-110) cc_final: 0.8902 (ptp-110) REVERT: G 17 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8588 (mm-30) REVERT: G 18 GLN cc_start: 0.8961 (tp40) cc_final: 0.8498 (tp40) REVERT: N 5 GLN cc_start: 0.8411 (tp-100) cc_final: 0.8052 (tp40) REVERT: N 34 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8508 (mmm) REVERT: N 43 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7676 (tptt) REVERT: N 46 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: N 53 GLN cc_start: 0.7987 (mp10) cc_final: 0.7632 (mp10) REVERT: N 73 ASP cc_start: 0.7871 (t0) cc_final: 0.7394 (t0) REVERT: N 87 LYS cc_start: 0.9123 (mttp) cc_final: 0.8733 (mttm) outliers start: 18 outliers final: 11 residues processed: 164 average time/residue: 0.5891 time to fit residues: 102.4104 Evaluate side-chains 156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 384 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.103742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.072225 restraints weight = 16216.144| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.62 r_work: 0.2852 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8324 Z= 0.152 Angle : 0.624 10.369 11266 Z= 0.321 Chirality : 0.043 0.210 1266 Planarity : 0.004 0.057 1440 Dihedral : 4.601 45.538 1141 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.54 % Allowed : 19.06 % Favored : 77.40 % 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 aren not related in a simple way. whole: 0.64 (0.27), residues: 1015 helix: 2.03 (0.26), residues: 409 sheet: 0.53 (0.37), residues: 199 loop : -1.37 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.013 0.001 TYR R 141 PHE 0.021 0.001 PHE R 371 TRP 0.023 0.002 TRP R 287 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8321) covalent geometry : angle 0.62069 (11260) SS BOND : bond 0.00333 ( 3) SS BOND : angle 3.02957 ( 6) hydrogen bonds : bond 0.03875 ( 423) hydrogen bonds : angle 4.04912 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8426 (m110) cc_final: 0.8180 (m-40) REVERT: R 293 LYS cc_start: 0.6576 (pptt) cc_final: 0.6304 (pptt) REVERT: R 396 ASN cc_start: 0.8265 (t0) cc_final: 0.7973 (t0) REVERT: R 408 HIS cc_start: 0.8327 (m170) cc_final: 0.7975 (m-70) REVERT: A 311 TYR cc_start: 0.7729 (m-10) cc_final: 0.7283 (m-10) REVERT: A 356 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7612 (mtp-110) REVERT: B 8 ARG cc_start: 0.9051 (mpt-90) cc_final: 0.8721 (mpt-90) REVERT: B 15 LYS cc_start: 0.9275 (mtmm) cc_final: 0.8769 (tmmt) REVERT: B 23 LYS cc_start: 0.9532 (tmmm) cc_final: 0.9237 (tptp) REVERT: G 13 ARG cc_start: 0.9275 (ptp-110) cc_final: 0.9025 (ptp-110) REVERT: G 18 GLN cc_start: 0.8875 (tp40) cc_final: 0.8492 (tp40) REVERT: N 5 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8043 (tp40) REVERT: N 46 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: N 53 GLN cc_start: 0.8038 (mp10) cc_final: 0.7691 (mp10) REVERT: N 73 ASP cc_start: 0.7818 (t0) cc_final: 0.7330 (t0) REVERT: N 87 LYS cc_start: 0.9064 (mttp) cc_final: 0.8719 (mttm) outliers start: 31 outliers final: 14 residues processed: 167 average time/residue: 0.5422 time to fit residues: 96.6022 Evaluate side-chains 161 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 93 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 384 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073616 restraints weight = 15758.341| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.58 r_work: 0.2892 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8324 Z= 0.136 Angle : 0.643 10.718 11266 Z= 0.329 Chirality : 0.043 0.192 1266 Planarity : 0.004 0.059 1440 Dihedral : 4.504 46.094 1141 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.74 % Allowed : 21.80 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.27), residues: 