Starting phenix.real_space_refine on Tue Sep 24 08:58:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/09_2024/7x1r_32947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/09_2024/7x1r_32947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/09_2024/7x1r_32947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/09_2024/7x1r_32947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/09_2024/7x1r_32947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/09_2024/7x1r_32947.cif" } resolution = 3.9 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Au 2 10.57 5 P 4 5.49 5 S 38 5.16 5 C 4824 2.51 5 N 1298 2.21 5 O 1442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7608 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3750 Classifications: {'peptide': 485} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 465} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' AU': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1419 SG CYS A 189 73.629 62.408 61.033 1.00 28.54 S Restraints were copied for chains: B Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="AU AU A 502 " occ=0.30 residue: pdb="AU AU B 502 " occ=0.30 Time building chain proxies: 6.38, per 1000 atoms: 0.84 Number of scatterers: 7608 At special positions: 0 Unit cell: (116.8, 104, 76.8, 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) Au 2 78.96 S 38 16.00 P 4 15.00 O 1442 8.00 N 1298 7.00 C 4824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 64 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.679A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 removed outlier: 4.346A pdb=" N VAL A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 84 removed outlier: 4.127A pdb=" N ARG A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 123 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 180 through 184 removed outlier: 4.188A pdb=" N PHE A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 444 through 458 removed outlier: 4.208A pdb=" N GLY A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.679A pdb=" N TYR B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 removed outlier: 4.347A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 84 removed outlier: 4.127A pdb=" N ARG B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 123 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 180 through 184 removed outlier: 4.188A pdb=" N PHE B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 342 through 359 Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 444 through 458 removed outlier: 4.208A pdb=" N GLY B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 468 Processing helix chain 'B' and resid 474 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128 removed outlier: 7.235A pdb=" N MET A 39 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 15 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU A 41 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 17 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP A 14 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU A 158 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 16 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 135 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 removed outlier: 7.235A pdb=" N MET A 39 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 15 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU A 41 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 17 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP A 14 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU A 158 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 16 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N TYR A 330 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE A 157 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.828A pdb=" N ILE A 178 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 260 removed outlier: 5.997A pdb=" N GLN A 272 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 