Starting phenix.real_space_refine on Sun May 11 06:32:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u65_41944/05_2025/8u65_41944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u65_41944/05_2025/8u65_41944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u65_41944/05_2025/8u65_41944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u65_41944/05_2025/8u65_41944.map" model { file = "/net/cci-nas-00/data/ceres_data/8u65_41944/05_2025/8u65_41944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u65_41944/05_2025/8u65_41944.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4827 2.51 5 N 1325 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7636 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3785 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 458} Chain breaks: 2 Chain: "A" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3765 Classifications: {'peptide': 482} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 455} Chain breaks: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.20, per 1000 atoms: 0.94 Number of scatterers: 7636 At special positions: 0 Unit cell: (120.888, 80.811, 101.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1438 8.00 N 1325 7.00 C 4827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 379 " distance=2.02 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 909.6 milliseconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 45.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.608A pdb=" N VAL B 11 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 294 through 341 removed outlier: 3.564A pdb=" N SER B 341 " --> pdb=" O MET B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.541A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 358 " --> pdb=" O GLN B 354 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.978A pdb=" N ILE B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 393 " --> pdb=" O HIS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 4.033A pdb=" N ALA B 414 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 416 " --> pdb=" O GLU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.764A pdb=" N SER B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 480 Processing helix chain 'B' and resid 488 through 512 Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.544A pdb=" N ALA A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.785A pdb=" N VAL A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.559A pdb=" N LEU A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.163A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.717A pdb=" N GLY A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 294 through 341 removed outlier: 4.039A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 341 " --> pdb=" O MET A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.871A pdb=" N LEU A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 349' Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.822A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 389 through 394 removed outlier: 4.182A pdb=" N MET A 393 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 389 through 394' Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.710A pdb=" N SER A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.504A pdb=" N LEU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 removed outlier: 4.282A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 27 removed outlier: 3.695A pdb=" N GLN B 64 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.588A pdb=" N THR B 35 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL B 46 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU B 33 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU B 101 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 93 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 198 through 199 removed outlier: 6.061A pdb=" N VAL B 182 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG B 173 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 184 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 376 removed outlier: 3.735A pdb=" N GLY B 364 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 434 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.642A pdb=" N ILE A 27 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 228 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 231 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 46 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 42 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 35 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL A 46 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 33 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU