Starting phenix.real_space_refine on Sun May 3 14:37:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11mt_75845/05_2026/11mt_75845.cif Found real_map, /net/cci-nas-00/data/ceres_data/11mt_75845/05_2026/11mt_75845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11mt_75845/05_2026/11mt_75845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11mt_75845/05_2026/11mt_75845.map" model { file = "/net/cci-nas-00/data/ceres_data/11mt_75845/05_2026/11mt_75845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11mt_75845/05_2026/11mt_75845.cif" } resolution = 2.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 54 5.16 5 C 7182 2.51 5 N 2067 2.21 5 O 4217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13520 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "A" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 644 Classifications: {'water': 644} Link IDs: {None: 643} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 653 Classifications: {'water': 653} Link IDs: {None: 652} Chain: "C" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 670 Classifications: {'water': 670} Link IDs: {None: 669} Time building chain proxies: 3.69, per 1000 atoms: 0.27 Number of scatterers: 13520 At special positions: 0 Unit cell: (88.2, 83.79, 149.94, 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 54 16.00 O 4217 8.00 N 2067 7.00 C 7182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 482 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 293 " distance=2.07 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 293 " distance=2.07 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 293 " distance=2.07 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 297 " - pdb=" SG CYS C 321 " 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=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 517.9 milliseconds 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 26.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.561A pdb=" N ASP A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 96 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 420 through 472 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.657A pdb=" N ASP B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 96 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.527A pdb=" N THR B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 472 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.557A pdb=" N ASP C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY C 94 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 383 through 399 Processing helix chain 'C' and resid 420 through 472 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 507 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 4.753A pdb=" N TYR A 367 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.217A pdb=" N ILE A 67 " --> pdb=" O GLY A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 74 through 76 removed outlier: 6.806A pdb=" N LEU A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE A 103 " --> pdb=" O MET A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 117 removed outlier: 5.024A pdb=" N ILE A 195 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY A 272 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 116 through 117 removed outlier: 7.491A pdb=" N ILE A 195 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'A' and resid 152 through 156 removed outlier: 4.662A pdb=" N CYS A 155 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 185 Processing sheet with id=AB3, first strand: chain 'A' and resid 302 through 304 removed outlier: 4.172A pdb=" N CYS A 297 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 321 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 405 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 377 through 381 Processing sheet with id=AB5, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AB6, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AB7, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AB8, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.236A pdb=" N ILE B 67 " --> pdb=" O GLY B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 74 through 76 removed outlier: 6.800A pdb=" N LEU B 75 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 117 removed outlier: 5.022A pdb=" N ILE B 195 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY B 272 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 117 removed outlier: 7.663A pdb=" N