1015 helix: 2.13 (0.26), residues: 404 sheet: 0.55 (0.37), residues: 211 loop : -1.39 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.013 0.001 TYR R 141 PHE 0.021 0.001 PHE R 379 TRP 0.020 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8321) covalent geometry : angle 0.63996 (11260) SS BOND : bond 0.00273 ( 3) SS BOND : angle 2.85529 ( 6) hydrogen bonds : bond 0.03802 ( 423) hydrogen bonds : angle 4.02862 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8414 (m110) cc_final: 0.8138 (m-40) REVERT: R 293 LYS cc_start: 0.6722 (pptt) cc_final: 0.6411 (pptt) REVERT: R 341 ARG cc_start: 0.7762 (mmm160) cc_final: 0.7266 (mmm160) REVERT: R 396 ASN cc_start: 0.8234 (t0) cc_final: 0.7641 (t0) REVERT: R 408 HIS cc_start: 0.8321 (m170) cc_final: 0.7979 (m-70) REVERT: A 311 TYR cc_start: 0.7842 (m-10) cc_final: 0.7390 (m-10) REVERT: A 356 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7614 (mtp-110) REVERT: A 390 GLN cc_start: 0.8764 (tt0) cc_final: 0.8348 (tp-100) REVERT: B 8 ARG cc_start: 0.9067 (mpt-90) cc_final: 0.8699 (mpt-90) REVERT: B 12 GLU cc_start: 0.8947 (pp20) cc_final: 0.8730 (pp20) REVERT: B 15 LYS cc_start: 0.9260 (mtmm) cc_final: 0.8784 (tmmt) REVERT: B 23 LYS cc_start: 0.9538 (tmmm) cc_final: 0.9248 (tptp) REVERT: G 18 GLN cc_start: 0.8828 (tp40) cc_final: 0.8403 (tp40) REVERT: G 32 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8520 (tppp) REVERT: G 36 ASP cc_start: 0.8847 (m-30) cc_final: 0.8645 (m-30) REVERT: N 1 GLN cc_start: 0.7214 (tp40) cc_final: 0.6940 (tp40) REVERT: N 5 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8061 (tp40) REVERT: N 46 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: N 53 GLN cc_start: 0.8287 (mp10) cc_final: 0.7917 (mp10) REVERT: N 73 ASP cc_start: 0.7847 (t0) cc_final: 0.7339 (t0) REVERT: N 76 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9195 (mmmm) REVERT: N 87 LYS cc_start: 0.9140 (mttp) cc_final: 0.8776 (mttm) outliers start: 24 outliers final: 13 residues processed: 167 average time/residue: 0.5572 time to fit residues: 98.8503 Evaluate side-chains 162 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain R residue 384 GLN Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 384 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.105117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072759 restraints weight = 15388.337| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.54 r_work: 0.2881 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8324 Z= 0.151 Angle : 0.656 9.843 11266 Z= 0.335 Chirality : 0.045 0.282 1266 Planarity : 0.004 0.061 1440 Dihedral : 4.545 45.525 1141 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.97 % Allowed : 22.49 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 aren not related in a simple way. whole: 0.68 (0.27), residues: 1015 helix: 2.09 (0.26), residues: 405 sheet: 0.57 (0.37), residues: 205 loop : -1.37 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 13 TYR 0.013 0.001 TYR R 335 PHE 0.021 0.001 PHE R 371 TRP 0.022 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8321) covalent geometry : angle 0.65185 (11260) SS BOND : bond 0.00149 ( 3) SS BOND : angle 3.13442 ( 6) hydrogen bonds : bond 0.03819 ( 423) hydrogen bonds : angle 4.07997 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8411 (m110) cc_final: 0.8151 (m-40) REVERT: R 293 LYS cc_start: 0.6713 (pptt) cc_final: 0.6390 (pptt) REVERT: R 384 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: R 396 ASN cc_start: 0.8236 (t0) cc_final: 0.7648 (t0) REVERT: R 408 HIS cc_start: 0.8321 (m170) cc_final: 0.7974 (m-70) REVERT: A 311 TYR cc_start: 0.7888 (m-10) cc_final: 0.7407 (m-10) REVERT: A 356 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7588 (mtp-110) REVERT: A 390 GLN cc_start: 0.8777 (tt0) cc_final: 0.8350 (tp-100) REVERT: B 8 ARG cc_start: 0.9084 (mpt-90) cc_final: 0.8716 (mtt-85) REVERT: B 10 GLU cc_start: 0.8322 (pp20) cc_final: 0.7997 (pp20) REVERT: B 12 GLU cc_start: 0.9018 (pp20) cc_final: 0.8765 (pp20) REVERT: B 15 LYS cc_start: 0.9237 (mtmm) cc_final: 0.8790 (tmmt) REVERT: B 23 LYS cc_start: 0.9538 (tmmm) cc_final: 0.9271 (tptp) REVERT: G 13 ARG cc_start: 0.9237 (ptp-110) cc_final: 0.8921 (mtm110) REVERT: G 18 GLN cc_start: 0.8864 (tp40) cc_final: 0.8471 (tp40) REVERT: G 32 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8507 (tppp) REVERT: G 36 ASP cc_start: 0.8862 (m-30) cc_final: 0.8641 (m-30) REVERT: N 1 GLN cc_start: 0.7260 (tp40) cc_final: 0.6987 (tp40) REVERT: N 5 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8058 (tp40) REVERT: N 46 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8483 (pt0) REVERT: N 53 GLN cc_start: 0.8361 (mp10) cc_final: 0.7987 (mp10) REVERT: N 73 ASP cc_start: 0.7888 (t0) cc_final: 0.7375 (t0) REVERT: N 76 LYS cc_start: 0.9473 (mmmm) cc_final: 0.9207 (mmmm) REVERT: N 87 LYS cc_start: 0.9164 (mttp) cc_final: 0.8782 (mttm) REVERT: N 105 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8595 (mtm180) outliers start: 26 outliers final: 14 residues processed: 166 average time/residue: 0.5868 time to fit residues: 103.3244 Evaluate side-chains 165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 384 GLN Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 0.0470 chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 384 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.106283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074079 restraints weight = 15791.555| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.59 r_work: 0.2906 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8324 Z= 0.129 Angle : 0.646 9.972 11266 Z= 0.330 Chirality : 0.044 0.316 1266 Planarity : 0.004 0.062 1440 Dihedral : 4.517 46.462 1141 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.63 % Allowed : 23.74 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 aren not related in a simple way. whole: 0.71 (0.27), residues: 1015 helix: 2.10 (0.26), residues: 405 sheet: 0.64 (0.38), residues: 209 loop : -1.38 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.013 0.001 TYR R 141 PHE 0.021 0.001 PHE R 371 TRP 0.025 0.001 TRP R 287 HIS 0.004 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8321) covalent geometry : angle 0.64306 (11260) SS BOND : bond 0.00302 ( 3) SS BOND : angle 2.61045 ( 6) hydrogen bonds : bond 0.03694 ( 423) hydrogen bonds : angle 4.05709 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.334 Fit side-chains REVERT: R 164 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8576 (tmm-80) REVERT: R 170 ASN cc_start: 0.8379 (m110) cc_final: 0.8091 (m-40) REVERT: R 293 LYS cc_start: 0.6709 (pptt) cc_final: 0.6378 (pptt) REVERT: R 396 ASN cc_start: 0.8165 (t0) cc_final: 0.7583 (t0) REVERT: R 408 HIS cc_start: 0.8319 (m170) cc_final: 0.7975 (m-70) REVERT: A 311 TYR cc_start: 0.7898 (m-10) cc_final: 0.7413 (m-10) REVERT: A 356 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7535 (mtp-110) REVERT: A 390 GLN cc_start: 0.8788 (tt0) cc_final: 0.8371 (tp-100) REVERT: B 8 ARG cc_start: 0.9041 (mpt-90) cc_final: 0.8696 (mmt90) REVERT: B 12 GLU cc_start: 0.8984 (pp20) cc_final: 0.8778 (pp20) REVERT: B 15 LYS cc_start: 0.9260 (mtmm) cc_final: 0.8805 (tmmt) REVERT: B 23 LYS cc_start: 0.9514 (tmmm) cc_final: 0.9242 (tptp) REVERT: G 13 ARG cc_start: 0.9265 (ptp-110) cc_final: 0.8916 (mtm110) REVERT: G 16 VAL cc_start: 0.9187 (t) cc_final: 0.8805 (p) REVERT: G 17 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8613 (mm-30) REVERT: G 18 GLN