Starting phenix.real_space_refine on Tue Jan 13 14:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mwg_24066/01_2026/7mwg_24066.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mwg_24066/01_2026/7mwg_24066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mwg_24066/01_2026/7mwg_24066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mwg_24066/01_2026/7mwg_24066.map" model { file = "/net/cci-nas-00/data/ceres_data/7mwg_24066/01_2026/7mwg_24066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mwg_24066/01_2026/7mwg_24066.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.119 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 50 5.16 5 C 4293 2.51 5 N 1167 2.21 5 O 1333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6849 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3413 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain: "B" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3366 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.63, per 1000 atoms: 0.24 Number of scatterers: 6849 At special positions: 0 Unit cell: (78.647, 70.649, 111.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 5 15.00 Mg 1 11.99 O 1333 8.00 N 1167 7.00 C 4293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 268.8 milliseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 52.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.570A pdb=" N THR A 51 " --> pdb=" O ALA A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.485A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.945A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.537A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.574A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.524A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.991A pdb=" N VAL A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.877A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.908A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.990A pdb=" N ASP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 108 through 127 removed outlier: 4.543A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.593A pdb=" N SER B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.256A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.618A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.792A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.919A pdb=" N GLU B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.874A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.768A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.061A pdb=" N VAL A 66 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS A 8 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASN A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER A 270 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASP A 205 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N TYR A 272 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE A 267 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER A 381 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.349A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N MET B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN B 8 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU B 3 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLN B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 5 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 136 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 7 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N SER B 138 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLY B 9 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N MET B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR B 166 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE B 268 " --> pdb=" O CYS B 199 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL B 201 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N PHE B 270 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 369 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N SER B 352 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA B 315 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 53 339 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.87 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: 2282 1.34 - 1.46: 1382 1.46 - 1.57: 3234 1.57 - 1.69: 8 1.69 - 1.80: 82 Bond restraints: 6988 Sorted by residual: bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.458 