ILE B 195 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 156 removed outlier: 4.624A pdb=" N CYS B 155 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 180 through 185 Processing sheet with id=AC6, first strand: chain 'B' and resid 302 through 304 removed outlier: 4.152A pdb=" N CYS B 297 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 321 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN B 405 " --> pdb=" O CYS B 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 377 through 382 removed outlier: 4.722A pdb=" N TYR C 367 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AD2, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.192A pdb=" N ILE C 67 " --> pdb=" O GLY C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 74 through 76 removed outlier: 6.797A pdb=" N LEU C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 116 through 117 removed outlier: 5.016A pdb=" N ILE C 195 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY C 272 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 117 removed outlier: 7.549A pdb=" N ILE C 195 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AD7, first strand: chain 'C' and resid 152 through 156 removed outlier: 4.670A pdb=" N CYS C 155 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 180 through 185 Processing sheet with id=AD9, first strand: chain 'C' and resid 302 through 304 removed outlier: 4.170A pdb=" N CYS C 297 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN C 405 " --> pdb=" O CYS C 321 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1479 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: 2.66 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1995 1.30 - 1.43: 3077 1.43 - 1.56: 6634 1.56 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 11778 Sorted by residual: bond pdb=" C PRO A 289 " pdb=" O PRO A 289 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.19e-02 7.06e+03 2.42e+01 bond pdb=" C PRO B 289 " pdb=" O PRO B 289 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.19e-02 7.06e+03 2.08e+01 bond pdb=" N SER B 70 " pdb=" CA SER B 70 " ideal model delta sigma weight residual 1.463 1.494 -0.031 6.90e-03 2.10e+04 2.03e+01 bond pdb=" C PRO C 289 " pdb=" O PRO C 289 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.19e-02 7.06e+03 1.87e+01 bond pdb=" C ALA C 122 " pdb=" O ALA C 122 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.17e-02 7.31e+03 1.32e+01 ... (remaining 11773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 14784 1.51 - 3.01: 950 3.01 - 4.52: 163 4.52 - 6.02: 25 6.02 - 7.53: 8 Bond angle restraints: 15930 Sorted by residual: angle pdb=" C ARG B 472 " pdb=" CA ARG B 472 " pdb=" CB ARG B 472 " ideal model delta sigma weight residual 116.54 111.17 5.37 1.15e+00 7.56e-01 2.18e+01 angle pdb=" CA TYR A 121 " pdb=" C TYR A 121 " pdb=" O TYR A 121 " ideal model delta sigma weight residual 120.70 115.91 4.79 1.03e+00 9.43e-01 2.16e+01 angle pdb=" C ARG A 472 " pdb=" CA ARG A 472 " pdb=" CB ARG A 472 " ideal model delta sigma weight residual 116.54 111.31 5.23 1.15e+00 7.56e-01 2.07e+01 angle pdb=" CA ASN A 47 " pdb=" CB ASN A 47 " pdb=" CG ASN A 47 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" C ARG C 472 " pdb=" CA ARG C 472 " pdb=" CB ARG C 472 " ideal model delta sigma weight residual 116.63 111.65 4.98 1.16e+00 7.43e-01 1.85e+01 ... (remaining 15925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6507 17.87 - 35.73: 510 35.73 - 53.60: 93 53.60 - 71.47: 23 71.47 - 89.34: 25 Dihedral angle restraints: 7158 sinusoidal: 2934 harmonic: 4224 Sorted by residual: dihedral pdb=" CA CYS B 80 " pdb=" C CYS B 80 " pdb=" N THR B 81 " pdb=" CA THR B 81 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA CYS C 80 " pdb=" C CYS C 80 " pdb=" N THR C 81 " pdb=" CA THR C 81 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TRP B 100 " pdb=" C TRP B 100 " pdb=" N ASP B 101 " pdb=" CA ASP B 101 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1203 0.047 - 0.094: 345 0.094 - 0.142: 129 0.142 - 0.189: 33 0.189 - 0.236: 18 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA VAL B 198 " pdb=" N VAL B 198 " pdb=" C VAL B 198 " pdb=" CB VAL B 198 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL C 118 " pdb=" N VAL C 118 " pdb=" C VAL C 118 " pdb=" CB VAL C 118 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA LEU A 397 " pdb=" N LEU A 397 " pdb=" C LEU A 397 " pdb=" CB LEU A 397 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1725 