cc_start: 0.8757 (tp40) cc_final: 0.8430 (tp40) REVERT: N 5 GLN cc_start: 0.8379 (tp-100) cc_final: 0.8028 (tp40) REVERT: N 43 LYS cc_start: 0.7969 (mmmm) cc_final: 0.7750 (tptt) REVERT: N 46 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8473 (pt0) REVERT: N 53 GLN cc_start: 0.8403 (mp10) cc_final: 0.8035 (mp10) REVERT: N 73 ASP cc_start: 0.7912 (t0) cc_final: 0.7446 (t0) REVERT: N 76 LYS cc_start: 0.9486 (mmmm) cc_final: 0.9228 (mmmm) REVERT: N 86 LEU cc_start: 0.9422 (mm) cc_final: 0.9217 (mm) REVERT: N 87 LYS cc_start: 0.9133 (mttp) cc_final: 0.8798 (mttm) REVERT: N 105 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8591 (mtm180) outliers start: 23 outliers final: 12 residues processed: 165 average time/residue: 0.5730 time to fit residues: 100.4658 Evaluate side-chains 161 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 164 ARG Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 0.0060 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 175 ASN ** R 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.069866 restraints weight = 16005.404| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.57 r_work: 0.2802 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8324 Z= 0.223 Angle : 0.719 9.945 11266 Z= 0.369 Chirality : 0.046 0.237 1266 Planarity : 0.004 0.064 1440 Dihedral : 4.716 44.617 1141 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.42 % Allowed : 23.97 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 aren not related in a simple way. whole: 0.55 (0.27), residues: 1015 helix: 2.00 (0.26), residues: 404 sheet: 0.40 (0.37), residues: 206 loop : -1.39 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 38 TYR 0.009 0.001 TYR R 141 PHE 0.023 0.002 PHE R 371 TRP 0.027 0.002 TRP R 287 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 8321) covalent geometry : angle 0.71583 (11260) SS BOND : bond 0.00351 ( 3) SS BOND : angle 3.13077 ( 6) hydrogen bonds : bond 0.04192 ( 423) hydrogen bonds : angle 4.23614 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: R 164 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8638 (tmm-80) REVERT: R 170 ASN cc_start: 0.8435 (m110) cc_final: 0.8187 (m-40) REVERT: R 293 LYS cc_start: 0.6603 (pptt) cc_final: 0.6271 (pptt) REVERT: R 335 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: R 341 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7380 (mmm160) REVERT: R 396 ASN cc_start: 0.8153 (t0) cc_final: 0.7121 (t0) REVERT: R 408 HIS cc_start: 0.8384 (m170) cc_final: 0.7998 (m-70) REVERT: A 311 TYR cc_start: 0.7958 (m-10) cc_final: 0.7500 (m-10) REVERT: A 356 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7481 (mtp-110) REVERT: B 8 ARG cc_start: 0.9029 (mpt-90) cc_final: 0.8698 (mpt-90) REVERT: B 12 GLU cc_start: 0.9027 (pp20) cc_final: 0.8768 (pp20) REVERT: B 15 LYS cc_start: 0.9249 (mtmm) cc_final: 0.8808 (tmmt) REVERT: B 23 LYS cc_start: 0.9520 (tmmm) cc_final: 0.9235 (tptp) REVERT: G 13 ARG cc_start: 0.9291 (ptp-110) cc_final: 0.8962 (mtm110) REVERT: G 17 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8620 (mp0) REVERT: G 18 GLN cc_start: 0.8803 (tp40) cc_final: 0.8393 (tp40) REVERT: G 28 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7975 (tp) REVERT: G 29 LYS cc_start: 0.8322 (tppt) cc_final: 0.8056 (tppp) REVERT: N 1 GLN cc_start: 0.7213 (tp40) cc_final: 0.6640 (tp40) REVERT: N 5 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8080 (tp40) REVERT: N 46 GLU cc_start: 0.8761 (tt0) cc_final: 0.8447 (pt0) REVERT: N 53 GLN cc_start: 0.8372 (mp10) cc_final: 0.7975 (mp10) REVERT: N 73 ASP cc_start: 0.8031 (t0) cc_final: 0.7449 (t0) REVERT: N 76 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9207 (mmmm) REVERT: N 87 LYS cc_start: 0.8994 (mttp) cc_final: 0.8653 (mttp) REVERT: N 105 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8591 (mtm180) outliers start: 30 outliers final: 16 residues processed: 159 average time/residue: 0.6394 time to fit residues: 107.8013 Evaluate side-chains 150 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 164 ARG Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 335 TYR Chi-restraints excluded: chain R residue 361 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 10 optimal weight: 0.0040 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.104760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.072735 restraints weight = 15895.094| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.63 r_work: 0.2867 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8324 Z= 0.135 Angle : 0.709 12.046 11266 Z= 0.357 Chirality : 0.046 0.354 1266 Planarity : 0.004 0.066 1440 Dihedral : 4.591 47.095 1141 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.83 % Allowed : 25.57 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 aren not related in a simple way. whole: 0.56 (0.27), residues: 1015 helix: 1.98 (0.26), residues: 405 sheet: 0.55 (0.38), residues: 204 loop : -1.44 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 326 TYR 0.012 0.001 TYR R 141 PHE 0.021 0.001 PHE R 371 TRP 0.025 0.001 TRP R 287 HIS 0.004 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8321) covalent geometry : angle 0.70714 (11260) SS BOND : bond 0.00238 ( 3) SS BOND : angle 2.49098 ( 6) hydrogen bonds : bond 0.03794 ( 423) hydrogen bonds : angle 4.08531 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8392 (m110) cc_final: 0.8122 (m-40) REVERT: R 293 LYS cc_start: 0.6597 (pptt) cc_final: 0.6300 (pptt) REVERT: R 341 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7385 (mmm160) REVERT: R 408 HIS cc_start: 0.8353 (m170) cc_final: 0.7970 (m-70) REVERT: A 311 TYR cc_start: 0.7974 (m-10) cc_final: 0.7508 (m-10) REVERT: A 356 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7431 (mtp-110) REVERT: A 390 GLN cc_start: 0.8850 (tt0) cc_final: 0.8254 (tp-100) REVERT: B 8 ARG cc_start: 0.8975 (mpt-90) cc_final: 0.8652 (mpt-90) REVERT: B 12 GLU cc_start: 0.8986 (pp20) cc_final: 0.8724 (pp20) REVERT: B 15 LYS cc_start: 0.9262 (mtmm) cc_final: 0.8810 (tmmt) REVERT: B 23 LYS cc_start: 0.9509 (tmmm) cc_final: 0.9212 (tptp) REVERT: B 61 MET cc_start: 0.9476 (pp-130) cc_final: 0.9161 (pp-130) REVERT: G 13 ARG cc_start: 0.9235 (ptp-110) cc_final: 0.8952 (mtm110) REVERT: G 16 VAL cc_start: 0.9205 (p) cc_final: 0.8990 (p) REVERT: G 18 GLN cc_start: 0.8721 (tp40) cc_final: 0.8321 (tp40) REVERT: G 28 ILE cc_start: 0.8197 (mm) cc_final: 0.7977 (tp) REVERT: G 29 LYS cc_start: 0.8258 (tppt) cc_final: 0.7999 (tppp) REVERT: N 1 GLN cc_start: 0.7176 (tp40) cc_final: 0.6577 (tp40) REVERT: N 5 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8084 (tp40) REVERT: N 46 GLU cc_start: 0.8738 (tt0) cc_final: 0.8449 (pt0) REVERT: N 53 GLN cc_start: 0.8435 (mp10) cc_final: 0.8047 (mp10) REVERT: N 73 ASP cc_start: 0.7992 (t0) cc_final: 0.7399 (t0) REVERT: N 76 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9187 (mmmm) REVERT: N 87 LYS cc_start: 0.9086 (mttp) cc_final: 0.8722 (mttm) outliers start: 16 outliers final: 12 residues processed: 155 average time/residue: 0.5890 time to fit residues: 97.1104 Evaluate side-chains 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 361 THR Chi-restraints excluded: chain R residue 379 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.0870 chunk 75 optimal weight: 0.3980 chunk 82 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.073921 restraints weight = 15595.159| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.56 r_work: 0.2898 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8324 