Starting phenix.real_space_refine on Sun May 11 16:12:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wa3_37390/05_2025/8wa3_37390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wa3_37390/05_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_37390/05_2025/8wa3_37390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wa3_37390/05_2025/8wa3_37390.map" model { file = "/net/cci-nas-00/data/ceres_data/8wa3_37390/05_2025/8wa3_37390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wa3_37390/05_2025/8wa3_37390.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG: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: 5.43, per 1000 atoms: 0.67 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.98 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: 2.33 Time building geometry restraints manager: 2.54 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: 1.290 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 22.510 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- 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 : 9.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (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 TRP 0.017 0.001 TRP R 296 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 371 TYR 0.027 0.001 TYR B 59 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.11881 ( 423) hydrogen bonds : angle 5.09090 ( 1233) SS BOND : bond 0.00306 ( 3) SS BOND : angle 2.81019 ( 6) covalent geometry : bond 0.00296 ( 8321) covalent geometry : angle 0.64634 (11260) *********************** 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 : 0.865 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: 0.8709 (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: 1.2708 time to fit residues: 241.6497 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 : 0.922 ------------------------------------------------------------------------------- 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 85 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 384 GLN A 387 HIS B 266 HIS B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.105692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073999 restraints weight = 16047.041| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.65 r_work: 0.2890 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8324 Z= 0.152 Angle : 0.634 10.077 11266 Z= 0.326 Chirality : 0.042 0.142 1266 Planarity : 0.004 0.053 1440 Dihedral : 4.796 44.591 1147 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.05 % Allowed : 12.56 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1015 helix: 2.19 (0.27), residues: 411 sheet: 0.33 (0.35), residues: 219 loop : -1.31 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 287 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.001 PHE R 371 TYR 0.015 0.001 TYR R 141 ARG 0.005 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 423) hydrogen bonds : angle 4.10572 ( 1233) SS BOND : bond 0.00304 ( 3) SS BOND : angle 3.20678 ( 6) covalent geometry : bond 0.00348 ( 8321) covalent geometry : angle 0.62961 (11260) *********************** 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 176 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8411 (m110) cc_final: 0.8178 (m-40) REVERT: R 181 MET cc_start: 0.8506 (mmm) cc_final: 0.8121 (mmt) REVERT: R 282 GLU cc_start: 0.7423 (pp20) cc_final: 0.7212 (pp20) REVERT: R 408 HIS cc_start: 0.8305 (m170) cc_final: 0.7956 (m-70) REVERT: A 311 TYR cc_start: 0.7389 (m-10) cc_final: 0.7026 (m-10) REVERT: A 356 ARG cc_start: 0.8092 (mtp-110) cc_final: 0.7721 (mtp-110) REVERT: B 7 LEU cc_start: 0.8989 (mm) cc_final: 0.8189 (mm) REVERT: B 8 ARG cc_start: 0.8991 (mpt-90) cc_final: 0.8645 (mpt-90) REVERT: B 15 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8721 (tmmt) REVERT: B 23 LYS cc_start: 0.9476 (tmmm) cc_final: 0.9257 (tptp) REVERT: G 13 ARG cc_start: 0.9349 (ptp-110) cc_final: 0.9057 (ptp-110) REVERT: G 18 GLN cc_start: 0.9042 (tp40) cc_final: 0.8489 (tp40) REVERT: G 20 LYS cc_start: 0.8988 (ptpp) cc_final: 0.8614 (ptpp) REVERT: N 5 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8042 (tp40) REVERT: N 46 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: N 53 GLN cc_start: 0.7853 (mp10) cc_final: 0.7516 (mp10) REVERT: N 73 ASP cc_start: 0.7725 (t0) cc_final: 0.7339 (t0) REVERT: N 87 LYS cc_start: 0.9123 (mttp) cc_final: 0.8760 (mttm) outliers start: 18 outliers final: 7 residues processed: 164 average time/residue: 1.2221 time to fit residues: 212.1186 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 : 0.880 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.106362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074413 restraints weight = 15957.308| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.61 r_work: 0.2902 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8324 Z= 0.133 Angle : 0.602 10.264 11266 Z= 0.309 Chirality : 0.042 0.161 1266 Planarity : 0.004 0.056 1440 Dihedral : 4.495 45.726 1141 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.71 % Allowed : 17.01 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1015 helix: 2.14 (0.26), residues: 410 sheet: 0.45 (0.36), residues: 205 loop : -1.31 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 287 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 371 TYR 0.015 0.001 TYR R 141 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 423) hydrogen bonds : angle 4.01081 ( 1233) SS BOND : bond 0.00262 ( 3) SS BOND : angle 3.09947 ( 6) covalent geometry : bond 0.00303 ( 8321) covalent geometry : angle 0.59817 (11260) *********************** 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 177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8434 (m110) cc_final: 0.8157 (m-40) REVERT: R 255 HIS cc_start: 0.7229 (m170) cc_final: 0.6981 (m-70) REVERT: R 293 LYS cc_start: 0.6575 (pptt) cc_final: 0.6333 (pptt) REVERT: R 408 HIS cc_start: 0.8305 (m170) cc_final: 0.7957 (m-70) REVERT: A 27 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 311 TYR cc_start: 0.7517 (m-10) cc_final: 0.7209 (m-10) REVERT: A 356 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7718 (mtp-110) REVERT: B 8 ARG cc_start: 0.9033 (mpt-90) cc_final: 0.8589 (mpt-90) REVERT: B 15 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8749 (tmmt) REVERT: B 23 LYS cc_start: 0.9526 (tmmm) cc_final: 0.9256 (tptp) REVERT: B 217 MET cc_start: 0.8422 (ppp) cc_final: 0.8196 (ppp) REVERT: G 13 ARG cc_start: 0.9343 (ptp-110) cc_final: 0.8896 (ptp-110) REVERT: G 17 GLU cc_start: 0.9551 (tp30) cc_final: 0.9126 (mm-30) REVERT: G 18 GLN cc_start: 0.8974 (tp40) cc_final: 0.8409 (tp40) REVERT: G 20 LYS cc_start: 0.8975 (ptpp) cc_final: 0.8395 (pttm) REVERT: N 5 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8033 (tp40) REVERT: N 43 LYS cc_start: 0.8008 (mmmm) cc_final: 0.7671 (tptt) REVERT: N 46 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8442 (pt0) REVERT: N 53 GLN cc_start: 0.7996 (mp10) cc_final: 0.7637 (mp10) REVERT: N 70 ILE cc_start: 0.8728 (pt) cc_final: 0.8401 (pp) REVERT: N 73 ASP cc_start: 0.7851 (t0) cc_final: 0.7368 (t0) REVERT: N 87 LYS cc_start: 0.9113 (mttp) cc_final: 0.8717 (mttm) outliers start: 15 outliers final: 9 residues processed: 168 average time/residue: 1.1767 time to fit residues: 210.4504 Evaluate side-chains 158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 90 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 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 = 0.3589 r_free = 0.3589 target = 0.104046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.072586 restraints weight = 15916.976| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.59 r_work: 0.2854 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8324 Z= 0.159 Angle : 0.625 9.967 11266 Z= 