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 294 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C LYS A 294 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS A 294 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 295 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 294 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C LYS C 294 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS C 294 " -0.014 2.00e-02 2.50e+03 pdb=" N SER C 295 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 294 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C LYS B 294 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS B 294 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B 295 " 0.012 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2604 2.77 - 3.30: 13341 3.30 - 3.83: 26774 3.83 - 4.37: 32594 4.37 - 4.90: 49267 Nonbonded interactions: 124580 Sorted by model distance: nonbonded pdb=" OD1 ASP A 84 " pdb=" OH TYR A 116 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP B 84 " pdb=" OH TYR B 116 " model vdw 2.269 3.040 nonbonded pdb=" O HOH A 634 " pdb=" O HOH A1178 " model vdw 2.300 3.040 nonbonded pdb=" O HOH C1049 " pdb=" O HOH C1074 " model vdw 2.301 3.040 nonbonded pdb=" OD2 ASP B 509 " pdb=" O HOH B 601 " model vdw 2.303 3.040 ... (remaining 124575 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 5.950 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.990 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.005 0.059 11793 Z= 0.374 Angle : 0.814 7.531 15960 Z= 0.536 Chirality : 0.057 0.236 1728 Planarity : 0.004 0.030 2106 Dihedral : 14.311 89.337 4395 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.31 % Allowed : 1.87 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1455 helix: 2.51 (0.25), residues: 360 sheet: 0.60 (0.27), residues: 336 loop : -0.60 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 498 TYR 0.012 0.002 TYR A 121 PHE 0.010 0.002 PHE B 483 TRP 0.010 0.001 TRP A 359 HIS 0.008 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00520 (11778) covalent geometry : angle 0.81027 (15930) SS BOND : bond 0.01733 ( 15) SS BOND : angle 2.05224 ( 30) hydrogen bonds : bond 0.09091 ( 499) hydrogen bonds : angle 5.81928 ( 1479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 0.515 Fit side-chains REVERT: A 91 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7029 (pt0) REVERT: A 110 ASN cc_start: 0.8235 (p0) cc_final: 0.7950 (p0) REVERT: A 277 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7480 (mtm-85) REVERT: A 296 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8679 (mm-30) REVERT: A 379 GLN cc_start: 0.8093 (tt0) cc_final: 0.7755 (tt0) REVERT: A 500 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7216 (mt-10) REVERT: B 49 ARG cc_start: 0.7618 (ttt90) cc_final: 0.7384 (ttm-80) REVERT: B 91 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7258 (pt0) REVERT: B 224 ARG cc_start: 0.7689 (mtp-110) cc_final: 0.7341 (mmt90) REVERT: B 258 ILE cc_start: 0.8599 (tt) cc_final: 0.8237 (pp) REVERT: B 277 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7656 (mtm-85) REVERT: B 280 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7801 (pttp) REVERT: C 277 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7675 (mtm-85) REVERT: C 469 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7847 (mttp) outliers start: 4 outliers final: 0 residues processed: 225 average time/residue: 0.6521 time to fit residues: 158.7332 Evaluate side-chains 149 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 469 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 206 ASN A 226 GLN A 262 ASN A 392 GLN A 394 ASN A 450 GLN A 470 GLN A 514 ASN B 34 HIS B 206 ASN B 226 GLN B 262 ASN B 379 GLN B 394 ASN ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 ASN C 34 HIS C 206 ASN C 226 GLN C 262 ASN C 379 GLN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110658 restraints weight = 11300.481| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.44 r_work: 0.3120 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11793 Z= 0.107 Angle : 0.513 7.198 15960 Z= 0.274 Chirality : 0.044 0.143 1728 Planarity : 0.003 0.030 2106 Dihedral : 4.679 57.833 1588 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.09 % Allowed : 7.03 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1455 helix: 3.15 (0.25), residues: 357 sheet: 0.66 (0.28), residues: 339 loop : -0.58 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.010 