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" CA LEU B 263 " pdb=" CB LEU B 263 " ideal model delta sigma weight residual 1.536 1.479 0.057 4.10e-02 5.95e+02 1.94e+00 bond pdb=" CA SER B 314 " pdb=" CB SER B 314 " ideal model delta sigma weight residual 1.535 1.510 0.025 1.90e-02 2.77e+03 1.79e+00 bond pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.23e-02 6.61e+03 1.67e+00 bond pdb=" CA VAL A 177 " pdb=" CB VAL A 177 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.34e-02 5.57e+03 1.41e+00 ... (remaining 6983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 8897 1.26 - 2.51: 470 2.51 - 3.77: 83 3.77 - 5.02: 22 5.02 - 6.28: 7 Bond angle restraints: 9479 Sorted by residual: angle pdb=" C VAL A 362 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta sigma weight residual 123.04 120.37 2.67 9.20e-01 1.18e+00 8.45e+00 angle pdb=" N VAL A 141 " pdb=" CA VAL A 141 " pdb=" C VAL A 141 " ideal model delta sigma weight residual 112.98 109.40 3.58 1.25e+00 6.40e-01 8.20e+00 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 106.32 110.67 -4.35 1.61e+00 3.86e-01 7.31e+00 angle pdb=" C GLU A 196 " pdb=" N HIS A 197 " pdb=" CA HIS A 197 " ideal model delta sigma weight residual 122.49 118.42 4.07 1.55e+00 4.16e-01 6.89e+00 angle pdb=" N ALA B 271 " pdb=" CA ALA B 271 " pdb=" C ALA B 271 " ideal model delta sigma weight residual 109.81 115.05 -5.24 2.21e+00 2.05e-01 5.62e+00 ... (remaining 9474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 4037 34.97 - 69.95: 111 69.95 - 104.92: 13 104.92 - 139.89: 1 139.89 - 174.87: 1 Dihedral angle restraints: 4163 sinusoidal: 1668 harmonic: 2495 Sorted by residual: dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 291.08 116.21 174.87 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -23.30 127.89 1 2.00e+01 2.50e-03 3.87e+01 dihedral pdb=" O2B GDP B 501 " pdb=" O3A GDP B 501 " pdb=" PB GDP B 501 " pdb=" PA GDP B 501 " ideal model delta sinusoidal sigma weight residual 180.00 79.88 100.12 1 2.00e+01 2.50e-03 2.82e+01 ... (remaining 4160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 639 0.032 - 0.065: 264 0.065 - 0.097: 92 0.097 - 0.129: 39 0.129 - 0.161: 5 Chirality restraints: 1039 Sorted by residual: chirality pdb=" CB VAL A 182 " pdb=" CA VAL A 182 " pdb=" CG1 VAL A 182 " pdb=" CG2 VAL A 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 275 " pdb=" N ILE A 275 " pdb=" C ILE A 275 " pdb=" CB ILE A 275 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1036 not shown) Planarity restraints: 1235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 62 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 63 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 111 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C GLY A 111 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY A 111 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 112 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 183 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 184 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 184 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 184 " 0.019 5.00e-02 4.00e+02 ... (remaining 1232 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 81 2.49 - 3.09: 5593 3.09 - 3.69: 11295 3.69 - 4.30: 16144 4.30 - 4.90: 26210 Nonbonded interactions: 59323 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 1.882 2.170 nonbonded pdb=" O1A GTP A 501 " pdb="MG MG A 502 " model vdw 1.954 2.170 nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 1.988 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.094 2.170 nonbonded pdb=" OH TYR A 210 " pdb=" OG1 THR B 323 " model vdw 2.146 3.040 ... (remaining 59318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.150 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.007 0.057 6988 Z= 0.330 Angle : 0.682 6.281 9479 Z= 0.375 Chirality : 0.043 0.161 1039 Planarity : 0.003 0.038 1235 Dihedral : 17.021 174.868 2567 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.39 % Allowed : 20.82 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.25), residues: 866 helix: -1.42 (0.22), residues: 368 sheet: -2.00 (0.45), residues: 122 loop : -2.17 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 84 TYR 0.010 0.001 TYR B 51 PHE 0.012 0.001 PHE B 294 TRP 0.013 0.002 TRP A 21 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 6988) covalent geometry : angle 0.68182 ( 9479) hydrogen bonds : bond 0.13627 ( 339) hydrogen bonds : angle 6.20876 ( 