A 101 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 199 removed outlier: 7.026A pdb=" N ILE A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU A 185 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 169 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A 273 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU A 282 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 271 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 284 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N MET A 269 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 377 removed outlier: 3.521A pdb=" N VAL A 365 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 425 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 423 " --> pdb=" O TRP A 437 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1409 1.32 - 1.45: 1884 1.45 - 1.57: 4422 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 7793 Sorted by residual: bond pdb=" C PRO B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.339 1.395 -0.056 3.40e-02 8.65e+02 2.69e+00 bond pdb=" CB ASN A 49 " pdb=" CG ASN A 49 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.91e-01 bond pdb=" CB LYS B 56 " pdb=" CG LYS B 56 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.29e-01 bond pdb=" CB GLU B 369 " pdb=" CG GLU B 369 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.34e-01 bond pdb=" CA ASN A 49 " pdb=" CB ASN A 49 " ideal model delta sigma weight residual 1.529 1.542 -0.014 1.64e-02 3.72e+03 6.88e-01 ... (remaining 7788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 10293 1.51 - 3.01: 234 3.01 - 4.52: 47 4.52 - 6.02: 14 6.02 - 7.53: 4 Bond angle restraints: 10592 Sorted by residual: angle pdb=" N VAL A 422 " pdb=" CA VAL A 422 " pdb=" C VAL A 422 " ideal model delta sigma weight residual 106.53 110.51 -3.98 1.41e+00 5.03e-01 7.97e+00 angle pdb=" CA LYS B 56 " pdb=" CB LYS B 56 " pdb=" CG LYS B 56 " ideal model delta sigma weight residual 114.10 119.47 -5.37 2.00e+00 2.50e-01 7.22e+00 angle pdb=" CA GLU B 381 " pdb=" CB GLU B 381 " pdb=" CG GLU B 381 " ideal model delta sigma weight residual 114.10 119.34 -5.24 2.00e+00 2.50e-01 6.88e+00 angle pdb=" CB MET B 263 " pdb=" CG MET B 263 " pdb=" SD MET B 263 " ideal model delta sigma weight residual 112.70 119.91 -7.21 3.00e+00 1.11e-01 5.77e+00 angle pdb=" CA GLN B 329 " pdb=" CB GLN B 329 " pdb=" CG GLN B 329 " ideal model delta sigma weight residual 114.10 118.85 -4.75 2.00e+00 2.50e-01 5.63e+00 ... (remaining 10587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.30: 3996 18.30 - 36.60: 527 36.60 - 54.89: 143 54.89 - 73.19: 49 73.19 - 91.49: 12 Dihedral angle restraints: 4727 sinusoidal: 1929 harmonic: 2798 Sorted by residual: dihedral pdb=" CB CYS B 375 " pdb=" SG CYS B 375 " pdb=" SG CYS B 379 " pdb=" CB CYS B 379 " ideal model delta sinusoidal sigma weight residual -86.00 -148.61 62.61 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CA GLY A 55 " pdb=" C GLY A 55 " pdb=" N LYS A 56 " pdb=" CA LYS A 56 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLU B 381 " pdb=" C GLU B 381 " pdb=" N PRO B 382 " pdb=" CA PRO B 382 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 809 0.033 - 0.067: 253 0.067 - 0.100: 89 0.100 - 0.134: 35 0.134 - 0.167: 3 Chirality restraints: 1189 Sorted by residual: chirality pdb=" CB VAL B 155 " pdb=" CA VAL B 155 " pdb=" CG1 VAL B 155 " pdb=" CG2 VAL B 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CG LEU A 331 " pdb=" CB LEU A 331 " pdb=" CD1 LEU A 331 " pdb=" CD2 LEU A 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CB VAL A 155 " pdb=" CA VAL A 155 " pdb=" CG1 VAL A 155 " pdb=" CG2 VAL A 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1186 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 429 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO A 430 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 188 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 189 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 57 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 58 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " -0.022 5.00e-02 4.00e+02 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 257 2.71 - 3.26: 7623 3.26 - 3.81: 12501 3.81 - 4.35: 15795 4.35 - 4.90: 25870 Nonbonded interactions: 62046 Sorted by model distance: nonbonded pdb=" O THR A 326 " pdb=" OG1 THR A 330 " model vdw 2.164 3.040 nonbonded pdb=" O GLY A 305 " pdb=" OG SER A 309 " model vdw 2.164 3.040 nonbonded pdb=" O THR B 326 " pdb=" OG1 THR B 330 " model vdw 2.176 3.040 nonbonded pdb=" O ILE A 160 " pdb=" OG1 THR A 164 " model vdw 2.206 3.040 nonbonded pdb=" O ILE B 160 " pdb=" OG1 THR B 164 " model vdw 2.218 3.040 ... (remaining 