266 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 374 removed outlier: 5.929A pdb=" N VAL A 435 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN A 428 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 128 removed outlier: 7.235A pdb=" N MET B 39 " --> pdb=" O TYR B 13 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 15 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 41 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 17 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 14 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 158 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 16 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 135 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 128 removed outlier: 7.235A pdb=" N MET B 39 " --> pdb=" O TYR B 13 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 15 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 41 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 17 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 14 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 158 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 16 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N TYR B 330 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE B 157 " --> pdb=" O TYR B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.829A pdb=" N ILE B 178 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 260 removed outlier: 5.997A pdb=" N GLN B 272 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG B 266 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 374 removed outlier: 5.929A pdb=" N VAL B 435 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN B 428 " --> pdb=" O VAL B 435 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 948 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: 2.39 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2486 1.35 - 1.47: 1858 1.47 - 1.60: 3368 1.60 - 1.72: 0 1.72 - 1.85: 52 Bond restraints: 7764 Sorted by residual: bond pdb=" O3P FAD B 501 " pdb=" P FAD B 501 " ideal model delta sigma weight residual 1.660 1.559 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.559 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5B FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sigma weight residual 1.634 1.557 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" O5B FAD B 501 " pdb=" PA FAD B 501 " ideal model delta sigma weight residual 1.634 1.557 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O5' FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.637 1.573 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 7759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10120 1.67 - 3.33: 354 3.33 - 5.00: 33 5.00 - 6.66: 21 6.66 - 8.33: 4 Bond angle restraints: 10532 Sorted by residual: angle pdb=" N VAL A 305 " pdb=" CA VAL A 305 " pdb=" C VAL A 305 " ideal model delta sigma weight residual 113.47 109.63 3.84 1.01e+00 9.80e-01 1.45e+01 angle pdb=" N VAL B 305 " pdb=" CA VAL B 305 " pdb=" C VAL B 305 " ideal model delta sigma weight residual 113.47 109.63 3.84 1.01e+00 9.80e-01 1.45e+01 angle pdb=" C GLY A 207 " pdb=" N PHE A 208 " pdb=" CA PHE A 208 " ideal model delta sigma weight residual 121.14 115.43 5.71 1.75e+00 3.27e-01 1.06e+01 angle pdb=" C GLY B 207 " pdb=" N PHE B 208 " pdb=" CA PHE B 208 " ideal model delta sigma weight residual 121.14 115.45 5.69 1.75e+00 3.27e-01 1.06e+01 angle pdb=" C ARG B 221 " pdb=" N SER B 222 " pdb=" CA SER B 222 " ideal model delta sigma weight residual 122.17 117.21 4.96 1.54e+00 4.22e-01 1.04e+01 ... (remaining 10527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4240 17.52 - 35.03: 327 35.03 - 52.55: 65 52.55 - 70.06: 16 70.06 - 87.58: 15 Dihedral angle restraints: 4663 sinusoidal: 1909 harmonic: 2754 Sorted by residual: dihedral pdb=" CA CYS A 59 " pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 64 " ideal model delta sinusoidal sigma weight residual -73.00 1.60 -74.60 1 2.00e+01 