960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8622 (mtm-85) REVERT: A 68 LEU cc_start: 0.9188 (tp) cc_final: 0.8958 (mt) REVERT: A 102 ASN cc_start: 0.9052 (t0) cc_final: 0.8359 (t0) REVERT: A 120 ASP cc_start: 0.9364 (t0) cc_final: 0.9134 (t0) REVERT: A 211 ASP cc_start: 0.9234 (m-30) cc_final: 0.8976 (m-30) REVERT: A 268 MET cc_start: 0.8938 (mtt) cc_final: 0.8435 (mpp) REVERT: A 317 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8576 (mmm) REVERT: A 318 MET cc_start: 0.8845 (mtp) cc_final: 0.8568 (mtp) REVERT: A 398 MET cc_start: 0.8937 (mtt) cc_final: 0.8648 (mtp) REVERT: B 37 HIS cc_start: 0.7566 (m-70) cc_final: 0.7286 (m170) REVERT: B 73 MET cc_start: 0.9300 (ttm) cc_final: 0.8314 (tmm) REVERT: B 122 LYS cc_start: 0.8521 (ttpt) cc_final: 0.7842 (tptt) REVERT: B 125 GLU cc_start: 0.8587 (pp20) cc_final: 0.7971 (pp20) REVERT: B 164 MET cc_start: 0.8974 (tpt) cc_final: 0.8764 (tpp) REVERT: B 203 ASP cc_start: 0.8921 (t0) cc_final: 0.8532 (t0) REVERT: B 267 MET cc_start: 0.7926 (ptm) cc_final: 0.6983 (ptm) REVERT: B 268 ILE cc_start: 0.8937 (pt) cc_final: 0.8586 (pt) REVERT: B 288 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8740 (mt-10) REVERT: B 299 MET cc_start: 0.9164 (mmt) cc_final: 0.8750 (mmt) REVERT: B 344 TRP cc_start: 0.8754 (p90) cc_final: 0.8404 (p90) REVERT: B 348 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8622 (m-40) REVERT: B 375 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8518 (tm-30) outliers start: 47 outliers final: 31 residues processed: 151 average time/residue: 0.0843 time to fit residues: 17.1731 Evaluate side-chains 121 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 197 HIS ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 131 GLN B 137 HIS B 190 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.050152 restraints weight = 24836.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.052114 restraints weight = 11564.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053451 restraints weight = 6764.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054357 restraints weight = 4498.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055087 restraints weight = 3292.729| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6988 Z= 0.196 Angle : 0.616 6.986 9479 Z= 0.310 Chirality : 0.043 0.152 1039 Planarity : 0.004 0.029 1235 Dihedral : 11.021 155.553 1023 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.63 % Allowed : 24.35 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.28), residues: 866 helix: 0.27 (0.25), residues: 377 sheet: -1.30 (0.47), residues: 125 loop : -1.16 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 390 TYR 0.011 0.001 TYR B 425 PHE 0.013 0.001 PHE B 90 TRP 0.014 0.002 TRP A 21 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6988) covalent geometry : angle 0.61608 ( 9479) hydrogen bonds : bond 0.04482 ( 339) hydrogen bonds : angle 4.94013 ( 960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 66 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 98 ASP cc_start: 0.8075 (p0) cc_final: 0.7685 (p0) REVERT: A 120 ASP cc_start: 0.9261 (t0) cc_final: 0.9043 (t0) REVERT: A 233 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: A 268 MET cc_start: 0.8909 (mtt) cc_final: 0.8547 (mpp) REVERT: A 317 MET cc_start: 0.9000 (mmm) cc_final: 0.8598 (mmm) REVERT: A 398 MET cc_start: 0.8846 (mtt) cc_final: 0.8575 (mtp) REVERT: B 37 HIS cc_start: 0.7429 (m90) cc_final: 0.7217 (m170) REVERT: B 45 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: B 73 MET cc_start: 0.9201 (ttm) cc_final: 0.8931 (tmm) REVERT: B 122 LYS cc_start: 0.8653 (ttpt) cc_final: 0.7904 (tptt) REVERT: B 125 GLU cc_start: 0.8531 (pp20) cc_final: 0.7980 (pp20) REVERT: B 164 MET cc_start: 0.8789 (tpt) cc_final: 0.8546 (tpp) REVERT: B 203 ASP cc_start: 0.8764 (t0) cc_final: 0.8362 (t0) REVERT: B 267 MET cc_start: 0.7884 (ptm) cc_final: 0.7366 (ptp) REVERT: B 268 ILE cc_start: 0.8986 (pt) cc_final: 0.8518 (pt) REVERT: B 344 TRP cc_start: 0.8699 (p90) cc_final: 0.8371 (p90) outliers start: 34 outliers final: 15 residues processed: 129 average time/residue: 0.0683 time to fit residues: 12.5592 Evaluate side-chains 106 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 35 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 0.0000 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 195 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.058869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.050283 restraints weight = 24740.