0.001 TYR B 502 PHE 0.009 0.001 PHE A 369 TRP 0.007 0.001 TRP B 437 HIS 0.008 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00229 (11778) covalent geometry : angle 0.51200 (15930) SS BOND : bond 0.00214 ( 15) SS BOND : angle 1.01663 ( 30) hydrogen bonds : bond 0.04679 ( 499) hydrogen bonds : angle 5.00895 ( 1479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.574 Fit side-chains REVERT: A 49 ARG cc_start: 0.7583 (mtp-110) cc_final: 0.7288 (ttm-80) REVERT: A 91 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7001 (pt0) REVERT: A 277 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7675 (mtm180) REVERT: A 296 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8546 (mm-30) REVERT: A 417 GLU cc_start: 0.7645 (pt0) cc_final: 0.6970 (mp0) REVERT: B 91 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7071 (pt0) REVERT: B 224 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7255 (mmt90) REVERT: B 277 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7562 (mtm-85) REVERT: B 280 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7625 (pttp) REVERT: C 91 GLN cc_start: 0.7858 (mp10) cc_final: 0.6924 (pt0) outliers start: 14 outliers final: 3 residues processed: 174 average time/residue: 0.6499 time to fit residues: 122.6960 Evaluate side-chains 149 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 258 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 226 GLN A 392 GLN A 394 ASN A 470 GLN A 514 ASN B 34 HIS B 226 GLN B 379 GLN B 392 GLN B 394 ASN B 470 GLN B 514 ASN C 34 HIS C 112 ASN C 226 GLN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106215 restraints weight = 11363.843| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.46 r_work: 0.3050 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11793 Z= 0.170 Angle : 0.591 8.062 15960 Z= 0.316 Chirality : 0.048 0.174 1728 Planarity : 0.004 0.038 2106 Dihedral : 4.666 22.047 1584 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.25 % Allowed : 8.43 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1455 helix: 2.99 (0.25), residues: 357 sheet: 0.45 (0.27), residues: 354 loop : -0.61 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 166 TYR 0.010 0.002 TYR A 439 PHE 0.013 0.002 PHE B 483 TRP 0.007 0.001 TRP A 143 HIS 0.010 0.002 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00379 (11778) covalent geometry : angle 0.58930 (15930) SS BOND : bond 0.00312 ( 15) SS BOND : angle 1.08275 ( 30) hydrogen bonds : bond 0.05633 ( 499) hydrogen bonds : angle 5.28853 ( 1479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.519 Fit side-chains REVERT: A 49 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7313 (ttm-80) REVERT: A 91 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6814 (pt0) REVERT: A 117 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8614 (p0) REVERT: A 224 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7152 (mmt90) REVERT: A 277 ARG cc_start: 0.8192 (mtt180) cc_final: 0.7720 (mtp180) REVERT: A 296 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 417 GLU cc_start: 0.7768 (pt0) cc_final: 0.6475 (mm-30) REVERT: B 50 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8178 (mp) REVERT: B 91 GLN cc_start: 0.7511 (mm-40) cc_final: 0.6975 (pt0) REVERT: B 224 ARG cc_start: 0.7848 (mtp-110) cc_final: 0.7288 (mmt90) REVERT: B 277 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7750 (mtm-85) REVERT: B 280 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7581 (pttp) REVERT: C 91 GLN cc_start: 0.7842 (mp10) cc_final: 0.6832 (pt0) REVERT: C 417 GLU cc_start: 0.7853 (pt0) cc_final: 0.7253 (pm20) outliers start: 16 outliers final: 7 residues processed: 159 average time/residue: 0.6477 time to fit residues: 111.9328 Evaluate side-chains 147 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 0.0060 chunk 15 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 392 GLN A 394 ASN A 470 GLN A 514 ASN B 34 HIS B 226 GLN B 379 GLN B 392 GLN B 394 ASN B 514 ASN C 34 HIS C 226 GLN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108616 restraints weight = 11332.691| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.37 r_work: 0.3101 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11793 Z= 0.100 Angle : 0.491 8.061 15960 Z= 0.261 Chirality : 0.043 0.141 1728 Planarity : 0.003 0.037 2106 Dihedral : 4.236 19.320 1584 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.56 % Allowed : 9.29 