2.50e-03 1.76e+01 dihedral pdb=" CA ALA B 160 " pdb=" C ALA B 160 " pdb=" N THR B 161 " pdb=" CA THR B 161 " ideal model delta harmonic sigma weight residual 180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ALA A 160 " pdb=" C ALA A 160 " pdb=" N THR A 161 " pdb=" CA THR A 161 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 653 0.034 - 0.068: 317 0.068 - 0.102: 141 0.102 - 0.136: 54 0.136 - 0.169: 9 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CA PHE B 208 " pdb=" N PHE B 208 " pdb=" C PHE B 208 " pdb=" CB PHE B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA PHE A 208 " pdb=" N PHE A 208 " pdb=" C PHE A 208 " pdb=" CB PHE A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" C2B FAD B 501 " pdb=" C1B FAD B 501 " pdb=" C3B FAD B 501 " pdb=" O2B FAD B 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1171 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 170 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 171 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 171 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 171 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 170 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 171 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 208 " 0.011 2.00e-02 2.50e+03 9.59e-03 1.61e+00 pdb=" CG PHE B 208 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 208 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 208 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 208 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 208 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 208 " 0.002 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 67 2.61 - 3.18: 6725 3.18 - 3.75: 11359 3.75 - 4.33: 16219 4.33 - 4.90: 26855 Nonbonded interactions: 61225 Sorted by model distance: nonbonded pdb=" SG CYS B 59 " pdb=" SG CYS B 64 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS B 189 " pdb="AU AU B 502 " model vdw 2.205 2.980 nonbonded pdb=" SG CYS A 189 " pdb="AU AU A 502 " model vdw 2.205 2.980 nonbonded pdb=" O LEU A 55 " pdb=" ND2 ASN A 113 " model vdw 2.207 3.120 nonbonded pdb=" O LEU B 55 " pdb=" ND2 ASN B 113 " model vdw 2.207 3.120 ... (remaining 61220 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' selection = chain 'B' } 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=0.30 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.710 Find NCS groups from input model: 0.210 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 0.101 7764 Z= 0.470 Angle : 0.755 8.330 10532 Z= 0.413 Chirality : 0.049 0.169 1174 Planarity : 0.004 0.032 1336 Dihedral : 14.250 87.578 2916 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.25 % Allowed : 7.02 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.91 (0.24), residues: 966 helix: 0.38 (0.27), residues: 290 sheet: -0.35 (0.32), residues: 264 loop : -1.43 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 53 HIS 0.005 0.002 HIS A 71 PHE 0.022 0.003 PHE B 208 TYR 0.015 0.002 TYR B 200 ARG 0.003 0.001 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 0.881 Fit side-chains REVERT: A 25 LEU cc_start: 0.9074 (mt) cc_final: 0.8771 (mt) REVERT: A 30 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6698 (mm-30) REVERT: A 81 GLN cc_start: 0.8038 (tt0) cc_final: 0.7754 (tt0) REVERT: A 85 ASN cc_start: 0.8588 (m110) cc_final: 0.8295 (m-40) REVERT: A 139 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7828 (mtp85) REVERT: A 140 ILE cc_start: 0.8785 (pt) cc_final: 0.8420 (pt) REVERT: A 222 SER cc_start: 0.8721 (p) cc_final: 0.8229 (t) REVERT: A 308 LYS cc_start: 0.7830 (mttp) cc_final: 0.7463 (tttm) REVERT: A 353 LEU cc_start: 0.9041 (tp) cc_final: 0.8723 (tp) REVERT: A 396 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 397 GLU cc_start: 0.7205 (pt0) cc_final: 0.6688 (mt-10) REVERT: A 450 GLN cc_start: 0.8877 (tp40) cc_final: 0.8558 (tp-100) REVERT: B 44 VAL cc_start: 0.8996 (p) cc_final: 0.8793 (m) REVERT: B 85 ASN cc_start: 0.8554 (m110) cc_final: 