0.321 Chirality : 0.044 0.258 1266 Planarity : 0.004 0.057 1440 Dihedral : 4.562 45.374 1141 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.54 % Allowed : 18.72 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 1015 helix: 2.01 (0.26), residues: 410 sheet: 0.49 (0.37), residues: 205 loop : -1.33 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 287 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.001 PHE R 371 TYR 0.013 0.001 TYR R 141 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 423) hydrogen bonds : angle 4.09163 ( 1233) SS BOND : bond 0.00423 ( 3) SS BOND : angle 2.99114 ( 6) covalent geometry : bond 0.00365 ( 8321) covalent geometry : angle 0.62138 (11260) *********************** 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 182 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8424 (m110) cc_final: 0.8148 (m-40) REVERT: R 293 LYS cc_start: 0.6599 (pptt) cc_final: 0.6324 (pptt) REVERT: R 396 ASN cc_start: 0.8276 (t0) cc_final: 0.7934 (t0) REVERT: R 408 HIS cc_start: 0.8330 (m170) cc_final: 0.7982 (m-70) REVERT: A 311 TYR cc_start: 0.7690 (m-10) cc_final: 0.7284 (m-10) REVERT: A 356 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7638 (mtp-110) REVERT: B 8 ARG cc_start: 0.9060 (mpt-90) cc_final: 0.8732 (mpt-90) REVERT: B 15 LYS cc_start: 0.9276 (mtmm) cc_final: 0.8776 (tmmt) REVERT: B 23 LYS cc_start: 0.9528 (tmmm) cc_final: 0.9254 (tptp) REVERT: B 217 MET cc_start: 0.8325 (ppp) cc_final: 0.8003 (ppp) REVERT: G 13 ARG cc_start: 0.9365 (ptp-110) cc_final: 0.9087 (ptp-110) REVERT: G 18 GLN cc_start: 0.8936 (tp40) cc_final: 0.8413 (tp40) REVERT: G 20 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8568 (ptpp) REVERT: N 5 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8046 (tp40) REVERT: N 46 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8445 (pt0) REVERT: N 53 GLN cc_start: 0.8014 (mp10) cc_final: 0.7653 (mp10) REVERT: N 70 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8415 (pp) REVERT: N 73 ASP cc_start: 0.7849 (t0) cc_final: 0.7360 (t0) REVERT: N 87 LYS cc_start: 0.9089 (mttp) cc_final: 0.8732 (mttm) outliers start: 31 outliers final: 11 residues processed: 166 average time/residue: 1.1599 time to fit residues: 205.0453 Evaluate side-chains 152 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 B residue 59 TYR 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 46 GLU Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.103826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.072118 restraints weight = 15891.684| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.61 r_work: 0.2855 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8324 Z= 0.148 Angle : 0.641 10.581 11266 Z= 0.328 Chirality : 0.044 0.258 1266 Planarity : 0.004 0.058 1440 Dihedral : 4.513 45.703 1141 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.65 % Allowed : 20.32 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 1015 helix: 2.08 (0.26), residues: 404 sheet: 0.54 (0.37), residues: 211 loop : -1.38 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.001 PHE R 379 TYR 0.013 0.001 TYR R 141 ARG 0.003 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 423) hydrogen bonds : angle 4.07332 ( 1233) SS BOND : bond 0.00286 ( 3) SS BOND : angle 2.85812 ( 6) covalent geometry : bond 0.00344 ( 8321) covalent geometry : angle 0.63776 (11260) *********************** 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 190 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8393 (m110) cc_final: 0.8134 (m-40) REVERT: R 293 LYS cc_start: 0.6690 (pptt) cc_final: 0.6378 (pptt) REVERT: R 396 ASN cc_start: 0.8185 (t0) cc_final: 0.7544 (t0) REVERT: R 408 HIS cc_start: 0.8328 (m170) cc_final: 0.7991 (m-70) REVERT: A 311 TYR cc_start: 0.7817 (m-10) cc_final: 0.7387 (m-10) REVERT: A 356 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7609 (mtp-110) REVERT: A 390 