Starting phenix.real_space_refine on Sat Aug 3 13:21:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa3_37390/08_2024/8wa3_37390.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa3_37390/08_2024/8wa3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa3_37390/08_2024/8wa3_37390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa3_37390/08_2024/8wa3_37390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa3_37390/08_2024/8wa3_37390.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa3_37390/08_2024/8wa3_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 Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.68, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 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: 0.77 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: 2.18 Time building geometry restraints manager: 3.38 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: 98.69 - 105.76: 105 105.76 - 112.83: 4467 112.83 - 119.90: 2713 119.90 - 126.97: 3879 126.97 - 134.04: 96 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: 0.850 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.210 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- 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 8321 Z= 0.195 Angle : 0.646 12.032 11260 Z= 0.378 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 0.947 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: 1.2172 time to fit residues: 231.8983 Evaluate side-chains 146 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8321 Z= 0.226 Angle : 0.631 10.070 11260 Z= 0.325 Chirality : 0.042 0.151 1266 Planarity : 0.004 0.053 1440 Dihedral : 4.798 44.573 1147 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.17 % Allowed : 12.44 % 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: 0.75 (0.27), residues: 1015 helix: 2.18 (0.27), residues: 411 sheet: 0.32 (0.35), residues: 219 loop : -1.31 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 287 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.001 PHE R 371 TYR 0.015 0.001 TYR R 141 ARG 0.005 0.000 ARG A 38 *********************** 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 177 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.8655 (mmm) cc_final: 0.8260 (mmt) REVERT: R 408 HIS cc_start: 0.8109 (m170) cc_final: 0.7785 (m-70) REVERT: A 311 TYR cc_start: 0.7257 (m-10) cc_final: 0.7027 (m-10) REVERT: A 356 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7408 (mtp-110) REVERT: B 7 LEU cc_start: 0.9176 (mm) cc_final: 0.8579 (mm) REVERT: B 8 ARG cc_start: 0.9017 (mpt-90) cc_final: 0.8620 (mpt-90) REVERT: B 15 LYS cc_start: 0.9323 (mtmm) cc_final: 0.8848 (tmtm) REVERT: B 23 LYS cc_start: 0.9519 (tmmm) cc_final: 0.9282 (tptp) REVERT: G 13 ARG cc_start: 0.9284 (ptp-110) cc_final: 0.8988 (ptp-110) REVERT: G 18 GLN cc_start: 0.9211 (tp40) cc_final: 0.8704 (tp40) REVERT: G 20 LYS cc_start: 0.9011 (ptpp) cc_final: 0.8571 (ptpp) REVERT: G 29 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8368 (mmpt) REVERT: N 5 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8136 (tp40) REVERT: N 43 LYS cc_start: 0.7930 (mmpt) cc_final: 0.7682 (mmmm) REVERT: N 46 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: N 53 GLN cc_start: 0.8122 (mp10) cc_final: 0.7771 (mp10) REVERT: N 73 ASP cc_start: 0.7961 (t0) cc_final: 0.7586 (t0) REVERT: N 87 LYS cc_start: 0.9324 (mttp) cc_final: 0.8959 (mttm) outliers start: 19 outliers final: 7 residues processed: 165 average time/residue: 1.2214 time to fit residues: 213.2952 Evaluate side-chains 152 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 50 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 0.0060 chunk 91 optimal weight: 0.0070 chunk 99 optimal weight: 0.0770 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 overall best weight: 0.