0.8342 (m-40) REVERT: B 93 THR cc_start: 0.8339 (t) cc_final: 0.8067 (p) REVERT: B 192 LYS cc_start: 0.7898 (tttt) cc_final: 0.7447 (ttmm) REVERT: B 222 SER cc_start: 0.8527 (p) cc_final: 0.8124 (t) REVERT: B 252 VAL cc_start: 0.9111 (p) cc_final: 0.8899 (m) REVERT: B 308 LYS cc_start: 0.7904 (mttp) cc_final: 0.7443 (tttm) REVERT: B 396 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 397 GLU cc_start: 0.7094 (pt0) cc_final: 0.6768 (mt-10) REVERT: B 425 ILE cc_start: 0.8846 (pt) cc_final: 0.8392 (mt) REVERT: B 450 GLN cc_start: 0.8890 (tp40) cc_final: 0.8554 (tp-100) outliers start: 2 outliers final: 2 residues processed: 276 average time/residue: 0.2301 time to fit residues: 81.5177 Evaluate side-chains 187 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.1980 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.0030 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A 472 HIS B 113 ASN B 144 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7764 Z= 0.206 Angle : 0.562 5.673 10532 Z= 0.301 Chirality : 0.046 0.152 1174 Planarity : 0.004 0.051 1336 Dihedral : 6.429 45.804 1148 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.75 % Allowed : 14.79 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.23 (0.26), residues: 966 helix: 1.91 (0.29), residues: 294 sheet: 0.08 (0.33), residues: 256 loop : -1.08 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 98 HIS 0.006 0.002 HIS B 96 PHE 0.026 0.002 PHE B 208 TYR 0.014 0.002 TYR B 13 ARG 0.005 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 0.948 Fit side-chains REVERT: A 25 LEU cc_start: 0.9019 (mt) cc_final: 0.8698 (mt) REVERT: A 44 VAL cc_start: 0.8896 (p) cc_final: 0.8694 (m) REVERT: A 157 PHE cc_start: 0.8534 (m-80) cc_final: 0.8329 (m-10) REVERT: A 222 SER cc_start: 0.8702 (p) cc_final: 0.8256 (t) REVERT: A 308 LYS cc_start: 0.7902 (mttp) cc_final: 0.7456 (tttm) REVERT: A 397 GLU cc_start: 0.7359 (pt0) cc_final: 0.6736 (mt-10) REVERT: A 450 GLN cc_start: 0.8722 (tp40) cc_final: 0.8473 (tp-100) REVERT: A 479 PHE cc_start: 0.8663 (m-80) cc_final: 0.8392 (m-80) REVERT: B 29 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7626 (mttt) REVERT: B 44 VAL cc_start: 0.9127 (p) cc_final: 0.8876 (m) REVERT: B 93 THR cc_start: 0.8423 (t) cc_final: 0.8218 (p) REVERT: B 139 ARG cc_start: 0.8301 (mtm110) cc_final: 0.7746 (mtp85) REVERT: B 150 LYS cc_start: 0.8154 (mtmt) cc_final: 0.7886 (mtmt) REVERT: B 157 PHE cc_start: 0.8466 (m-80) cc_final: 0.8239 (m-10) REVERT: B 192 LYS cc_start: 0.7897 (tttt) cc_final: 0.7545 (ttmm) REVERT: B 222 SER cc_start: 0.8510 (p) cc_final: 0.8127 (t) REVERT: B 252 VAL cc_start: 0.8880 (p) cc_final: 0.8651 (m) REVERT: B 308 LYS cc_start: 0.7857 (mttp) cc_final: 0.7428 (tttm) REVERT: B 386 SER cc_start: 0.8671 (t) cc_final: 0.8255 (p) REVERT: B 450 GLN cc_start: 0.8732 (tp40) cc_final: 0.8370 (tp-100) outliers start: 14 outliers final: 9 residues processed: 216 average time/residue: 0.1854 time to fit residues: 54.4848 Evaluate side-chains 193 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 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 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 7764 Z= 0.518 Angle : 0.760 5.886 10532 Z= 0.398 Chirality : 0.052 0.159 1174 Planarity : 0.005 0.042 1336 Dihedral : 7.339 50.794 1148 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.51 % Allowed : 17.92 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.08 (0.26), residues: 966 helix: 1.85 (0.30), residues: 282 sheet: -0.14 (0.32), residues: 258 loop : -1.32 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 53 HIS 0.008 0.003 HIS B 138 PHE 0.021 0.003 PHE B 184 TYR 0.015 0.002 TYR A 358 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 time to evaluate : 0.907 Fit side-chains REVERT: A 49 LEU cc_start: 0.8729 (mp) cc_final: 0.8518 (mp) REVERT: A 163 GLU cc_start: 0.7772 (pt0) cc_final: 0.7407 (pm20) REVERT: A 205 CYS cc_start: 0.7817 (m) cc_final: 0.7440 (m) REVERT: A 222 SER