GLN cc_start: 0.8754 (tt0) cc_final: 0.8339 (tp-100) REVERT: B 7 LEU cc_start: 0.8691 (mm) cc_final: 0.8480 (mm) REVERT: B 8 ARG cc_start: 0.9116 (mpt-90) cc_final: 0.8756 (mpt-90) REVERT: B 15 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8788 (tmmt) REVERT: B 23 LYS cc_start: 0.9530 (tmmm) cc_final: 0.9273 (tptp) REVERT: B 217 MET cc_start: 0.8293 (ppp) cc_final: 0.7962 (ppp) REVERT: G 18 GLN cc_start: 0.8975 (tp40) cc_final: 0.8472 (tp40) REVERT: N 5 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8049 (tp40) REVERT: N 46 GLU cc_start: 0.8721 (tt0) cc_final: 0.8403 (pt0) REVERT: N 53 GLN cc_start: 0.8098 (mp10) cc_final: 0.7756 (mp10) REVERT: N 70 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8451 (pp) REVERT: N 73 ASP cc_start: 0.7841 (t0) cc_final: 0.7368 (t0) REVERT: N 87 LYS cc_start: 0.9062 (mttp) cc_final: 0.8711 (mttm) outliers start: 32 outliers final: 15 residues processed: 171 average time/residue: 0.9919 time to fit residues: 181.8203 Evaluate side-chains 164 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 260 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 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 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.104080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.071781 restraints weight = 15919.877| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.65 r_work: 0.2851 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8324 Z= 0.145 Angle : 0.656 10.011 11266 Z= 0.335 Chirality : 0.045 0.276 1266 Planarity : 0.004 0.061 1440 Dihedral : 4.569 45.879 1141 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.31 % Allowed : 22.37 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1015 helix: 1.98 (0.26), residues: 403 sheet: 0.54 (0.38), residues: 205 loop : -1.37 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE R 371 TYR 0.013 0.001 TYR R 141 ARG 0.006 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 423) hydrogen bonds : angle 4.08589 ( 1233) SS BOND : bond 0.00505 ( 3) SS BOND : angle 3.01014 ( 6) covalent geometry : bond 0.00336 ( 8321) covalent geometry : angle 0.65256 (11260) *********************** 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 184 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8380 (m110) cc_final: 0.8097 (m-40) REVERT: R 293 LYS cc_start: 0.6684 (pptt) cc_final: 0.6366 (pptt) REVERT: R 341 ARG cc_start: 0.7765 (mmm160) cc_final: 0.7396 (mmm160) REVERT: R 396 ASN cc_start: 0.8152 (t0) cc_final: 0.7539 (t0) REVERT: R 408 HIS cc_start: 0.8323 (m170) cc_final: 0.7980 (m-70) REVERT: A 311 TYR cc_start: 0.7870 (m-10) cc_final: 0.7435 (m-10) REVERT: A 356 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.7570 (mtp-110) REVERT: A 390 GLN cc_start: 0.8767 (tt0) cc_final: 0.8319 (tp-100) REVERT: B 8 ARG cc_start: 0.9085 (mpt-90) cc_final: 0.8696 (mpt-90) REVERT: B 12 GLU cc_start: 0.8976 (pp20) cc_final: 0.8727 (pp20) REVERT: B 15 LYS cc_start: 0.9263 (mtmm) cc_final: 0.8813 (tmmt) REVERT: B 23 LYS cc_start: 0.9531 (tmmm) cc_final: 0.9266 (tptp) REVERT: B 217 MET cc_start: 0.8352 (ppp) cc_final: 0.7995 (ppp) REVERT: G 13 ARG cc_start: 0.9341 (ptp-110) cc_final: 0.9108 (mtm110) REVERT: G 18 GLN cc_start: 0.8910 (tp40) cc_final: 0.8400 (tp40) REVERT: N 1 GLN cc_start: 0.7119 (tp40) cc_final: 0.6849 (tp40) REVERT: N 5 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8074 (tp40) REVERT: N 43 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7620 (tptt) REVERT: N 46 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8392 (pt0) REVERT: N 53 GLN cc_start: 0.8118 (mp10) cc_final: 0.7784 (mp10) REVERT: N 70 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8465 (pp) REVERT: N 73 ASP cc_start: 0.7824 (t0) cc_final: 0.7305 (t0) REVERT: N 76 LYS cc_start: 0.9456 (mmmm) cc_final: 0.9191 (mmmm) REVERT: N 87 LYS cc_start: 0.9052 (mttp) cc_final: 0.8705 (mttm) REVERT: N 