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 ASN R 384 GLN ** R 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8321 Z= 0.155 Angle : 0.592 10.628 11260 Z= 0.302 Chirality : 0.041 0.151 1266 Planarity : 0.004 0.055 1440 Dihedral : 4.430 46.494 1141 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.71 % Allowed : 16.78 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.27), residues: 1015 helix: 2.13 (0.26), residues: 412 sheet: 0.48 (0.36), residues: 205 loop : -1.27 (0.31), residues: 398 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 0.017 0.001 PHE R 371 TYR 0.017 0.001 TYR R 141 ARG 0.003 0.000 ARG A 38 *********************** 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 179 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: R 181 MET cc_start: 0.8811 (mmm) cc_final: 0.8554 (tpp) REVERT: R 255 HIS cc_start: 0.7470 (m170) cc_final: 0.7087 (m-70) REVERT: R 293 LYS cc_start: 0.7000 (pptt) cc_final: 0.6751 (pptt) REVERT: R 408 HIS cc_start: 0.8119 (m170) cc_final: 0.7790 (m-70) REVERT: A 27 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8416 (mm-30) REVERT: A 311 TYR cc_start: 0.7312 (m-10) cc_final: 0.7059 (m-10) REVERT: A 356 ARG cc_start: 0.7826 (mtp-110) cc_final: 0.7495 (mtp-110) REVERT: B 8 ARG cc_start: 0.9056 (mpt-90) cc_final: 0.8603 (mpt-90) REVERT: B 15 LYS cc_start: 0.9317 (mtmm) cc_final: 0.8820 (tmmt) REVERT: B 23 LYS cc_start: 0.9543 (tmmm) cc_final: 0.9256 (tptp) REVERT: G 13 ARG cc_start: 0.9279 (ptp-110) cc_final: 0.8858 (ptp-110) REVERT: G 17 GLU cc_start: 0.9472 (tp30) cc_final: 0.9087 (mm-30) REVERT: G 18 GLN cc_start: 0.9161 (tp40) cc_final: 0.8703 (tp40) REVERT: G 20 LYS cc_start: 0.8943 (ptpp) cc_final: 0.8229 (pttm) REVERT: G 29 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8274 (mmtm) REVERT: N 5 GLN cc_start: 0.8396 (tp-100) cc_final: 0.8122 (tp40) REVERT: N 38 ARG cc_start: 0.8927 (ttp-110) cc_final: 0.8638 (mtm110) REVERT: N 53 GLN cc_start: 0.8170 (mp10) cc_final: 0.7820 (mp10) REVERT: N 70 ILE cc_start: 0.8614 (pt) cc_final: 0.8310 (pp) REVERT: N 73 ASP cc_start: 0.7999 (t0) cc_final: 0.7501 (t0) REVERT: N 87 LYS cc_start: 0.9309 (mttp) cc_final: 0.8924 (mttm) outliers start: 15 outliers final: 7 residues processed: 173 average time/residue: 1.0865 time to fit residues: 200.6184 Evaluate side-chains 154 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 ASN R 384 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8321 Z= 0.212 Angle : 0.613 10.358 11260 Z= 0.312 Chirality : 0.043 0.265 1266 Planarity : 0.004 0.056 1440 Dihedral : 4.403 45.176 1141 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.85 % Allowed : 19.06 % Favored : 78.08 % 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: 2.05 (0.26), residues: 410 sheet: 0.56 (0.37), residues: 205 loop : -1.31 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.001 PHE R 371 TYR 0.013 0.001 TYR R 141 ARG 0.005 0.000 ARG N 38 *********************** 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 180 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: R 255 HIS cc_start: 0.7577 (m170) cc_final: 0.7285 (m170) REVERT: R 293 LYS cc_start: 0.7019 (pptt) cc_final: 0.6737 (pptt) REVERT: R 396 ASN cc_start: 0.8189 (t0) cc_final: 0.7814 (t0) REVERT: R 408 HIS cc_start: 0.8135 (m170) cc_final: 0.7804 (m-70) REVERT: A 27 