cc_start: 0.9038 (p) cc_final: 0.8623 (t) REVERT: A 308 LYS cc_start: 0.8152 (mttp) cc_final: 0.7568 (tttm) REVERT: A 397 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: B 29 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7543 (mttt) REVERT: B 163 GLU cc_start: 0.7719 (pt0) cc_final: 0.7360 (pm20) REVERT: B 205 CYS cc_start: 0.7840 (m) cc_final: 0.7485 (m) REVERT: B 222 SER cc_start: 0.9051 (p) cc_final: 0.8629 (t) REVERT: B 252 VAL cc_start: 0.8792 (p) cc_final: 0.8521 (m) REVERT: B 289 LEU cc_start: 0.9061 (mt) cc_final: 0.8691 (mp) REVERT: B 308 LYS cc_start: 0.8150 (mttp) cc_final: 0.7564 (tttm) REVERT: B 397 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7203 (mt-10) outliers start: 44 outliers final: 35 residues processed: 210 average time/residue: 0.1745 time to fit residues: 50.6097 Evaluate side-chains 201 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 328 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.0010 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 0.0050 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN B 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7764 Z= 0.179 Angle : 0.541 5.797 10532 Z= 0.289 Chirality : 0.045 0.149 1174 Planarity : 0.004 0.034 1336 Dihedral : 6.395 47.558 1148 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.88 % Allowed : 21.55 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.48 (0.26), residues: 966 helix: 2.50 (0.31), residues: 280 sheet: -0.05 (0.32), residues: 254 loop : -0.93 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 407 HIS 0.007 0.002 HIS B 96 PHE 0.025 0.002 PHE B 208 TYR 0.017 0.001 TYR A 13 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 0.896 Fit side-chains REVERT: A 49 LEU cc_start: 0.8674 (mp) cc_final: 0.8282 (mp) REVERT: A 163 GLU cc_start: 0.7507 (pt0) cc_final: 0.7149 (pm20) REVERT: A 222 SER cc_start: 0.8958 (p) cc_final: 0.8675 (t) REVERT: A 308 LYS cc_start: 0.8134 (mttp) cc_final: 0.7522 (tttm) REVERT: A 334 ASP cc_start: 0.7425 (p0) cc_final: 0.6873 (p0) REVERT: A 397 GLU cc_start: 0.7537 (pt0) cc_final: 0.7205 (mt-10) REVERT: A 403 HIS cc_start: 0.8341 (p90) cc_final: 0.8098 (p90) REVERT: A 479 PHE cc_start: 0.8640 (m-80) cc_final: 0.8078 (m-80) REVERT: B 29 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7795 (mttt) REVERT: B 70 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6892 (mtp) REVERT: B 76 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 103 GLU cc_start: 0.8136 (tp30) cc_final: 0.7885 (tp30) REVERT: B 139 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7654 (mtp85) REVERT: B 222 SER cc_start: 0.9024 (p) cc_final: 0.8717 (t) REVERT: B 252 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8277 (m) REVERT: B 289 LEU cc_start: 0.9006 (mt) cc_final: 0.8538 (mp) REVERT: B 334 ASP cc_start: 0.7468 (p0) cc_final: 0.6970 (p0) REVERT: B 353 LEU cc_start: 0.8919 (tp) cc_final: 0.8694 (tp) REVERT: B 397 GLU cc_start: 0.7502 (pt0) cc_final: 0.7250 (mt-10) REVERT: B 403 HIS cc_start: 0.8395 (p90) cc_final: 0.8095 (p90) outliers start: 31 outliers final: 23 residues processed: 218 average time/residue: 0.1776 time to fit residues: 53.4618 Evaluate side-chains 207 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 69 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 0.0070 overall best weight: 1.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 243 HIS A 250 GLN A 444 ASN B 129 ASN B 243 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7764 Z= 0.210 Angle : 0.553 6.679 10532 Z= 0.292 Chirality : 0.045 0.147 1174 Planarity : 0.004 0.032 1336 Dihedral : 6.317 47.637 1148 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.64 % Allowed : 22.68 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.58 (0.26), residues: 966 helix: 2.51 (0.31), residues: 280 sheet: 0.13 (0.33), residues: 244 loop : -0.87 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 88 HIS 0.013 0.002 HIS B 243 PHE 0.025 0.002 PHE B 208 TYR 0.013 0.001 TYR A 13 