105 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8552 (mtm180) outliers start: 29 outliers final: 16 residues processed: 169 average time/residue: 1.1321 time to fit residues: 203.6187 Evaluate side-chains 164 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 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 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE 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 51 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 175 ASN R 329 GLN R 384 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.069406 restraints weight = 15992.830| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.61 r_work: 0.2791 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8324 Z= 0.218 Angle : 0.695 9.478 11266 Z= 0.358 Chirality : 0.046 0.269 1266 Planarity : 0.004 0.062 1440 Dihedral : 4.693 45.019 1141 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.65 % Allowed : 22.95 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.27), residues: 1015 helix: 1.96 (0.26), residues: 404 sheet: 0.32 (0.37), residues: 206 loop : -1.36 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 287 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.002 PHE R 371 TYR 0.010 0.001 TYR R 141 ARG 0.006 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 423) hydrogen bonds : angle 4.23527 ( 1233) SS BOND : bond 0.00356 ( 3) SS BOND : angle 3.15913 ( 6) covalent geometry : bond 0.00512 ( 8321) covalent geometry : angle 0.69098 (11260) *********************** 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: 32 poor density : 145 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 164 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8578 (tmm-80) REVERT: R 170 ASN cc_start: 0.8425 (m110) cc_final: 0.8189 (m-40) REVERT: R 293 LYS cc_start: 0.6635 (pptt) cc_final: 0.6286 (pptt) REVERT: R 335 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6275 (m-10) REVERT: R 341 ARG cc_start: 0.7801 (mmm160) cc_final: 0.7406 (mmm160) REVERT: R 384 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: R 396 ASN cc_start: 0.8156 (t0) cc_final: 0.7343 (t0) REVERT: R 408 HIS cc_start: 0.8373 (m170) cc_final: 0.7984 (m-70) REVERT: A 311 TYR cc_start: 0.8004 (m-10) cc_final: 0.7559 (m-10) REVERT: A 356 ARG cc_start: 0.8114 (mtp-110) cc_final: 0.7534 (mtp-110) REVERT: B 8 ARG cc_start: 0.9063 (mpt-90) cc_final: 0.8674 (mtt-85) REVERT: B 12 GLU cc_start: 0.9016 (pp20) cc_final: 0.8739 (pp20) REVERT: B 15 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8814 (tmmt) REVERT: B 23 LYS cc_start: 0.9530 (tmmm) cc_final: 0.9276 (tptp) REVERT: B 217 MET cc_start: 0.8179 (ppp) cc_final: 0.7779 (ppp) REVERT: G 13 ARG cc_start: 0.9345 (ptp-110) cc_final: 0.8915 (mtm110) REVERT: G 16 VAL cc_start: 0.9346 (p) cc_final: 0.8938 (p) REVERT: G 17 GLU cc_start: 0.9550 (tp30) cc_final: 0.9245 (mm-30) REVERT: G 18 GLN cc_start: 0.8828 (tp40) cc_final: 0.8207 (tp40) REVERT: N 1 GLN cc_start: 0.7229 (tp40) cc_final: 0.6839 (tp40) REVERT: N 5 GLN cc_start: 0.8379 (tp-100) cc_final: 0.8044 (tp40) REVERT: N 43 LYS cc_start: 0.8026 (mmmm) cc_final: 0.7598 (tptt) REVERT: N 46 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8452 (pt0) REVERT: N 53 GLN cc_start: 0.8061 (mp10) cc_final: 0.7684 (mp10) REVERT: N 70 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8482 (pp) REVERT: N 73 ASP cc_start: 0.7847 (t0) cc_final: 0.7347 (t0) REVERT: N 76 LYS cc_start: 0.9479 (mmmm) cc_final: 0.9249 (mmmm) REVERT: N 87 LYS cc_start: 0.9068 (mttp) cc_final: 0.8723 (mttm) REVERT: N 105 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8610 (mtm180) outliers start: 32 outliers final: 16 residues processed: 163 average time/residue: 1.1311 time to fit residues: 196.0518 Evaluate side-chains 158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 349 LEU 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 