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8481 (mm-30) REVERT: A 311 TYR cc_start: 0.7402 (m-10) cc_final: 0.7151 (m-10) REVERT: A 356 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7461 (mtp-110) REVERT: B 8 ARG cc_start: 0.9066 (mpt-90) cc_final: 0.8661 (mpt-90) REVERT: B 15 LYS cc_start: 0.9333 (mtmm) cc_final: 0.8829 (tmmt) REVERT: B 23 LYS cc_start: 0.9553 (tmmm) cc_final: 0.9244 (tptp) REVERT: G 13 ARG cc_start: 0.9282 (ptp-110) cc_final: 0.9000 (ptp-110) REVERT: G 18 GLN cc_start: 0.9152 (tp40) cc_final: 0.8730 (tp40) REVERT: G 20 LYS cc_start: 0.8956 (ptpp) cc_final: 0.8616 (ptpp) REVERT: G 29 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8302 (mmtm) REVERT: G 32 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8564 (ttpp) REVERT: N 5 GLN cc_start: 0.8413 (tp-100) cc_final: 0.8108 (tp40) REVERT: N 43 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7820 (tptt) REVERT: N 53 GLN cc_start: 0.8211 (mp10) cc_final: 0.7837 (mp10) REVERT: N 70 ILE cc_start: 0.8638 (pt) cc_final: 0.8336 (pp) REVERT: N 73 ASP cc_start: 0.8056 (t0) cc_final: 0.7567 (t0) REVERT: N 87 LYS cc_start: 0.9318 (mttp) cc_final: 0.8939 (mttm) outliers start: 25 outliers final: 11 residues processed: 166 average time/residue: 1.1263 time to fit residues: 199.2855 Evaluate side-chains 157 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 ASN R 384 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8321 Z= 0.246 Angle : 0.632 9.636 11260 Z= 0.324 Chirality : 0.044 0.267 1266 Planarity : 0.004 0.059 1440 Dihedral : 4.507 45.349 1141 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.54 % Allowed : 20.43 % 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: 0.70 (0.27), residues: 1015 helix: 2.11 (0.26), residues: 403 sheet: 0.57 (0.37), residues: 205 loop : -1.35 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.001 PHE R 379 TYR 0.012 0.001 TYR R 141 ARG 0.003 0.000 ARG N 38 *********************** 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 188 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: R 293 LYS cc_start: 0.7035 (pptt) cc_final: 0.6709 (pptt) REVERT: R 307 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8376 (tp) REVERT: R 396 ASN cc_start: 0.8235 (t0) cc_final: 0.7810 (t0) REVERT: R 408 HIS cc_start: 0.8127 (m170) cc_final: 0.7808 (m-70) REVERT: A 311 TYR cc_start: 0.7578 (m-10) cc_final: 0.7320 (m-10) REVERT: A 356 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.7415 (mtp-110) REVERT: A 390 GLN cc_start: 0.8696 (tt0) cc_final: 0.8261 (tp-100) REVERT: B 8 ARG cc_start: 0.9063 (mpt-90) cc_final: 0.8680 (mtt-85) REVERT: B 23 LYS cc_start: 0.9558 (tmmm) cc_final: 0.9219 (tptp) REVERT: G 18 GLN cc_start: 0.9162 (tp40) cc_final: 0.8736 (tp40) REVERT: G 20 LYS cc_start: 0.8935 (ptpp) cc_final: 0.8659 (ptpp) REVERT: G 29 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8338 (mmtm) REVERT: G 32 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8651 (ttpp) REVERT: N 5 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8171 (tp40) REVERT: N 43 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7763 (tptt) REVERT: N 53 GLN cc_start: 0.8303 (mp10) cc_final: 0.7946 (mp10) REVERT: N 70 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8317 (pp) REVERT: N 73 ASP cc_start: 0.8092 (t0) cc_final: 0.7617 (t0) REVERT: N 87 LYS cc_start: 0.9341 (mttp) cc_final: 0.8979 (mttm) outliers start: 31 outliers final: 14 residues processed: 169 average time/residue: 1.0359 time to fit residues: 187.1253 Evaluate side-chains 163 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 