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.052238 restraints weight = 11693.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053636 restraints weight = 6891.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054555 restraints weight = 4593.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055237 restraints weight = 3346.402| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6988 Z= 0.199 Angle : 0.606 6.976 9479 Z= 0.301 Chirality : 0.043 0.175 1039 Planarity : 0.004 0.031 1235 Dihedral : 10.273 155.743 980 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.17 % Allowed : 24.35 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.28), residues: 866 helix: 0.78 (0.26), residues: 383 sheet: -0.93 (0.47), residues: 126 loop : -1.00 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 221 TYR 0.011 0.001 TYR B 51 PHE 0.008 0.001 PHE B 90 TRP 0.012 0.002 TRP A 21 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6988) covalent geometry : angle 0.60552 ( 9479) hydrogen bonds : bond 0.04399 ( 339) hydrogen bonds : angle 4.76465 ( 960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: A 96 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9157 (mmmm) REVERT: A 98 ASP cc_start: 0.7940 (p0) cc_final: 0.7585 (p0) REVERT: A 120 ASP cc_start: 0.9259 (t0) cc_final: 0.9022 (t0) REVERT: A 233 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.8641 (mp10) REVERT: A 268 MET cc_start: 0.8899 (mtt) cc_final: 0.8461 (mpp) REVERT: A 291 ILE cc_start: 0.9207 (mt) cc_final: 0.8999 (mp) REVERT: A 317 MET cc_start: 0.9036 (mmm) cc_final: 0.8595 (mmm) REVERT: A 398 MET cc_start: 0.8798 (mtt) cc_final: 0.8516 (mtp) REVERT: B 45 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: B 73 MET cc_start: 0.9239 (ttm) cc_final: 0.8964 (tmm) REVERT: B 122 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8325 (tptt) REVERT: B 198 GLU cc_start: 0.8909 (pt0) cc_final: 0.8373 (pt0) REVERT: B 203 ASP cc_start: 0.8754 (t0) cc_final: 0.8343 (t0) REVERT: B 292 GLN cc_start: 0.9198 (tt0) cc_final: 0.8944 (tt0) REVERT: B 344 TRP cc_start: 0.8695 (p90) cc_final: 0.8422 (p90) outliers start: 38 outliers final: 26 residues processed: 122 average time/residue: 0.0641 time to fit residues: 11.4604 Evaluate side-chains 118 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 40.0000 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.058797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.050271 restraints weight = 25054.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.052217 restraints weight = 11787.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053579 restraints weight = 6981.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054508 restraints weight = 4673.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055177 restraints weight = 3398.186| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6988 Z= 0.214 Angle : 0.614 7.219 9479 Z= 0.304 Chirality : 0.043 0.176 1039 Planarity : 0.004 0.032 1235 Dihedral : 10.136 155.941 978 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.94 % Allowed : 22.18 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.29), residues: 866 helix: 0.96 (0.26), residues: 384 sheet: -0.65 (0.46), residues: 126 loop : -0.78 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.011 0.001 TYR B 51 PHE 0.007 0.001 PHE A 388 TRP 0.012 0.002 TRP B 344 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 6988) covalent geometry : angle 0.61366 ( 9479) hydrogen bonds : bond 0.04350 ( 339) hydrogen bonds : angle 4.69190 ( 960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 91 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8900 (tm-30) REVERT: A 98 ASP cc_start: 0.7918 (p0) cc_final: 0.7563 (p0) REVERT: A 120 ASP cc_start: 0.9258 (t0) cc_final: 0.9016 (t0) REVERT: A 166 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8126 (mttm) REVERT: A 233 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: A 259 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9086 (mm) REVERT: A 268 MET cc_start: 0.8912 (mtt) cc_final: 0.8503 (mpp) REVERT: A 317 MET cc_start: 0.8986 (mmm) cc_final: 0.8578 (mmm) REVERT: A 318 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8611 (mtm) REVERT: A 398 MET cc_start: 0.8769 (mtt) cc_final: 0.8410 (mtp) REVERT: A 401 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8542 (tppt) REVERT: B 1 MET cc_start: 0.8535 (tpp) cc_final: 0.8299 (tpp) REVERT: B 37 HIS cc_start: 0.7373 (m90) cc_final: 0.7157 (m90) REVERT: B 45 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: B 73 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8997 (tmm) REVERT: B 122 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8341 (tptt) REVERT: B 203 ASP cc_start: 0.8762 (t0) cc_final: 0.8349 (t0) REVERT: B 344 TRP cc_start: 0.8727 (p90) cc_final: 0.8191 (p90) outliers start: 51 outliers final: 28 residues processed: 127 average time/residue: 0.0704 time to fit residues: 12.6439 Evaluate side-chains 123 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.050787 restraints weight = 24946.