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 57 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE 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: 3.9990 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.103311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.071338 restraints weight = 16006.679| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.62 r_work: 0.2838 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8324 Z= 0.144 Angle : 0.693 10.974 11266 Z= 0.349 Chirality : 0.045 0.226 1266 Planarity : 0.004 0.064 1440 Dihedral : 4.609 46.348 1141 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.08 % Allowed : 23.97 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1015 helix: 1.93 (0.26), residues: 404 sheet: 0.49 (0.37), residues: 204 loop : -1.39 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE R 371 TYR 0.012 0.001 TYR R 141 ARG 0.012 0.000 ARG R 326 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 423) hydrogen bonds : angle 4.12934 ( 1233) SS BOND : bond 0.00330 ( 3) SS BOND : angle 2.74524 ( 6) covalent geometry : bond 0.00336 ( 8321) covalent geometry : angle 0.69005 (11260) *********************** 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 180 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8422 (m110) cc_final: 0.8161 (m-40) REVERT: R 293 LYS cc_start: 0.6642 (pptt) cc_final: 0.6320 (pptt) REVERT: R 341 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7402 (mmm160) REVERT: R 408 HIS cc_start: 0.8362 (m170) cc_final: 0.7985 (m-70) REVERT: A 311 TYR cc_start: 0.8058 (m-10) cc_final: 0.7622 (m-10) REVERT: A 356 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7463 (mtp-110) REVERT: A 390 GLN cc_start: 0.8829 (tt0) cc_final: 0.8156 (tp-100) REVERT: B 8 ARG cc_start: 0.9031 (mpt-90) cc_final: 0.8649 (mmt90) REVERT: B 12 GLU cc_start: 0.9007 (pp20) cc_final: 0.8699 (pp20) REVERT: B 15 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8802 (tmmt) REVERT: B 23 LYS cc_start: 0.9518 (tmmm) cc_final: 0.9233 (tptp) REVERT: B 61 MET cc_start: 0.9490 (pp-130) cc_final: 0.9129 (pp-130) REVERT: B 217 MET cc_start: 0.8313 (ppp) cc_final: 0.7950 (ppp) REVERT: G 13 ARG cc_start: 0.9376 (ptp-110) cc_final: 0.8948 (mtm110) REVERT: G 17 GLU cc_start: 0.9535 (tp30) cc_final: 0.9214 (mm-30) REVERT: G 18 GLN cc_start: 0.8842 (tp40) cc_final: 0.8269 (tp40) REVERT: G 29 LYS cc_start: 0.8302 (mmtm) cc_final: 0.8065 (tppp) REVERT: N 1 GLN cc_start: 0.7206 (tp40) cc_final: 0.6821 (tp40) REVERT: N 5 GLN cc_start: 0.8364 (tp-100) cc_final: 0.8038 (tp40) REVERT: N 46 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: N 53 GLN cc_start: 0.8084 (mp10) cc_final: 0.7697 (mp10) REVERT: N 70 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8488 (pp) REVERT: N 73 ASP cc_start: 0.7841 (t0) cc_final: 0.7375 (t0) REVERT: N 76 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9248 (mmmm) REVERT: N 87 LYS cc_start: 0.9075 (mttp) cc_final: 0.8728 (mttm) outliers start: 27 outliers final: 12 residues processed: 167 average time/residue: 1.1018 time to fit residues: 196.7545 Evaluate side-chains 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 270 PHE 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 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.0050 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.104368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.072304 restraints weight = 16161.174| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.67 r_work: 0.2855 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8324 Z= 0.138 Angle : 0.695 10.580 11266 Z= 0.352 Chirality : 0.045 0.326 1266 Planarity : 0.004 0.066 1440 Dihedral : 4.536 46.265 1141 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.17 % Allowed : 25.00 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1015 helix: 1.92 (0.26), residues: 405 sheet: 0.44 (0.37), residues: 