307 ILE 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 B residue 158 VAL Chi-restraints excluded: chain G residue 32 LYS 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 87 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 94 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: R 384 GLN B 13 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8321 Z= 0.226 Angle : 0.648 10.612 11260 Z= 0.330 Chirality : 0.045 0.276 1266 Planarity : 0.004 0.060 1440 Dihedral : 4.518 46.114 1141 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.54 % Allowed : 22.60 % Favored : 73.86 % 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: 0.70 (0.27), residues: 1015 helix: 2.09 (0.26), residues: 405 sheet: 0.47 (0.37), residues: 213 loop : -1.31 (0.31), residues: 397 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 335 ARG 0.007 0.000 ARG G 13 *********************** 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 181 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: R 293 LYS cc_start: 0.7017 (pptt) cc_final: 0.6680 (pptt) REVERT: R 396 ASN cc_start: 0.8195 (t0) cc_final: 0.7682 (t0) REVERT: R 408 HIS cc_start: 0.8114 (m170) cc_final: 0.7791 (m-70) REVERT: A 311 TYR cc_start: 0.7629 (m-10) cc_final: 0.7371 (m-10) REVERT: A 356 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7399 (mtp-110) REVERT: A 390 GLN cc_start: 0.8693 (tt0) cc_final: 0.8248 (tp-100) REVERT: B 8 ARG cc_start: 0.9059 (mpt-90) cc_final: 0.8748 (mpt-90) REVERT: B 23 LYS cc_start: 0.9562 (tmmm) cc_final: 0.9276 (tptp) REVERT: G 18 GLN cc_start: 0.9136 (tp40) cc_final: 0.8737 (tp40) REVERT: G 20 LYS cc_start: 0.8934 (ptpp) cc_final: 0.8662 (ptpp) REVERT: G 29 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8334 (mmtm) REVERT: N 5 GLN cc_start: 0.8454 (tp-100) cc_final: 0.8178 (tp40) REVERT: N 43 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7760 (tptt) REVERT: N 53 GLN cc_start: 0.8314 (mp10) cc_final: 0.7956 (mp10) REVERT: N 70 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8401 (pt) REVERT: N 73 ASP cc_start: 0.8066 (t0) cc_final: 0.7562 (t0) REVERT: N 76 LYS cc_start: 0.9467 (mmmm) cc_final: 0.9184 (mmmm) REVERT: N 87 LYS cc_start: 0.9339 (mttp) cc_final: 0.8996 (mttm) REVERT: N 105 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8177 (mtm180) outliers start: 31 outliers final: 15 residues processed: 164 average time/residue: 1.0923 time to fit residues: 191.0650 Evaluate side-chains 159 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 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 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 LEU 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 11 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8321 Z= 0.208 Angle : 0.641 9.401 11260 Z= 0.327 Chirality : 0.044 0.264 1266 Planarity : 0.004 0.062 1440 Dihedral : 4.512 45.623 1141 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.74 % Allowed : 24.09 % Favored : 73.17 % 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: 0.73 (0.27), residues: 1015 helix: 2.11 (0.26), residues: 405 sheet: 0.55 (0.37), residues: 210 loop : -1.31 (0.30), residues: 400 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 0.010 0.000 ARG G 13 *********************** 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 178 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: R 293 LYS cc_start: 0.7007 (pptt) cc_final: 0.6661 (pptt) REVERT: R 396 ASN cc_start: 0.8159 (t0) cc_final: 0.7597 (t0) REVERT: R 408 HIS cc_start: 0.8116 (m170) cc_final: 0.7801 (m-70) REVERT: A 311 TYR