ARG 0.006 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 0.870 Fit side-chains REVERT: A 37 LYS cc_start: 0.8087 (tptt) cc_final: 0.7816 (mtpp) REVERT: A 81 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: A 163 GLU cc_start: 0.7493 (pt0) cc_final: 0.7213 (pm20) REVERT: A 222 SER cc_start: 0.9043 (p) cc_final: 0.8758 (t) REVERT: A 243 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.6867 (t70) REVERT: A 308 LYS cc_start: 0.8158 (mttp) cc_final: 0.7679 (tmtt) REVERT: A 334 ASP cc_start: 0.7486 (p0) cc_final: 0.7073 (p0) REVERT: A 403 HIS cc_start: 0.8394 (p90) cc_final: 0.8066 (p90) REVERT: A 479 PHE cc_start: 0.8638 (m-80) cc_final: 0.8159 (m-80) REVERT: B 29 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7441 (mttt) REVERT: B 76 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 139 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7692 (mtp85) REVERT: B 150 LYS cc_start: 0.8044 (mttt) cc_final: 0.7706 (tptt) REVERT: B 205 CYS cc_start: 0.7879 (m) cc_final: 0.7362 (m) REVERT: B 222 SER cc_start: 0.9083 (p) cc_final: 0.8752 (t) REVERT: B 289 LEU cc_start: 0.8979 (mt) cc_final: 0.8648 (mp) REVERT: B 353 LEU cc_start: 0.8968 (tp) cc_final: 0.8748 (tp) REVERT: B 397 GLU cc_start: 0.7511 (pt0) cc_final: 0.7272 (mt-10) REVERT: B 425 ILE cc_start: 0.8556 (pt) cc_final: 0.8253 (mt) outliers start: 37 outliers final: 26 residues processed: 215 average time/residue: 0.1884 time to fit residues: 56.2929 Evaluate side-chains 210 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7764 Z= 0.238 Angle : 0.567 7.086 10532 Z= 0.298 Chirality : 0.046 0.156 1174 Planarity : 0.004 0.033 1336 Dihedral : 6.326 47.439 1148 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.26 % Allowed : 23.06 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.47 (0.27), residues: 966 helix: 2.38 (0.31), residues: 284 sheet: 0.04 (0.33), residues: 244 loop : -0.93 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 88 HIS 0.008 0.002 HIS A 243 PHE 0.027 0.002 PHE A 208 TYR 0.016 0.001 TYR B 284 ARG 0.007 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 193 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9292 (mp) cc_final: 0.8981 (mm) REVERT: A 81 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: A 139 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7550 (mtp85) REVERT: A 149 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6179 (tm-30) REVERT: A 163 GLU cc_start: 0.7606 (pt0) cc_final: 0.7330 (pm20) REVERT: A 205 CYS cc_start: 0.8163 (m) cc_final: 0.7768 (m) REVERT: A 222 SER cc_start: 0.9102 (p) cc_final: 0.8806 (t) REVERT: A 308 LYS cc_start: 0.8086 (mttp) cc_final: 0.7573 (tmtt) REVERT: A 334 ASP cc_start: 0.7522 (p0) cc_final: 0.7200 (p0) REVERT: A 479 PHE cc_start: 0.8670 (m-80) cc_final: 0.8253 (m-80) REVERT: B 29 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7464 (mttt) REVERT: B 76 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8501 (mp) REVERT: B 81 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: B 139 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7682 (mtp85) REVERT: B 222 SER cc_start: 0.9134 (p) cc_final: 0.8820 (t) REVERT: B 308 LYS cc_start: 0.8215 (mttp) cc_final: 0.7626 (tmtt) REVERT: B 425 ILE cc_start: 0.8563 (pt) cc_final: 0.8275 (mt) outliers start: 42 outliers final: 34 residues processed: 223 average time/residue: 0.1722 time to fit residues: 53.6207 Evaluate side-chains 223 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.0050 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7764 Z= 0.166 Angle : 0.546 10.212 10532 Z= 0.284 Chirality : 0.045 0.172 1174 Planarity : 0.003 0.033 1336 Dihedral : 6.062 46.573 1148 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.51 % Allowed : 23.93 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 966 helix: 2.57 (0.31), residues: 284 sheet: 0.13 (0.33), residues: 244 loop : -0.81 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 88 HIS 0.005 0.001 HIS B 96 PHE 0.028 0.002 PHE A 