212 loop : -1.34 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE R 371 TYR 0.012 0.001 TYR R 141 ARG 0.011 0.000 ARG R 326 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 423) hydrogen bonds : angle 4.09204 ( 1233) SS BOND : bond 0.00274 ( 3) SS BOND : angle 2.39545 ( 6) covalent geometry : bond 0.00319 ( 8321) covalent geometry : angle 0.69312 (11260) *********************** 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 173 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.991 Fit side-chains REVERT: R 170 ASN cc_start: 0.8393 (m110) cc_final: 0.8130 (m-40) REVERT: R 181 MET cc_start: 0.8441 (mmt) cc_final: 0.8181 (mmm) REVERT: R 293 LYS cc_start: 0.6623 (pptt) cc_final: 0.6325 (pptt) REVERT: R 335 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5998 (m-10) REVERT: R 341 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7420 (mmm160) REVERT: R 408 HIS cc_start: 0.8367 (m170) cc_final: 0.7988 (m-70) REVERT: A 311 TYR cc_start: 0.8025 (m-10) cc_final: 0.7591 (m-10) REVERT: A 356 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7436 (mtp-110) REVERT: A 390 GLN cc_start: 0.8743 (tt0) cc_final: 0.8241 (tp-100) REVERT: B 8 ARG cc_start: 0.9059 (mpt-90) cc_final: 0.8734 (mpt-90) REVERT: B 12 GLU cc_start: 0.8906 (pp20) cc_final: 0.8630 (pp20) REVERT: B 15 LYS cc_start: 0.9243 (mtmm) cc_final: 0.8812 (tmmt) REVERT: B 23 LYS cc_start: 0.9514 (tmmm) cc_final: 0.9221 (tptp) REVERT: B 61 MET cc_start: 0.9493 (pp-130) cc_final: 0.9146 (pp-130) REVERT: B 217 MET cc_start: 0.8299 (ppp) cc_final: 0.7923 (ppp) REVERT: G 13 ARG cc_start: 0.9383 (ptp-110) cc_final: 0.9114 (mtm110) REVERT: G 18 GLN cc_start: 0.8854 (tp40) cc_final: 0.8335 (tp40) REVERT: G 28 ILE cc_start: 0.8185 (mm) cc_final: 0.7919 (tp) REVERT: G 29 LYS cc_start: 0.8278 (mmtm) cc_final: 0.8074 (tppp) REVERT: N 1 GLN cc_start: 0.7173 (tp40) cc_final: 0.6797 (tp40) REVERT: N 5 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7939 (tp40) REVERT: N 43 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7639 (tptt) REVERT: N 46 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: N 53 GLN cc_start: 0.8183 (mp10) cc_final: 0.7800 (mp10) REVERT: N 70 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8448 (pp) REVERT: N 73 ASP cc_start: 0.8025 (t0) cc_final: 0.7430 (t0) REVERT: N 76 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9231 (mmmm) REVERT: N 87 LYS cc_start: 0.9102 (mttp) cc_final: 0.8751 (mttm) outliers start: 19 outliers final: 12 residues processed: 163 average time/residue: 1.0575 time to fit residues: 184.2274 Evaluate side-chains 164 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 315 ILE Chi-restraints excluded: chain R residue 335 TYR Chi-restraints excluded: chain R residue 384 GLN Chi-restraints excluded: chain A residue 51 SER 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 249 THR Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 384 GLN ** R 396 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 = 0.3587 r_free = 0.3587 target = 0.104016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072097 restraints weight = 15853.413| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.62 r_work: 0.2853 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8324 Z= 0.148 Angle : 0.717 11.872 11266 Z= 0.361 Chirality : 0.046 0.363 1266 Planarity : 0.004 0.067 1440 Dihedral : 4.518 45.731 1141 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.05 % Allowed : 25.80 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.27), residues: 1015 helix: 1.85 (0.26), residues: 405 sheet: 0.47 (0.37), residues: 212 loop : -1.34 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE R 371 TYR 0.012 0.001 TYR R 141 ARG 0.011 0.000 ARG R 326 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 423) hydrogen bonds : angle 4.11540 ( 1233) SS BOND : bond 0.00253 ( 3) SS BOND : angle 2.42034 ( 6) covalent