62041 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 120 or resid 135 through 512 or resid 900)) selection = (chain 'B' and (resid 2 through 120 or resid 135 through 342 or resid 345 throug \ h 512 or resid 900)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.250 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.160 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7796 Z= 0.151 Angle : 0.585 7.527 10594 Z= 0.299 Chirality : 0.041 0.167 1189 Planarity : 0.005 0.062 1377 Dihedral : 18.680 91.490 2908 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.36 % Allowed : 31.88 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.29), residues: 953 helix: 0.63 (0.28), residues: 375 sheet: -1.92 (0.44), residues: 131 loop : -0.79 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 391 HIS 0.004 0.001 HIS A 179 PHE 0.010 0.001 PHE A 102 TYR 0.017 0.001 TYR A 172 ARG 0.003 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.22099 ( 367) hydrogen bonds : angle 8.03843 ( 1047) SS BOND : bond 0.00753 ( 1) SS BOND : angle 1.29168 ( 2) covalent geometry : bond 0.00244 ( 7793) covalent geometry : angle 0.58475 (10592) Misc. bond : bond 0.06475 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8465 (mp) cc_final: 0.8126 (tt) outliers start: 3 outliers final: 2 residues processed: 160 average time/residue: 0.2120 time to fit residues: 44.9060 Evaluate side-chains 157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain A residue 374 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN A 302 GLN A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.180855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.162974 restraints weight = 11350.648| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.38 r_work: 0.4056 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7796 Z= 0.201 Angle : 0.626 6.846 10594 Z= 0.327 Chirality : 0.043 0.165 1189 Planarity : 0.005 0.051 1377 Dihedral : 7.386 82.575 1087 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.47 % Allowed : 27.29 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 953 helix: 0.39 (0.25), residues: 401 sheet: -1.81 (0.41), residues: 142 loop : -1.01 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 391 HIS 0.006 0.001 HIS B 30 PHE 0.012 0.002 PHE B 199 TYR 0.021 0.002 TYR A 172 ARG 0.003 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 367) hydrogen bonds : angle 5.71996 ( 1047) SS BOND : bond 0.00655 ( 1) SS BOND : angle 1.24685 ( 2) covalent geometry : bond 0.00433 ( 7793) covalent geometry : angle 0.62576 (10592) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: B 95 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6879 (mpp) REVERT: B 163 MET cc_start: 0.6241 (ptp) cc_final: 0.5900 (ptm) REVERT: B 332 GLN cc_start: 0.6579 (pp30) cc_final: 0.6222 (pp30) REVERT: A 304 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7644 (mt) outliers start: 37 outliers final: 19 residues processed: 186 average time/residue: 0.2046 time to fit residues: 50.8688 Evaluate side-chains 179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 56 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.180098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.162547 restraints weight = 11605.653| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.34 r_work: 0.4043 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7796 Z= 0.256 Angle : 0.656 6.828 10594 Z= 0.344 Chirality : 0.044 0.220 1189 Planarity : 0.005 0.051 1377 Dihedral : 7.573 77.953 1084 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.07 % Allowed : 27.42 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.27), residues: 953 helix: 0.21 (0.25), residues: 398 sheet: -1.89 (0.42), residues: 136 loop : -1.15 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 PHE 0.018 0.002 PHE B 199 TYR 0.016 0.002 TYR A 172 ARG 0.003 0.000 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 367) hydrogen bonds : angle 5.71897 ( 1047) SS BOND : bond 0.00809 ( 1) SS BOND : angle 0.51680 ( 2) covalent geometry : bond 0.00554 ( 7793) covalent geometry : angle 0.65612 (10592) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.754 Fit side-chains REVERT: B 10 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6987 (mm-30) REVERT: B 95 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6847 (mpp) REVERT: B 206 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: A 139 MET cc_start: 0.7739 (ptm) cc_final: 0.7489 (ptm) REVERT: A 172 TYR cc_start: 0.7703 (m-80) cc_final: 0.7270 (m-80) REVERT: A 304 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8076 (mt) REVERT: A 335 HIS cc_start: 0.6487 (OUTLIER) cc_final: 0.6145 (t70) outliers start: 42 outliers final: 22 