cc_start: 0.7649 (m-10) cc_final: 0.7405 (m-10) REVERT: A 356 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.7337 (mtp-110) REVERT: A 390 GLN cc_start: 0.8693 (tt0) cc_final: 0.8318 (tp-100) REVERT: B 8 ARG cc_start: 0.9069 (mpt-90) cc_final: 0.8718 (mpt-90) REVERT: B 10 GLU cc_start: 0.8362 (pp20) cc_final: 0.7880 (pp20) REVERT: B 12 GLU cc_start: 0.8736 (pp20) cc_final: 0.8522 (pp20) REVERT: B 15 LYS cc_start: 0.9325 (mtmm) cc_final: 0.8866 (tmtm) REVERT: B 23 LYS cc_start: 0.9558 (tmmm) cc_final: 0.9261 (tptp) REVERT: G 18 GLN cc_start: 0.9118 (tp40) cc_final: 0.8714 (tp40) REVERT: G 20 LYS cc_start: 0.8948 (ptpp) cc_final: 0.8694 (ptpp) REVERT: G 29 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8257 (mmtm) REVERT: N 5 GLN cc_start: 0.8432 (tp-100) cc_final: 0.8132 (tp40) REVERT: N 43 LYS cc_start: 0.7940 (mmmt) cc_final: 0.7714 (tptt) REVERT: N 53 GLN cc_start: 0.8276 (mp10) cc_final: 0.7909 (mp10) REVERT: N 70 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8314 (pp) REVERT: N 73 ASP cc_start: 0.8084 (t0) cc_final: 0.7578 (t0) REVERT: N 76 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9199 (mmmm) REVERT: N 87 LYS cc_start: 0.9368 (mttp) cc_final: 0.9006 (mttm) outliers start: 24 outliers final: 14 residues processed: 165 average time/residue: 1.0339 time to fit residues: 182.4435 Evaluate side-chains 163 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 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 57 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 0.0770 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8321 Z= 0.210 Angle : 0.665 10.915 11260 Z= 0.338 Chirality : 0.045 0.307 1266 Planarity : 0.004 0.064 1440 Dihedral : 4.495 45.192 1141 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.74 % Allowed : 24.89 % Favored : 72.37 % 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: 0.67 (0.27), residues: 1015 helix: 2.02 (0.26), residues: 405 sheet: 0.57 (0.37), residues: 210 loop : -1.33 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 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 0.009 0.000 ARG G 13 *********************** 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 174 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: R 164 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8502 (tmm-80) REVERT: R 181 MET cc_start: 0.8537 (mmt) cc_final: 0.8238 (mmm) REVERT: R 293 LYS cc_start: 0.7029 (pptt) cc_final: 0.6686 (pptt) REVERT: R 396 ASN cc_start: 0.8119 (t0) cc_final: 0.7546 (t0) REVERT: R 408 HIS cc_start: 0.8120 (m170) cc_final: 0.7804 (m-70) REVERT: A 311 TYR cc_start: 0.7670 (m-10) cc_final: 0.7426 (m-10) REVERT: A 356 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7362 (mtp-110) REVERT: A 390 GLN cc_start: 0.8679 (tt0) cc_final: 0.8308 (tp-100) REVERT: B 8 ARG cc_start: 0.8977 (mpt-90) cc_final: 0.8610 (mpt-90) REVERT: B 12 GLU cc_start: 0.8715 (pp20) cc_final: 0.8497 (pp20) REVERT: B 15 LYS cc_start: 0.9333 (mtmm) cc_final: 0.8859 (tmtm) REVERT: B 23 LYS cc_start: 0.9560 (tmmm) cc_final: 0.9258 (tptp) REVERT: G 13 ARG cc_start: 0.9187 (ptp-110) cc_final: 0.8960 (mtm110) REVERT: G 16 VAL cc_start: 0.9441 (t) cc_final: 0.9181 (p) REVERT: G 18 GLN cc_start: 0.9101 (tp40) cc_final: 0.8676 (tp40) REVERT: G 29 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8209 (mmtm) REVERT: N 5 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8121 (tp40) REVERT: N 43 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7693 (tptt) REVERT: N 53 GLN cc_start: 0.8283 (mp10) cc_final: 0.7914 (mp10) REVERT: N 70 