geometry : bond 0.00346 ( 8321) covalent geometry : angle 0.71482 (11260) ********************** 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 171 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: R 170 ASN cc_start: 0.8405 (m110) cc_final: 0.8149 (m-40) REVERT: R 293 LYS cc_start: 0.6660 (pptt) cc_final: 0.6346 (pptt) REVERT: R 335 TYR cc_start: 0.6565 (OUTLIER) cc_final: 0.6019 (m-10) REVERT: R 341 ARG cc_start: 0.7718 (mmm160) cc_final: 0.7395 (mmm160) REVERT: R 384 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: R 396 ASN cc_start: 0.8088 (t0) cc_final: 0.7866 (t0) REVERT: R 408 HIS cc_start: 0.8373 (m170) cc_final: 0.7995 (m-70) REVERT: A 311 TYR cc_start: 0.8032 (m-10) cc_final: 0.7604 (m-10) REVERT: A 356 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7419 (mtp-110) REVERT: A 390 GLN cc_start: 0.8746 (tt0) cc_final: 0.8189 (tp-100) REVERT: B 8 ARG cc_start: 0.8994 (mpt-90) cc_final: 0.8631 (mpt-90) REVERT: B 12 GLU cc_start: 0.8920 (pp20) cc_final: 0.8587 (pp20) REVERT: B 15 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8809 (tmmt) REVERT: B 23 LYS cc_start: 0.9507 (tmmm) cc_final: 0.9200 (tptp) REVERT: B 61 MET cc_start: 0.9499 (pp-130) cc_final: 0.9113 (pp-130) REVERT: B 217 MET cc_start: 0.8338 (ppp) cc_final: 0.7965 (ppp) REVERT: G 13 ARG cc_start: 0.9385 (ptp-110) cc_final: 0.9096 (mtm110) REVERT: G 18 GLN cc_start: 0.8881 (tp40) cc_final: 0.8414 (tp40) REVERT: G 28 ILE cc_start: 0.8178 (mm) cc_final: 0.7911 (tp) REVERT: G 29 LYS cc_start: 0.8278 (mmtm) cc_final: 0.8073 (tppp) REVERT: N 1 GLN cc_start: 0.7207 (tp40) cc_final: 0.6834 (tp40) REVERT: N 5 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7953 (tp40) REVERT: N 46 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: N 53 GLN cc_start: 0.8191 (mp10) cc_final: 0.7811 (mp10) REVERT: N 70 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8461 (pp) REVERT: N 73 ASP cc_start: 0.7997 (t0) cc_final: 0.7398 (t0) REVERT: N 76 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9223 (mmmm) REVERT: N 87 LYS cc_start: 0.9114 (mttp) cc_final: 0.8773 (mttm) outliers start: 18 outliers final: 10 residues processed: 162 average time/residue: 1.0322 time to fit residues: 178.8260 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 : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 335 TYR Chi-restraints excluded: chain R residue 384 GLN Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 214 VAL 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 249 THR Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 0.0030 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 384 GLN ** R 396 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 = 0.3614 r_free = 0.3614 target = 0.105495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.074225 restraints weight = 15986.860| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.61 r_work: 0.2885 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2950 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= 0.132 Angle : 0.715 11.644 11266 Z= 0.360 Chirality : 0.046 0.355 1266 Planarity : 0.004 0.068 1440 Dihedral : 4.455 45.674 1141 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.71 % Allowed : 26.14 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1015 helix: 1.82 (0.26), residues: 407 sheet: 0.56 (0.38), residues: 206 loop : -1.32 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 287 HIS 0.003 0.001 HIS A 357 PHE 0.021 0.001 PHE R 371 TYR 0.012 0.001 TYR R 141 ARG 0.011 0.000 ARG R 326 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 423) hydrogen bonds : angle 4.10164 ( 1233) SS BOND : bond 0.00238 ( 3) SS BOND : angle 2.11765 ( 6) covalent geometry : bond 0.00298 ( 8321) covalent geometry : angle 0.71335 (11260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5999.43 seconds wall clock time: 103 minutes 55.82 seconds (6235.82 seconds total)