208 TYR 0.012 0.001 TYR B 284 ARG 0.007 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 0.875 Fit side-chains REVERT: A 64 CYS cc_start: 0.6577 (m) cc_final: 0.6266 (m) REVERT: A 67 LYS cc_start: 0.9092 (tmmt) cc_final: 0.8874 (ttpt) REVERT: A 76 LEU cc_start: 0.9192 (mp) cc_final: 0.8832 (mm) REVERT: A 86 TYR cc_start: 0.8743 (m-80) cc_final: 0.8482 (m-80) REVERT: A 139 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7520 (mtp85) REVERT: A 163 GLU cc_start: 0.7464 (pt0) cc_final: 0.7104 (pm20) REVERT: A 192 LYS cc_start: 0.8066 (tttt) cc_final: 0.7817 (ttmm) REVERT: A 205 CYS cc_start: 0.7834 (m) cc_final: 0.7254 (m) REVERT: A 221 ARG cc_start: 0.8415 (ttm110) cc_final: 0.8184 (ttm110) REVERT: A 222 SER cc_start: 0.9153 (p) cc_final: 0.8874 (t) REVERT: A 308 LYS cc_start: 0.8101 (mttp) cc_final: 0.7564 (tmtt) REVERT: A 479 PHE cc_start: 0.8458 (m-80) cc_final: 0.8014 (m-80) REVERT: B 76 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 139 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7620 (mtp85) REVERT: B 222 SER cc_start: 0.9168 (p) cc_final: 0.8914 (t) REVERT: B 279 ILE cc_start: 0.8767 (mm) cc_final: 0.8563 (tp) REVERT: B 280 ILE cc_start: 0.7017 (pt) cc_final: 0.6549 (tt) REVERT: B 308 LYS cc_start: 0.8200 (mttp) cc_final: 0.7588 (tmtt) REVERT: B 403 HIS cc_start: 0.8372 (p90) cc_final: 0.8042 (p90) REVERT: B 425 ILE cc_start: 0.8545 (pt) cc_final: 0.8252 (mt) outliers start: 36 outliers final: 29 residues processed: 240 average time/residue: 0.1961 time to fit residues: 64.5980 Evaluate side-chains 226 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7764 Z= 0.180 Angle : 0.567 12.130 10532 Z= 0.291 Chirality : 0.045 0.151 1174 Planarity : 0.004 0.040 1336 Dihedral : 5.974 46.990 1148 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.14 % Allowed : 25.31 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.66 (0.27), residues: 966 helix: 2.53 (0.31), residues: 284 sheet: 0.32 (0.34), residues: 232 loop : -0.88 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 88 HIS 0.006 0.001 HIS B 96 PHE 0.026 0.002 PHE B 208 TYR 0.012 0.001 TYR A 358 ARG 0.009 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9159 (mp) cc_final: 0.8826 (mm) REVERT: A 86 TYR cc_start: 0.8762 (m-80) cc_final: 0.8465 (m-80) REVERT: A 163 GLU cc_start: 0.7485 (pt0) cc_final: 0.7141 (pm20) REVERT: A 205 CYS cc_start: 0.8031 (m) cc_final: 0.7459 (m) REVERT: A 222 SER cc_start: 0.9021 (p) cc_final: 0.8768 (t) REVERT: A 308 LYS cc_start: 0.8100 (mttp) cc_final: 0.7539 (tmtt) REVERT: A 362 THR cc_start: 0.7741 (m) cc_final: 0.7268 (t) REVERT: A 479 PHE cc_start: 0.8438 (m-80) cc_final: 0.8180 (m-80) REVERT: B 76 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8516 (mp) REVERT: B 139 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7590 (mtp85) REVERT: B 279 ILE cc_start: 0.8819 (mm) cc_final: 0.8549 (tp) REVERT: B 280 ILE cc_start: 0.7085 (pt) cc_final: 0.6550 (tt) REVERT: B 308 LYS cc_start: 0.8218 (mttp) cc_final: 0.7554 (tmtt) REVERT: B 425 ILE cc_start: 0.8500 (pt) cc_final: 0.8265 (mt) outliers start: 41 outliers final: 32 residues processed: 232 average time/residue: 0.1808 time to fit residues: 57.8440 Evaluate side-chains 228 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN B 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7764 Z= 0.204 Angle : 0.588 11.363 10532 Z= 0.300 Chirality : 0.046 0.155 1174 Planarity : 0.004 0.049 1336 Dihedral : 6.008 47.662 1148 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.64 % Allowed : 26.44 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 966 helix: 2.53 (0.31), residues: 284 sheet: 0.10 (0.33), residues: 244 loop : -0.76 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 407 HIS 0.006 0.001 HIS B 96 PHE 0.026 0.002 PHE A 208 TYR 0.020 0.001 TYR A 358 ARG 0.010 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8911 (ppp) cc_final: 0.8671 (ppp) REVERT: A 67 LYS cc_start: 0.9122 (tmmt) cc_final: 0.8851 (tttt) REVERT: A 