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052749 restraints weight = 11731.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054054 restraints weight = 6948.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055052 restraints weight = 4723.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.055721 restraints weight = 3426.001| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6988 Z= 0.174 Angle : 0.604 7.057 9479 Z= 0.297 Chirality : 0.043 0.198 1039 Planarity : 0.003 0.034 1235 Dihedral : 10.018 155.896 978 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.44 % Allowed : 24.35 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.29), residues: 866 helix: 1.18 (0.26), residues: 385 sheet: -0.48 (0.46), residues: 120 loop : -0.75 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.010 0.001 TYR B 36 PHE 0.006 0.001 PHE B 260 TRP 0.012 0.002 TRP B 344 HIS 0.003 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6988) covalent geometry : angle 0.60354 ( 9479) hydrogen bonds : bond 0.04201 ( 339) hydrogen bonds : angle 4.58958 ( 960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8883 (tm-30) REVERT: A 96 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.8960 (mmmm) REVERT: A 98 ASP cc_start: 0.7927 (p0) cc_final: 0.7581 (p0) REVERT: A 120 ASP cc_start: 0.9234 (t0) cc_final: 0.9008 (t0) REVERT: A 233 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: A 259 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9000 (mm) REVERT: A 268 MET cc_start: 0.8793 (mtt) cc_final: 0.8391 (mpp) REVERT: A 317 MET cc_start: 0.8969 (mmm) cc_final: 0.8575 (mmm) REVERT: A 318 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8679 (mtm) REVERT: A 398 MET cc_start: 0.8710 (mtt) cc_final: 0.8352 (mtp) REVERT: A 401 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8438 (tppt) REVERT: A 417 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: B 45 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: B 73 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8996 (tmm) REVERT: B 122 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8347 (tptt) REVERT: B 164 MET cc_start: 0.8616 (mmm) cc_final: 0.8201 (tpp) REVERT: B 200 MET cc_start: 0.8695 (mpt) cc_final: 0.8192 (mpp) REVERT: B 203 ASP cc_start: 0.8723 (t0) cc_final: 0.8373 (t0) REVERT: B 307 HIS cc_start: 0.9181 (m90) cc_final: 0.8883 (m-70) outliers start: 40 outliers final: 22 residues processed: 127 average time/residue: 0.0687 time to fit residues: 12.5818 Evaluate side-chains 121 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.058772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.050214 restraints weight = 25055.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.052137 restraints weight = 11825.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053469 restraints weight = 7022.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.054411 restraints weight = 4723.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055139 restraints weight = 3455.120| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6988 Z= 0.229 Angle : 0.624 8.122 9479 Z= 0.310 Chirality : 0.044 0.199 1039 Planarity : 0.004 0.037 1235 Dihedral : 9.991 153.410 977 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.53 % Allowed : 22.86 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.29), residues: 866 helix: 1.21 (0.26), residues: 384 sheet: -0.68 (0.45), residues: 132 loop : -0.69 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.011 0.001 TYR B 36 PHE 0.008 0.001 PHE A 388 TRP 0.012 0.001 TRP B 21 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 6988) covalent geometry : angle 0.62367 ( 9479) hydrogen bonds : bond 0.04311 ( 339) hydrogen bonds : angle 4.69179 ( 960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 88 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8423 (tpp) cc_final: 