residues processed: 184 average time/residue: 0.1937 time to fit residues: 48.0482 Evaluate side-chains 187 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.176203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.158693 restraints weight = 11514.074| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.33 r_work: 0.4054 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7796 Z= 0.208 Angle : 0.623 6.714 10594 Z= 0.325 Chirality : 0.043 0.216 1189 Planarity : 0.005 0.050 1377 Dihedral : 7.595 77.553 1084 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.19 % Allowed : 27.29 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.27), residues: 953 helix: 0.23 (0.25), residues: 405 sheet: -1.88 (0.41), residues: 139 loop : -1.20 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 PHE 0.014 0.002 PHE B 199 TYR 0.014 0.002 TYR B 259 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 367) hydrogen bonds : angle 5.52821 ( 1047) SS BOND : bond 0.00654 ( 1) SS BOND : angle 0.52684 ( 2) covalent geometry : bond 0.00453 ( 7793) covalent geometry : angle 0.62320 (10592) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.794 Fit side-chains REVERT: B 10 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 118 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.5996 (mt-10) REVERT: B 206 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6584 (mm-30) REVERT: A 338 MET cc_start: 0.6476 (mmm) cc_final: 0.6207 (mmm) outliers start: 43 outliers final: 23 residues processed: 191 average time/residue: 0.2049 time to fit residues: 52.2911 Evaluate side-chains 186 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 63 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.177889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.160230 restraints weight = 11482.856| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.34 r_work: 0.4072 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7796 Z= 0.170 Angle : 0.602 6.730 10594 Z= 0.314 Chirality : 0.043 0.221 1189 Planarity : 0.005 0.047 1377 Dihedral : 7.546 78.539 1084 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.43 % Allowed : 28.38 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.28), residues: 953 helix: 0.36 (0.25), residues: 413 sheet: -1.92 (0.40), residues: 148 loop : -1.14 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.012 0.002 PHE B 199 TYR 0.014 0.002 TYR A 172 ARG 0.007 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 367) hydrogen bonds : angle 5.33073 ( 1047) SS BOND : bond 0.00524 ( 1) SS BOND : angle 0.46526 ( 2) covalent geometry : bond 0.00372 ( 7793) covalent geometry : angle 0.60182 (10592) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.729 Fit side-chains REVERT: B 10 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 95 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6871 (mpp) REVERT: B 118 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5951 (mt-10) REVERT: B 206 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6533 (mm-30) REVERT: A 120 GLN cc_start: 0.5911 (OUTLIER) cc_final: 0.5669 (mm-40) REVERT: A 263 MET cc_start: 0.6582 (tmm) cc_final: 0.6214 (tmm) REVERT: A 335 HIS cc_start: 0.6364 (OUTLIER) cc_final: 0.5940 (t70) outliers start: 45 outliers final: 27 residues processed: 180 average time/residue: 0.1880 time to fit residues: 45.5184 Evaluate side-chains 181 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.0570 chunk 84 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 0.0270 chunk 56 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.1672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.185383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.168048 restraints weight = 11500.203| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.32 r_work: 0.4091 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7796 Z= 0.120 Angle : 0.582 6.651 10594 Z= 0.302 Chirality : 0.042 0.217 1189 Planarity : 0.005 0.048 1377 Dihedral : 7.359 80.775 1084 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.35 % Allowed : 29.59 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.28), residues: 953 helix: 0.64 (0.25), residues: 412 sheet: -1.83 (0.42), residues: 142 loop : -1.10 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS B 30 PHE 0.010 0.001 PHE A 102 TYR 0.014 0.001 TYR A 172 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 367) hydrogen bonds : angle 4.94534 ( 1047) SS BOND : bond 0.00356 ( 1) SS BOND : angle 0.47917 ( 2) covalent geometry : bond 0.00266 ( 7793) covalent geometry : angle 0.58166 (10592) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.840 Fit side-chains REVERT: A 263 MET cc_start: 0.6384 (tmm) cc_final: 0.5858 (tmm) REVERT: A 