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8329 (pp) REVERT: N 73 ASP cc_start: 0.8117 (t0) cc_final: 0.7624 (t0) REVERT: N 76 LYS cc_start: 0.9479 (mmmm) cc_final: 0.9211 (mmmm) REVERT: N 87 LYS cc_start: 0.9360 (mttp) cc_final: 0.9033 (mttm) outliers start: 24 outliers final: 12 residues processed: 162 average time/residue: 1.0519 time to fit residues: 181.8651 Evaluate side-chains 159 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 R residue 361 THR 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 N residue 11 LEU Chi-restraints excluded: chain N residue 18 LEU 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 90 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8321 Z= 0.211 Angle : 0.685 10.510 11260 Z= 0.346 Chirality : 0.046 0.353 1266 Planarity : 0.004 0.066 1440 Dihedral : 4.527 46.304 1141 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.51 % Allowed : 25.00 % Favored : 72.49 % 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: 0.62 (0.27), residues: 1015 helix: 1.95 (0.26), residues: 405 sheet: 0.56 (0.37), residues: 210 loop : -1.33 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.001 PHE R 371 TYR 0.011 0.001 TYR R 141 ARG 0.008 0.000 ARG G 13 *********************** 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 167 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.009 Fit side-chains REVERT: R 293 LYS cc_start: 0.7006 (pptt) cc_final: 0.6676 (pptt) REVERT: R 335 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.6027 (m-10) REVERT: R 396 ASN cc_start: 0.8115 (t0) cc_final: 0.7517 (t0) REVERT: R 408 HIS cc_start: 0.8134 (m170) cc_final: 0.7820 (m-70) REVERT: A 311 TYR cc_start: 0.7686 (m-10) cc_final: 0.7448 (m-10) REVERT: A 356 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7349 (mtp-110) REVERT: A 390 GLN cc_start: 0.8678 (tt0) cc_final: 0.8255 (tp-100) REVERT: B 8 ARG cc_start: 0.8943 (mpt-90) cc_final: 0.8543 (mpt-90) REVERT: B 12 GLU cc_start: 0.8716 (pp20) cc_final: 0.8460 (pp20) REVERT: B 15 LYS cc_start: 0.9326 (mtmm) cc_final: 0.8857 (tmtm) REVERT: B 23 LYS cc_start: 0.9556 (tmmm) cc_final: 0.9247 (tptp) REVERT: G 13 ARG cc_start: 0.9229 (ptp-110) cc_final: 0.8921 (mtm110) REVERT: G 16 VAL cc_start: 0.9413 (t) cc_final: 0.8947 (p) REVERT: G 17 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8340 (mm-30) REVERT: G 18 GLN cc_start: 0.9059 (tp40) cc_final: 0.8662 (tp40) REVERT: G 20 LYS cc_start: 0.9290 (ptpp) cc_final: 0.8858 (pttp) REVERT: G 29 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8175 (mmtm) REVERT: G 47 GLU cc_start: 0.8257 (mp0) cc_final: 0.7039 (mp0) REVERT: N 5 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8110 (tp40) REVERT: N 43 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7698 (tptt) REVERT: N 53 GLN cc_start: 0.8297 (mp10) cc_final: 0.7917 (mp10) REVERT: N 70 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8336 (pp) REVERT: N 73 ASP cc_start: 0.8134 (t0) cc_final: 0.7688 (t0) REVERT: N 76 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9218 (mmmm) REVERT: N 87 LYS cc_start: 0.9363 (mttp) cc_final: 0.9024 (mttm) REVERT: N 105 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8174 (mtm180) outliers start: 22 outliers final: 14 residues processed: 154 average time/residue: 1.1333 time to fit residues: 185.9795 Evaluate side-chains 156 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 R residue 335 TYR Chi-restraints excluded: chain R residue 361 THR 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 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 70 