0.8130 (tpp) REVERT: A 22 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8920 (tm-30) REVERT: A 98 ASP cc_start: 0.7849 (p0) cc_final: 0.7496 (p0) REVERT: A 120 ASP cc_start: 0.9229 (t0) cc_final: 0.9009 (t0) REVERT: A 163 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8204 (mttp) REVERT: A 233 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.8646 (mp10) REVERT: A 259 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9056 (mm) REVERT: A 268 MET cc_start: 0.8805 (mtt) cc_final: 0.8363 (mpp) REVERT: A 317 MET cc_start: 0.8948 (mmm) cc_final: 0.8543 (mmm) REVERT: A 386 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8683 (pt0) REVERT: A 398 MET cc_start: 0.8719 (mtt) cc_final: 0.8355 (mtp) REVERT: A 401 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8618 (tppt) REVERT: B 45 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: B 73 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.9014 (tmm) REVERT: B 122 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8363 (tptt) REVERT: B 164 MET cc_start: 0.8500 (mmm) cc_final: 0.8060 (tpp) REVERT: B 200 MET cc_start: 0.8603 (mpt) cc_final: 0.8371 (mpp) REVERT: B 203 ASP cc_start: 0.8752 (t0) cc_final: 0.8336 (t0) outliers start: 48 outliers final: 35 residues processed: 123 average time/residue: 0.0745 time to fit residues: 12.9996 Evaluate side-chains 130 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 48 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 78 optimal weight: 0.0870 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.050420 restraints weight = 24759.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.052342 restraints weight = 11740.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053693 restraints weight = 6981.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.054609 restraints weight = 4681.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055323 restraints weight = 3426.670| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6988 Z= 0.223 Angle : 0.630 9.946 9479 Z= 0.311 Chirality : 0.044 0.200 1039 Planarity : 0.003 0.036 1235 Dihedral : 9.959 151.630 977 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.53 % Allowed : 23.81 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.29), residues: 866 helix: 1.27 (0.26), residues: 384 sheet: -0.58 (0.46), residues: 132 loop : -0.67 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.011 0.001 TYR B 51 PHE 0.007 0.001 PHE A 388 TRP 0.012 0.001 TRP B 21 HIS 0.008 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 6988) covalent geometry : angle 0.62951 ( 9479) hydrogen bonds : bond 0.04255 ( 339) hydrogen bonds : angle 4.68061 ( 960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8399 (tpp) cc_final: 0.8136 (tpp) REVERT: A 22 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8920 (tm-30) REVERT: A 96 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9038 (mmmm) REVERT: A 98 ASP cc_start: 0.7957 (p0) cc_final: 0.7609 (p0) REVERT: A 120 ASP cc_start: 0.9224 (t0) cc_final: 0.9012 (t0) REVERT: A 163 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8127 (mttt) REVERT: A 233 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: A 268 MET cc_start: 0.8812 (mtt) cc_final: 0.8382 (mpp) REVERT: A 317 MET cc_start: 0.8837 (mmm) cc_final: 0.8455 (mmm) REVERT: A 386 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8685 (pt0) REVERT: A 398 MET cc_start: 0.8706 (mtt) cc_final: 0.8362 (mtp) REVERT: A 401 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8643 (tppt) REVERT: B 45 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: B 73 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.9001 (tmm) REVERT: B 122 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8362 (tptt) REVERT: B 200 MET cc_start: 0.8891 (mpt) cc_final: 0.8484 (mpp) REVERT: B 203 ASP cc_start: 0.8755 (t0) cc_final: 0.8424 (t0) REVERT: B 293 MET cc_start: 0.9327 (tmm) cc_final: 0.9032 (tmm) outliers start: 48 outliers final: 34 residues processed: 126 average time/residue: 0.0697 time to fit residues: 12.4865 Evaluate side-chains 129 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 0.0050 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.052297 restraints weight = 24557.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054239 restraints weight = 11821.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055570 restraints weight = 7031.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056543 restraints weight = 4726.