335 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.5956 (t70) REVERT: A 363 THR cc_start: 0.7793 (p) cc_final: 0.7524 (p) outliers start: 36 outliers final: 25 residues processed: 177 average time/residue: 0.2247 time to fit residues: 52.1663 Evaluate side-chains 173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 433 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 90 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 332 GLN A 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.181454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.163780 restraints weight = 11542.400| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.32 r_work: 0.4057 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7796 Z= 0.214 Angle : 0.661 7.173 10594 Z= 0.342 Chirality : 0.044 0.195 1189 Planarity : 0.005 0.046 1377 Dihedral : 7.578 78.814 1084 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.80 % Allowed : 27.66 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.27), residues: 953 helix: 0.35 (0.25), residues: 420 sheet: -1.66 (0.42), residues: 140 loop : -1.33 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 PHE 0.018 0.002 PHE B 199 TYR 0.026 0.002 TYR B 376 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 367) hydrogen bonds : angle 5.31505 ( 1047) SS BOND : bond 0.00957 ( 1) SS BOND : angle 2.01120 ( 2) covalent geometry : bond 0.00469 ( 7793) covalent geometry : angle 0.66019 (10592) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.883 Fit side-chains REVERT: B 10 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6999 (mm-30) REVERT: B 95 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6798 (mpp) REVERT: B 118 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5896 (mt-10) REVERT: B 120 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.4783 (mm-40) REVERT: A 120 GLN cc_start: 0.5889 (OUTLIER) cc_final: 0.5576 (mt0) REVERT: A 263 MET cc_start: 0.6617 (tmm) cc_final: 0.6093 (tmm) REVERT: A 284 SER cc_start: 0.7763 (p) cc_final: 0.7478 (p) REVERT: A 322 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7327 (mtm-85) REVERT: A 335 HIS cc_start: 0.6395 (OUTLIER) cc_final: 0.5970 (t70) REVERT: A 338 MET cc_start: 0.6435 (mmm) cc_final: 0.6091 (mmm) outliers start: 48 outliers final: 33 residues processed: 186 average time/residue: 0.1885 time to fit residues: 47.3356 Evaluate side-chains 187 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 0.0980 chunk 90 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 0.0010 chunk 48 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.179453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.161392 restraints weight = 11530.687| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.38 r_work: 0.4087 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7796 Z= 0.160 Angle : 0.652 12.552 10594 Z= 0.330 Chirality : 0.043 0.193 1189 Planarity : 0.005 0.048 1377 Dihedral : 7.521 79.183 1084 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.68 % Allowed : 28.50 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.28), residues: 953 helix: 0.39 (0.25), residues: 418 sheet: -1.86 (0.41), residues: 148 loop : -1.15 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.011 0.001 PHE B 199 TYR 0.017 0.002 TYR B 376 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 367) hydrogen bonds : angle 5.18579 ( 1047) SS BOND : bond 0.00792 ( 1) SS BOND : angle 2.01679 ( 2) covalent geometry : bond 0.00361 ( 7793) covalent geometry : angle 0.65107 (10592) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.816 Fit side-chains REVERT: B 118 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5848 (mt-10) REVERT: B 120 GLN cc_start: 0.5938 (OUTLIER) cc_final: 0.4786 (mm-40) REVERT: A 120 GLN cc_start: 0.5871 (OUTLIER) cc_final: 0.5649 (mm-40) REVERT: A 263 MET cc_start: 0.6567 (tmm) cc_final: 0.6120 (tmm) REVERT: A 284 SER cc_start: 0.7735 (p) cc_final: 0.7485 (p) REVERT: A 335 HIS cc_start: 0.6349 (OUTLIER) cc_final: 0.5924 (t70) REVERT: A 338 MET cc_start: 0.6510 (mmm) cc_final: 0.6160 (mmm) outliers start: 47 outliers final: 34 residues processed: 178 average time/residue: 0.2002 time to fit residues: 47.3111 Evaluate side-chains 183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 13 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 378 ASN A 433 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.179747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.161848 restraints weight = 11637.436| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.37 r_work: 0.4070 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7796 Z= 0.185 Angle : 0.663 9.384 10594 Z= 0.338 Chirality : 0.044 0.191 1189 Planarity : 0.005 