76 LEU cc_start: 0.9209 (mp) cc_final: 0.8936 (mm) REVERT: A 222 SER cc_start: 0.8928 (p) cc_final: 0.8715 (t) REVERT: A 308 LYS cc_start: 0.8114 (mttp) cc_final: 0.7540 (tmtt) REVERT: A 362 THR cc_start: 0.7525 (m) cc_final: 0.6937 (t) REVERT: A 479 PHE cc_start: 0.8473 (m-80) cc_final: 0.8237 (m-80) REVERT: B 55 LEU cc_start: 0.8690 (tt) cc_final: 0.8453 (tt) REVERT: B 76 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 86 TYR cc_start: 0.8800 (m-80) cc_final: 0.8581 (m-80) REVERT: B 139 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7598 (mtp85) REVERT: B 205 CYS cc_start: 0.7988 (m) cc_final: 0.7475 (m) REVERT: B 280 ILE cc_start: 0.7122 (pt) cc_final: 0.6505 (tt) REVERT: B 308 LYS cc_start: 0.8225 (mttp) cc_final: 0.7552 (tmtt) REVERT: B 403 HIS cc_start: 0.8339 (p90) cc_final: 0.7999 (p90) REVERT: B 425 ILE cc_start: 0.8548 (pt) cc_final: 0.8280 (mt) outliers start: 37 outliers final: 35 residues processed: 220 average time/residue: 0.1795 time to fit residues: 55.3578 Evaluate side-chains 228 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 0.0270 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7764 Z= 0.182 Angle : 0.592 11.984 10532 Z= 0.305 Chirality : 0.046 0.154 1174 Planarity : 0.004 0.055 1336 Dihedral : 5.937 47.326 1148 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.64 % Allowed : 26.44 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 966 helix: 2.53 (0.31), residues: 284 sheet: 0.14 (0.33), residues: 244 loop : -0.73 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 407 HIS 0.007 0.001 HIS B 96 PHE 0.028 0.002 PHE B 208 TYR 0.018 0.001 TYR A 358 ARG 0.011 0.000 ARG B 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 206 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8922 (ppp) cc_final: 0.8706 (ppp) REVERT: A 64 CYS cc_start: 0.6387 (m) cc_final: 0.6013 (m) REVERT: A 67 LYS cc_start: 0.9095 (tmmt) cc_final: 0.8866 (tttt) REVERT: A 76 LEU cc_start: 0.9279 (mp) cc_final: 0.8952 (mm) REVERT: A 308 LYS cc_start: 0.8114 (mttp) cc_final: 0.7526 (tmtt) REVERT: A 362 THR cc_start: 0.7458 (m) cc_final: 0.6974 (t) REVERT: B 55 LEU cc_start: 0.8695 (tt) cc_final: 0.8401 (tt) REVERT: B 61 ASN cc_start: 0.8638 (m-40) cc_final: 0.8139 (m-40) REVERT: B 76 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8669 (mp) REVERT: B 139 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7587 (mtp85) REVERT: B 280 ILE cc_start: 0.7039 (pt) cc_final: 0.6509 (tt) REVERT: B 308 LYS cc_start: 0.8222 (mttp) cc_final: 0.7529 (tmtt) REVERT: B 362 THR cc_start: 0.7539 (m) cc_final: 0.7023 (t) REVERT: B 403 HIS cc_start: 0.8400 (p90) cc_final: 0.8106 (p90) REVERT: B 425 ILE cc_start: 0.8534 (pt) cc_final: 0.8269 (mt) outliers start: 37 outliers final: 33 residues processed: 228 average time/residue: 0.2081 time to fit residues: 64.9778 Evaluate side-chains 228 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS ** B 403 HIS ** 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 = 0.3391 r_free = 0.3391 target = 0.136222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.118750 restraints weight = 9085.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.118707 restraints weight = 8761.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.119081 restraints weight = 8280.123| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7764 Z= 0.290 Angle : 0.640 10.072 10532 Z= 0.332 Chirality : 0.047 0.158 1174 Planarity : 0.004 0.055 1336 Dihedral : 6.257 48.153 1148 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.39 % Allowed : 26.69 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.48 (0.27), residues: 966 helix: 2.37 (0.31), residues: 284 sheet: -0.02 (0.33), residues: 240 loop : -0.86 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.005 0.001 HIS B 96 PHE 0.024 0.002 PHE A 208 TYR 0.020 0.002 TYR A 358 ARG 0.010 0.000 ARG A 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.16 seconds wall clock time: 34 minutes 18.92 seconds (2058.92 seconds total)