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.057256 restraints weight = 3436.363| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6988 Z= 0.147 Angle : 0.624 11.301 9479 Z= 0.302 Chirality : 0.043 0.203 1039 Planarity : 0.003 0.034 1235 Dihedral : 9.684 153.748 975 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.99 % Allowed : 24.76 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.29), residues: 866 helix: 1.38 (0.27), residues: 385 sheet: -0.42 (0.46), residues: 132 loop : -0.56 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.011 0.001 TYR A 172 PHE 0.007 0.001 PHE B 90 TRP 0.012 0.001 TRP B 21 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6988) covalent geometry : angle 0.62392 ( 9479) hydrogen bonds : bond 0.04040 ( 339) hydrogen bonds : angle 4.57286 ( 960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8729 (mp0) REVERT: A 96 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9098 (mmmm) REVERT: A 98 ASP cc_start: 0.7980 (p0) cc_final: 0.7610 (p0) REVERT: A 120 ASP cc_start: 0.9210 (t0) cc_final: 0.8710 (t0) REVERT: A 124 LYS cc_start: 0.9413 (mmmm) cc_final: 0.9152 (mmtm) REVERT: A 145 THR cc_start: 0.8651 (m) cc_final: 0.8394 (m) REVERT: A 233 GLN cc_start: 0.9329 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: A 251 ASP cc_start: 0.8567 (p0) cc_final: 0.8332 (p0) REVERT: A 268 MET cc_start: 0.8517 (mtt) cc_final: 0.8302 (mpp) REVERT: A 317 MET cc_start: 0.8890 (mmm) cc_final: 0.8421 (mmm) REVERT: A 386 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: A 398 MET cc_start: 0.8647 (mtt) cc_final: 0.8324 (mtp) REVERT: A 401 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8410 (tppt) REVERT: B 45 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7842 (pt0) REVERT: B 73 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8994 (tmm) REVERT: B 122 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8365 (tptt) REVERT: B 203 ASP cc_start: 0.8671 (t0) cc_final: 0.8319 (t0) REVERT: B 293 MET cc_start: 0.9320 (tmm) cc_final: 0.9038 (tmm) REVERT: B 307 HIS cc_start: 0.9126 (m90) cc_final: 0.8838 (m-70) outliers start: 44 outliers final: 32 residues processed: 136 average time/residue: 0.0707 time to fit residues: 13.6750 Evaluate side-chains 134 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.060034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.051469 restraints weight = 24924.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.053371 restraints weight = 12029.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054692 restraints weight = 7179.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055647 restraints weight = 4834.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.056345 restraints weight = 3513.824| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6988 Z= 0.231 Angle : 0.669 12.097 9479 Z= 0.330 Chirality : 0.045 0.233 1039 Planarity : 0.004 0.037 1235 Dihedral : 9.794 153.980 975 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.99 % Allowed : 24.76 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.29), residues: 866 helix: 1.29 (0.26), residues: 385 sheet: -0.40 (0.46), residues: 132 loop : -0.57 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.011 0.001 TYR A 172 PHE 0.009 0.001 PHE A 267 TRP 0.018 0.002 TRP A 21 HIS 0.004 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 6988) covalent geometry : angle 0.66858 ( 9479) hydrogen bonds : bond 0.04291 ( 339) hydrogen bonds : angle 4.72438 ( 960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8940 (tm-30) REVERT: A 84 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7810 (ptt180) REVERT: A 96 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9064 (mmmm) REVERT: A 98 ASP cc_start: 0.8070 (p0) cc_final: 0.7737 (p0) REVERT: A 120 ASP cc_start: 0.9215 (t0) cc_final: 0.9008 (t0) REVERT: A 145 THR cc_start: 0.8619 (m) cc_final: 0.8339 (m) REVERT: A 233 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: A 268 MET cc_start: 0.8729 (mtt) cc_final: 0.8334 (mpp) REVERT: A 317 MET cc_start: 0.8923 (mmm) cc_final: 0.8531 (mmm) REVERT: A 386 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: A 398 MET cc_start: 0.8668 (mtt) cc_final: 0.8319 (mtp) REVERT: A 401 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8597 (tppt) REVERT: B 37 HIS cc_start: 0.7472 (p-80) cc_final: 0.7226 (p-80) REVERT: B 45 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: B 73 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.9002 (tmm) REVERT: B 122 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8374 (tptt) REVERT: B 198 GLU cc_start: 0.9104 (pt0) cc_final: 0.8864 (pt0) REVERT: B 200 MET cc_start: 0.8250 (mpp) cc_final: 0.7798 (mpp) REVERT: B 203 ASP cc_start: 0.8733 (t0) cc_final: 0.8435 (t0) REVERT: B 293 MET cc_start: 0.9333 (tmm) cc_final: 0.9032 (tmm) outliers start: 44 outliers final: 32 residues processed: 123 average time/residue: 0.0755 time to fit residues: 12.9919 Evaluate side-chains 128 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.052252 restraints weight = 24583.