0.053 1377 Dihedral : 7.578 78.565 1084 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.68 % Allowed : 28.14 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.28), residues: 953 helix: 0.35 (0.25), residues: 418 sheet: -1.88 (0.41), residues: 148 loop : -1.21 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 391 HIS 0.006 0.001 HIS B 30 PHE 0.014 0.002 PHE B 199 TYR 0.023 0.002 TYR B 376 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 367) hydrogen bonds : angle 5.25602 ( 1047) SS BOND : bond 0.00786 ( 1) SS BOND : angle 1.89238 ( 2) covalent geometry : bond 0.00410 ( 7793) covalent geometry : angle 0.66225 (10592) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.838 Fit side-chains REVERT: B 10 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 118 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5853 (mt-10) REVERT: B 120 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.4832 (mm-40) REVERT: A 120 GLN cc_start: 0.5887 (OUTLIER) cc_final: 0.5568 (mt0) REVERT: A 263 MET cc_start: 0.6620 (tmm) cc_final: 0.6176 (tmm) REVERT: A 335 HIS cc_start: 0.6348 (OUTLIER) cc_final: 0.5960 (t70) REVERT: A 338 MET cc_start: 0.6489 (mmm) cc_final: 0.6164 (mmm) outliers start: 47 outliers final: 35 residues processed: 180 average time/residue: 0.2031 time to fit residues: 48.5999 Evaluate side-chains 183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.0470 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.180113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.162145 restraints weight = 11613.048| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.38 r_work: 0.4064 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7796 Z= 0.194 Angle : 0.672 9.126 10594 Z= 0.344 Chirality : 0.044 0.197 1189 Planarity : 0.005 0.048 1377 Dihedral : 7.631 77.927 1084 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.95 % Allowed : 28.14 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.28), residues: 953 helix: 0.27 (0.25), residues: 422 sheet: -1.88 (0.41), residues: 148 loop : -1.28 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 391 HIS 0.007 0.001 HIS B 30 PHE 0.015 0.002 PHE B 199 TYR 0.022 0.002 TYR B 376 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 367) hydrogen bonds : angle 5.29253 ( 1047) SS BOND : bond 0.00780 ( 1) SS BOND : angle 1.91402 ( 2) covalent geometry : bond 0.00429 ( 7793) covalent geometry : angle 0.67133 (10592) Misc. bond : bond 0.00003 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.783 Fit side-chains REVERT: B 10 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7019 (mm-30) REVERT: B 95 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6821 (mpp) REVERT: B 118 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5899 (mt-10) REVERT: B 120 GLN cc_start: 0.6011 (OUTLIER) cc_final: 0.4865 (mm-40) REVERT: A 120 GLN cc_start: 0.5890 (OUTLIER) cc_final: 0.5577 (mt0) REVERT: A 263 MET cc_start: 0.6679 (tmm) cc_final: 0.6120 (tmm) REVERT: A 335 HIS cc_start: 0.6398 (OUTLIER) cc_final: 0.6049 (t70) REVERT: A 338 MET cc_start: 0.6506 (mmm) cc_final: 0.6197 (mmm) outliers start: 41 outliers final: 35 residues processed: 177 average time/residue: 0.2321 time to fit residues: 55.4951 Evaluate side-chains 185 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 335 HIS Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 441 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.0030 chunk 21 optimal weight: 0.0570 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.0070 chunk 12 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.184341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.166095 restraints weight = 11482.278| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.45 r_work: 0.4113 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7796 Z= 0.117 Angle : 0.616 8.531 10594 Z= 0.317 Chirality : 0.043 0.211 1189 Planarity : 0.005 0.046 1377 Dihedral : 7.405 82.026 1084 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.26 % Allowed : 29.95 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.28), residues: 953 helix: 0.54 (0.25), residues: 424 sheet: -1.59 (0.41), residues: 147 loop : -1.28 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 391 HIS 0.005 0.001 HIS A 179 PHE 0.010 0.001 PHE A 102 TYR 0.016 0.001 TYR B 376 ARG 0.004 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 367) hydrogen bonds : angle 4.75215 ( 1047) SS BOND : bond 0.00650 ( 1) SS BOND : angle 1.97379 ( 2) covalent geometry : bond 0.00261 ( 7793) covalent geometry : angle 0.61586 (10592) Misc. bond : bond 0.00022 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.39 seconds wall clock time: 71 minutes 51.04 seconds (4311.04 seconds total)