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.21), residues: 1455 helix: 3.31 (0.25), residues: 357 sheet: 0.57 (0.27), residues: 354 loop : -0.54 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 224 TYR 0.008 0.001 TYR B 502 PHE 0.008 0.001 PHE A 369 TRP 0.007 0.001 TRP A 437 HIS 0.004 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00210 (11778) covalent geometry : angle 0.49046 (15930) SS BOND : bond 0.00245 ( 15) SS BOND : angle 0.81730 ( 30) hydrogen bonds : bond 0.04580 ( 499) hydrogen bonds : angle 4.87277 ( 1479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.541 Fit side-chains REVERT: A 49 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7368 (ttm-80) REVERT: A 91 GLN cc_start: 0.7681 (mm-40) cc_final: 0.6871 (pt0) REVERT: A 117 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8630 (p0) REVERT: A 224 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7121 (mmt90) REVERT: A 277 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7700 (mtp180) REVERT: A 296 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8503 (mm-30) REVERT: A 417 GLU cc_start: 0.7705 (pt0) cc_final: 0.7138 (pm20) REVERT: B 50 ILE cc_start: 0.8416 (mt) cc_final: 0.8212 (mp) REVERT: B 91 GLN cc_start: 0.7464 (mm-40) cc_final: 0.6929 (pt0) REVERT: B 224 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7272 (mmt90) REVERT: B 277 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7739 (mtm-85) REVERT: B 280 LYS cc_start: 0.8244 (mmtm) cc_final: 0.7571 (pttp) REVERT: B 292 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7857 (mttp) REVERT: C 91 GLN cc_start: 0.7847 (mp10) cc_final: 0.6877 (pt0) REVERT: C 417 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7221 (pm20) outliers start: 20 outliers final: 5 residues processed: 160 average time/residue: 0.6454 time to fit residues: 112.3393 Evaluate side-chains 149 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 392 GLN A 394 ASN A 470 GLN A 514 ASN B 34 HIS B 226 GLN B 379 GLN B 392 GLN B 394 ASN B 514 ASN C 34 HIS C 79 ASN C 226 GLN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108136 restraints weight = 11455.054| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.45 r_work: 0.3053 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11793 Z= 0.137 Angle : 0.541 8.137 15960 Z= 0.288 Chirality : 0.045 0.144 1728 Planarity : 0.004 0.041 2106 Dihedral : 4.453 21.143 1584 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.33 % Allowed : 9.76 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1455 helix: 3.16 (0.25), residues: 357 sheet: 0.51 (0.27), residues: 354 loop : -0.57 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.009 0.001 TYR A 439 PHE 0.011 0.002 PHE C 369 TRP 0.006 0.001 TRP A 143 HIS 0.005 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00302 (11778) covalent geometry : angle 0.53980 (15930) SS BOND : bond 0.00252 ( 15) SS BOND : angle 0.88226 ( 30) hydrogen bonds : bond 0.05186 ( 499) hydrogen bonds : angle 5.08638 ( 1479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.530 Fit side-chains REVERT: A 49 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7314 (ttm-80) REVERT: A 91 GLN cc_start: 0.7709 (mm-40) cc_final: 0.6784 (pt0) REVERT: A 117 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8576 (p0) REVERT: A 224 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7170 (mmt90) REVERT: A 277 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7755 (mtp180) REVERT: A 296 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8533 (mm-30) REVERT: A 417 GLU cc_start: 0.7739 (pt0) cc_final: 0.7161 (pm20) REVERT: A 457 ASP cc_start: 0.8588 (m-30) cc_final: 0.8381 (m-30) REVERT: B 50 ILE cc_start: 0.8386 (mt) cc_final: 0.8166 (mp) REVERT: B 91 GLN cc_start: 0.7557 (mm-40) cc_final: 0.6881 (pt0) REVERT: B 224 ARG cc_start: 0.7811 (mtp-110) cc_final: 0.7256 (mmt90) REVERT: B 277 ARG cc_start: 0.8364 (mtt180) cc_final: 0.7762 (mtm-85) REVERT: B 280 LYS cc_start: 0.8267 (mmtm) cc_final: 0.7547 (pttp) REVERT: B 292 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7930 (mttp) REVERT: C 91 GLN cc_start: 0.7830 (mp10) cc_final: 0.6786 (pt0) REVERT: C 337 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8407 (ttp-110) REVERT: C 417 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7331 (pm20) outliers start: 17 outliers final: 6 residues processed: 156 average time/residue: 0.6346 time to fit residues: 107.8652 Evaluate side-chains 150 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 