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.054115 restraints weight = 11901.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055440 restraints weight = 7140.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056350 restraints weight = 4794.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057049 restraints weight = 3525.082| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6988 Z= 0.203 Angle : 0.664 11.943 9479 Z= 0.324 Chirality : 0.045 0.228 1039 Planarity : 0.004 0.037 1235 Dihedral : 9.737 156.524 975 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.44 % Allowed : 25.17 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.29), residues: 866 helix: 1.32 (0.26), residues: 384 sheet: -0.32 (0.47), residues: 132 loop : -0.55 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.013 0.001 TYR A 172 PHE 0.010 0.001 PHE A 267 TRP 0.017 0.002 TRP A 21 HIS 0.004 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 6988) covalent geometry : angle 0.66367 ( 9479) hydrogen bonds : bond 0.04169 ( 339) hydrogen bonds : angle 4.72759 ( 960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8915 (tm-30) REVERT: A 76 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8587 (m-30) REVERT: A 84 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7793 (ptt180) REVERT: A 96 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9106 (mmmm) REVERT: A 98 ASP cc_start: 0.7967 (p0) cc_final: 0.7615 (p0) REVERT: A 120 ASP cc_start: 0.9233 (t0) cc_final: 0.9008 (t0) REVERT: A 145 THR cc_start: 0.8576 (m) cc_final: 0.8291 (m) REVERT: A 268 MET cc_start: 0.8561 (mtt) cc_final: 0.8236 (mpp) REVERT: A 317 MET cc_start: 0.8979 (mmm) cc_final: 0.8530 (mmm) REVERT: A 386 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8622 (pt0) REVERT: A 398 MET cc_start: 0.8685 (mtt) cc_final: 0.8442 (mtp) REVERT: A 401 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8559 (tppt) REVERT: B 37 HIS cc_start: 0.7449 (p-80) cc_final: 0.7121 (p-80) REVERT: B 45 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: B 73 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.9012 (tmm) REVERT: B 122 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8375 (tptt) REVERT: B 198 GLU cc_start: 0.9111 (pt0) cc_final: 0.8846 (pt0) REVERT: B 203 ASP cc_start: 0.8728 (t0) cc_final: 0.8305 (t0) REVERT: B 293 MET cc_start: 0.9337 (tmm) cc_final: 0.9046 (tmm) REVERT: B 307 HIS cc_start: 0.9185 (m90) cc_final: 0.8868 (m-70) outliers start: 40 outliers final: 30 residues processed: 120 average time/residue: 0.0672 time to fit residues: 11.4955 Evaluate side-chains 127 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.051232 restraints weight = 25024.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.053124 restraints weight = 12094.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054441 restraints weight = 7226.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055341 restraints weight = 4858.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.056053 restraints weight = 3585.248| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6988 Z= 0.229 Angle : 0.683 12.675 9479 Z= 0.336 Chirality : 0.045 0.231 1039 Planarity : 0.004 0.037 1235 Dihedral : 9.783 158.534 975 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.85 % Allowed : 25.17 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.29), residues: 866 helix: 1.22 (0.26), residues: 386 sheet: -0.37 (0.47), residues: 132 loop : -0.55 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.013 0.001 TYR A 172 PHE 0.009 0.001 PHE B 378 TRP 0.016 0.002 TRP A 21 HIS 0.004 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 6988) covalent geometry : angle 0.68266 ( 9479) hydrogen bonds : bond 0.04305 ( 339) hydrogen bonds : angle 4.77149 ( 960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.79 seconds wall clock time: 26 minutes 24.38 seconds (1584.38 seconds total)