Z= 0.136 Angle : 0.709 12.387 11266 Z= 0.358 Chirality : 0.046 0.364 1266 Planarity : 0.004 0.067 1440 Dihedral : 4.564 46.652 1141 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.48 % Allowed : 26.71 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 aren not related in a simple way. whole: 0.60 (0.27), residues: 1015 helix: 1.99 (0.26), residues: 405 sheet: 0.60 (0.38), residues: 204 loop : -1.42 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 326 TYR 0.012 0.001 TYR R 141 PHE 0.020 0.001 PHE R 371 TRP 0.026 0.001 TRP R 287 HIS 0.004 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8321) covalent geometry : angle 0.70688 (11260) SS BOND : bond 0.00297 ( 3) SS BOND : angle 2.28853 ( 6) hydrogen bonds : bond 0.03743 ( 423) hydrogen bonds : angle 4.03600 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8399 (m110) cc_final: 0.8113 (m-40) REVERT: R 293 LYS cc_start: 0.6701 (pptt) cc_final: 0.6393 (pptt) REVERT: R 341 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7451 (mmm160) REVERT: R 396 ASN cc_start: 0.8177 (t0) cc_final: 0.7787 (t0) REVERT: R 408 HIS cc_start: 0.8352 (m170) cc_final: 0.7972 (m-70) REVERT: A 311 TYR cc_start: 0.7989 (m-10) cc_final: 0.7523 (m-10) REVERT: A 356 ARG cc_start: 0.8071 (mtp-110) cc_final: 0.7465 (mtp-110) REVERT: A 390 GLN cc_start: 0.8771 (tt0) cc_final: 0.8269 (tp-100) REVERT: B 8 ARG cc_start: 0.8992 (mpt-90) cc_final: 0.8652 (mpt-90) REVERT: B 12 GLU cc_start: 0.8964 (pp20) cc_final: 0.8693 (pp20) REVERT: B 15 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8806 (tmmt) REVERT: B 23 LYS cc_start: 0.9512 (tmmm) cc_final: 0.9206 (tptp) REVERT: B 61 MET cc_start: 0.9501 (pp-130) cc_final: 0.9165 (pp-130) REVERT: G 13 ARG cc_start: 0.9209 (ptp-110) cc_final: 0.8993 (mtm110) REVERT: G 18 GLN cc_start: 0.8771 (tp40) cc_final: 0.8407 (tp40) REVERT: G 29 LYS cc_start: 0.8283 (tppt) cc_final: 0.8033 (tppp) REVERT: N 5 GLN cc_start: 0.8395 (tp-100) cc_final: 0.8038 (tp40) REVERT: N 38 ARG cc_start: 0.8742 (ttp-170) cc_final: 0.8382 (mtm110) REVERT: N 46 GLU cc_start: 0.8777 (tt0) cc_final: 0.8455 (pt0) REVERT: N 53 GLN cc_start: 0.8475 (mp10) cc_final: 0.8106 (mp10) REVERT: N 73 ASP cc_start: 0.8042 (t0) cc_final: 0.7432 (t0) REVERT: N 76 LYS cc_start: 0.9435 (mmmm) cc_final: 0.9166 (mmmm) REVERT: N 87 LYS cc_start: 0.9173 (mttp) cc_final: 0.8803 (mttm) outliers start: 13 outliers final: 10 residues processed: 153 average time/residue: 0.5518 time to fit residues: 89.6055 Evaluate side-chains 157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 361 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073024 restraints weight = 15931.395| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.57 r_work: 0.2852 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8324 Z= 0.154 Angle : 0.707 12.335 11266 Z= 0.361 Chirality : 0.047 0.363 1266 Planarity : 0.004 0.067 1440 Dihedral : 4.579 46.091 1141 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.71 % Allowed : 26.60 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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 aren not related in a simple way. whole: 0.55 (0.27), residues: 1015 helix: 1.98 (0.26), residues: 405 sheet: 0.47 (0.37), residues: 206 loop : -1.43 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 326 TYR 0.011 0.001 TYR R 141 PHE 0.023 0.001 PHE R 371 TRP 0.029 0.001 TRP R 287 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8321) covalent geometry : angle 0.70474 (11260) SS BOND : bond 0.00280 ( 3) SS BOND : angle 2.37114 ( 6) hydrogen bonds : bond 0.03806 ( 423) hydrogen bonds : angle 4.05254 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3125.26 seconds wall clock time: 54 minutes 4.81 seconds (3244.81 seconds total)