392 GLN A 394 ASN A 470 GLN A 514 ASN B 34 HIS B 206 ASN B 226 GLN B 379 GLN B 392 GLN B 394 ASN B 514 ASN C 34 HIS C 226 GLN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106810 restraints weight = 11275.698| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.25 r_work: 0.3039 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11793 Z= 0.276 Angle : 0.701 8.971 15960 Z= 0.377 Chirality : 0.054 0.238 1728 Planarity : 0.005 0.048 2106 Dihedral : 4.997 23.116 1584 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.95 % Allowed : 9.52 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1455 helix: 2.72 (0.24), residues: 357 sheet: 0.30 (0.26), residues: 336 loop : -0.72 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 166 TYR 0.016 0.003 TYR C 439 PHE 0.017 0.003 PHE C 310 TRP 0.010 0.002 TRP A 143 HIS 0.007 0.002 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00630 (11778) covalent geometry : angle 0.69964 (15930) SS BOND : bond 0.00497 ( 15) SS BOND : angle 1.30665 ( 30) hydrogen bonds : bond 0.06512 ( 499) hydrogen bonds : angle 5.62812 ( 1479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.464 Fit side-chains REVERT: A 49 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7357 (ttm-80) REVERT: A 117 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8560 (p0) REVERT: A 224 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7206 (mmt90) REVERT: A 277 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7749 (mtm180) REVERT: A 296 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8545 (mm-30) REVERT: A 417 GLU cc_start: 0.7842 (pt0) cc_final: 0.6439 (mm-30) REVERT: B 50 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 224 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.7256 (mmt90) REVERT: B 277 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7823 (mtm180) REVERT: B 280 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7475 (pttp) REVERT: B 292 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7959 (mttp) REVERT: C 417 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7285 (pm20) outliers start: 25 outliers final: 9 residues processed: 157 average time/residue: 0.6437 time to fit residues: 110.0749 Evaluate side-chains 151 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 262 ASN A 392 GLN A 394 ASN A 451 HIS A 470 GLN A 514 ASN B 34 HIS B 206 ASN B 226 GLN B 379 GLN B 392 GLN B 394 ASN B 514 ASN C 34 HIS C 226 GLN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107291 restraints weight = 11333.440| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.36 r_work: 0.3080 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11793 Z= 0.109 Angle : 0.506 8.863 15960 Z= 0.270 Chirality : 0.044 0.142 1728 Planarity : 0.003 0.043 2106 Dihedral : 4.374 20.105 1584 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.80 % Allowed : 10.07 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1455 helix: 3.23 (0.25), residues: 357 sheet: 0.57 (0.27), residues: 348 loop : -0.53 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 236 TYR 0.008 0.001 TYR B 502 PHE 0.010 0.001 PHE C 369 TRP 0.007 0.001 TRP B 437 HIS 0.005 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00231 (11778) covalent geometry : angle 0.50560 (15930) SS BOND : bond 0.00242 ( 15) SS BOND : angle 0.82781 ( 30) hydrogen bonds : bond 0.04795 ( 499) hydrogen bonds : angle 4.98389 ( 1479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.454 Fit side-chains REVERT: A 49 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7341 (ttm-80) REVERT: A 117 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8560 (p0) REVERT: A 224 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7194 (mmt90) REVERT: A 277 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7732 (mtp180) REVERT: A 296 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8504 (mm-30) REVERT: A 417 GLU cc_start: 0.7735 (pt0) cc_final: 0.7161 (pm20) REVERT: B 91 GLN cc_start: 0.7994 (mm110) cc_final: 0.6977 (pt0) REVERT: B 224 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7298 (mmt90) REVERT: B 277 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7817 (mtm-85) REVERT: B 280 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7510 (pttp) REVERT: B 292 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7943 (mttp) REVERT: B 500 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: C 292 LYS cc_start: 0.8153 (mttp) cc_final: 0.7648 (mtpt) REVERT: C 417 