ILE Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8321 Z= 0.204 Angle : 0.697 10.407 11260 Z= 0.352 Chirality : 0.045 0.341 1266 Planarity : 0.004 0.067 1440 Dihedral : 4.511 45.827 1141 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.05 % Allowed : 26.03 % Favored : 71.92 % 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: 0.61 (0.27), residues: 1015 helix: 1.90 (0.26), residues: 407 sheet: 0.58 (0.37), residues: 210 loop : -1.32 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 287 HIS 0.003 0.001 HIS A 357 PHE 0.022 0.001 PHE R 371 TYR 0.012 0.001 TYR R 141 ARG 0.013 0.000 ARG R 326 ********************** 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 159 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.838 Fit side-chains REVERT: R 293 LYS cc_start: 0.6964 (pptt) cc_final: 0.6664 (pptt) REVERT: R 408 HIS cc_start: 0.8136 (m170) cc_final: 0.7822 (m-70) REVERT: A 311 TYR cc_start: 0.7694 (m-10) cc_final: 0.7461 (m-10) REVERT: A 356 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.7322 (mtp-110) REVERT: A 390 GLN cc_start: 0.8705 (tt0) cc_final: 0.8459 (tp-100) REVERT: B 8 ARG cc_start: 0.8923 (mpt-90) cc_final: 0.8536 (mpt-90) REVERT: B 12 GLU cc_start: 0.8722 (pp20) cc_final: 0.8459 (pp20) REVERT: B 15 LYS cc_start: 0.9321 (mtmm) cc_final: 0.8855 (tmtm) REVERT: B 23 LYS cc_start: 0.9556 (tmmm) cc_final: 0.9244 (tptp) REVERT: G 13 ARG cc_start: 0.9207 (ptp-110) cc_final: 0.8902 (mtm110) REVERT: G 16 VAL cc_start: 0.9394 (t) cc_final: 0.8916 (p) REVERT: G 17 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8246 (mm-30) REVERT: G 18 GLN cc_start: 0.9058 (tp40) cc_final: 0.8664 (tp40) REVERT: G 20 LYS cc_start: 0.9280 (ptpp) cc_final: 0.8822 (pttp) REVERT: G 29 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8164 (mmtm) REVERT: N 5 GLN cc_start: 0.8380 (tp-100) cc_final: 0.8073 (tp40) REVERT: N 43 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7692 (tptt) REVERT: N 53 GLN cc_start: 0.8324 (mp10) cc_final: 0.7945 (mp10) REVERT: N 70 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8295 (pp) REVERT: N 73 ASP cc_start: 0.8273 (t0) cc_final: 0.7667 (t0) REVERT: N 76 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9215 (mmmm) REVERT: N 87 LYS cc_start: 0.9358 (mttp) cc_final: 0.9034 (mttm) REVERT: N 105 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8165 (mtm180) outliers start: 18 outliers final: 9 residues processed: 149 average time/residue: 1.0662 time to fit residues: 169.6435 Evaluate side-chains 148 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 317 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.0570 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.106285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.074042 restraints weight = 15578.226| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.59 r_work: 0.2908 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8321 Z= 0.212 Angle : 0.697 9.782 11260 Z= 0.353 Chirality : 0.045 0.317 1266 Planarity : 0.004 0.067 1440 Dihedral : 4.516 45.434 1141 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.94 % Allowed : 26.48 % Favored : 71.58 % 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: 0.61 (0.27), residues: 1015 helix: 1.95 (0.26), residues: 407 sheet: 0.57 (0.37), residues: 210 loop : -1.37 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 287 HIS 0.004 0.001 HIS A 357 PHE 0.025 0.001 PHE N 103 TYR 0.011 0.001 TYR R 141 ARG 0.014 0.000 ARG R 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.85 seconds wall clock time: 62 minutes 9.00 seconds (3729.00 seconds total)