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: C 491 ASN cc_start: 0.7490 (m-40) cc_final: 0.7137 (m110) outliers start: 23 outliers final: 7 residues processed: 161 average time/residue: 0.6184 time to fit residues: 108.3469 Evaluate side-chains 155 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 262 ASN A 392 GLN A 394 ASN A 451 HIS A 470 GLN A 514 ASN B 34 HIS B 206 ASN B 226 GLN B 379 GLN B 392 GLN B 394 ASN B 514 ASN C 34 HIS C 226 GLN C 262 ASN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107887 restraints weight = 11288.756| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.36 r_work: 0.3090 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11793 Z= 0.105 Angle : 0.500 8.918 15960 Z= 0.265 Chirality : 0.043 0.140 1728 Planarity : 0.003 0.044 2106 Dihedral : 4.253 19.753 1584 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.72 % Allowed : 9.99 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.21), residues: 1455 helix: 3.40 (0.25), residues: 357 sheet: 0.63 (0.27), residues: 348 loop : -0.47 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 236 TYR 0.008 0.001 TYR B 502 PHE 0.010 0.001 PHE C 369 TRP 0.008 0.001 TRP A 437 HIS 0.006 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00225 (11778) covalent geometry : angle 0.49978 (15930) SS BOND : bond 0.00227 ( 15) SS BOND : angle 0.75735 ( 30) hydrogen bonds : bond 0.04672 ( 499) hydrogen bonds : angle 4.88344 ( 1479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.552 Fit side-chains REVERT: A 49 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.7315 (ttm-80) REVERT: A 117 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8522 (p0) REVERT: A 224 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7179 (mmt90) REVERT: A 277 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7791 (mtp180) REVERT: A 296 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8515 (mm-30) REVERT: A 417 GLU cc_start: 0.7729 (pt0) cc_final: 0.7140 (pm20) REVERT: B 91 GLN cc_start: 0.8000 (mm110) cc_final: 0.7037 (pt0) REVERT: B 224 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7287 (mmt90) REVERT: B 277 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7809 (mtm-85) REVERT: B 280 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7510 (pttp) REVERT: B 292 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7926 (mttp) REVERT: B 500 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: C 277 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7663 (mtm180) REVERT: C 292 LYS cc_start: 0.8140 (mttp) cc_final: 0.7644 (mtpt) REVERT: C 417 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7287 (pm20) REVERT: C 491 ASN cc_start: 0.7507 (m-40) cc_final: 0.7163 (m110) outliers start: 22 outliers final: 7 residues processed: 160 average time/residue: 0.6819 time to fit residues: 118.4736 Evaluate side-chains 156 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 262 ASN A 392 GLN A 394 ASN A 451 HIS A 470 GLN A 514 ASN B 34 HIS B 206 ASN B 226 GLN B 379 GLN B 392 GLN B 394 ASN B 514 ASN C 34 HIS C 226 GLN C 262 ASN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106578 restraints weight = 11437.958| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.25 r_work: 0.3020 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11793 Z= 0.258 Angle : 0.680 10.204 15960 Z= 0.364 Chirality : 0.053 0.219 1728 Planarity : 0.005 0.051 2106 Dihedral : 4.908 22.745 1584 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.72 % Allowed : 9.99 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1455 helix: 2.91 (0.24), residues: 357 sheet: 0.39 (0.26), residues: 330 loop : -0.63 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 166 TYR 0.016 0.003 TYR C 439 PHE 0.016 0.003 PHE C 310 TRP 0.010 0.002 TRP A 143 HIS 0.006 0.002 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00591 (11778) covalent geometry : angle 0.67891 (15930) SS BOND : bond 0.00462 ( 15) SS BOND : angle 1.24866 ( 30) hydrogen bonds : bond 0.06314 ( 499) hydrogen bonds : angle 5.53737 ( 1479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.547 Fit side-chains REVERT: A 49 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7379 (ttm-80) REVERT: A 117 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8659 (p0) REVERT: A 224 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7260 (mmt90) REVERT: A 277 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7872 (mtm180) REVERT: A 296 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8626 (mm-30) REVERT: A 417 GLU cc_start: 0.7916 (pt0) cc_final: 0.7315 (pm20) REVERT: B 91 GLN cc_start: 0.8082 (mm110) cc_final: 0.7072 (pt0) REVERT: B 224 ARG cc_start: 0.7878 (mtp-110) cc_final: 0.7354 (mmt90) REVERT: B 277 ARG cc_start: 0.8450 (mtt180) cc_final: 0.7880 (mtm-85) REVERT: B 280 LYS cc_start: 0.8311 (mmtm) cc_final: 0.7600 (pttp) REVERT: B 292 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7988 (mttp) REVERT: C 417 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7355 (pm20) outliers start: 22 outliers final: 9 residues processed: 163 average time/residue: 0.6939 time to fit residues: 122.9288 Evaluate side-chains 153 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 262 ASN A 372 GLN A 392 GLN A 394 ASN A 451 HIS A 470 GLN A 514 ASN B 34 HIS B 206 ASN B 226 GLN B 392 GLN B 394 ASN B 514 ASN C 34 HIS C 226 GLN C 262 ASN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105452 restraints weight = 11333.631| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.37 r_work: 0.3052 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11793 Z= 0.145 Angle : 0.558 9.324 15960 Z= 0.298 Chirality : 0.046 0.146 1728 Planarity : 0.004 0.049 2106 Dihedral : 4.606 21.345 1584 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.48 % Allowed : 10.30 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1455 helix: 3.13 (0.25), residues: 357 sheet: 0.45 (0.26), residues: 348 loop : -0.54 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 166 TYR 0.010 0.002 TYR A 439 PHE 0.012 0.002 PHE B 369 TRP 0.007 0.001 TRP A 143 HIS 0.006 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00321 (11778) covalent geometry : angle 0.55723 (15930) SS BOND : bond 0.00278 ( 15) SS BOND : angle 0.93003 ( 30) hydrogen bonds : bond 0.05330 ( 499) hydrogen bonds : angle 5.21571 ( 1479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.523 Fit side-chains REVERT: A 49 ARG cc_start: 0.7610 (mtp-110) cc_final: 0.7338 (ttm-80) REVERT: A 117 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8588 (p0) REVERT: A 224 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7163 (mmt90) REVERT: A 277 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7846 (mtm180) REVERT: A 296 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8529 (mm-30) REVERT: A 417 GLU cc_start: 0.7833 (pt0) cc_final: 0.6461 (mm-30) REVERT: B 91 GLN cc_start: 0.8005 (mm110) cc_final: 0.6977 (pt0) REVERT: B 224 ARG cc_start: 0.7831 (mtp-110) cc_final: 0.7316 (mmt90) REVERT: B 277 ARG cc_start: 0.8398 (mtt180) cc_final: 0.7837 (mtm-85) REVERT: B 280 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7521 (pttp) REVERT: B 292 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7927 (mttp) REVERT: B 296 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8691 (mm-30) REVERT: C 292 LYS cc_start: 0.8160 (mttp) cc_final: 0.7655 (mtpt) REVERT: C 417 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: C 491 ASN cc_start: 0.7659 (m-40) cc_final: 0.7273 (m110) outliers start: 19 outliers final: 8 residues processed: 161 average time/residue: 0.6864 time to fit residues: 120.2320 Evaluate side-chains 158 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 262 ASN A 392 GLN A 394 ASN A 451 HIS A 470 GLN A 514 ASN B 34 HIS B 206 ASN B 226 GLN B 392 GLN B 394 ASN B 514 ASN C 34 HIS C 226 GLN C 262 ASN C 394 ASN C 470 GLN C 514 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108265 restraints weight = 11452.600| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.26 r_work: 0.3056 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11793 Z= 0.173 Angle : 0.592 9.448 15960 Z= 0.316 Chirality : 0.047 0.168 1728 Planarity : 0.004 0.052 2106 Dihedral : 4.714 21.974 1584 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.64 % Allowed : 10.38 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1455 helix: 3.04 (0.24), residues: 357 sheet: 0.41 (0.26), residues: 348 loop : -0.56 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 166 TYR 0.012 0.002 TYR A 439 PHE 0.013 0.002 PHE B 369 TRP 0.008 0.002 TRP A 143 HIS 0.007 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00388 (11778) covalent geometry : angle 0.59106 (15930) SS BOND : bond 0.00310 ( 15) SS BOND : angle 1.01620 ( 30) hydrogen bonds : bond 0.05649 ( 499) hydrogen bonds : angle 5.32373 ( 1479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5743.73 seconds wall clock time: 98 minutes 46.67 seconds (5926.67 seconds total)