Starting phenix.real_space_refine on Tue Feb 3 18:38:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ua5_63979/02_2026/9ua5_63979.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ua5_63979/02_2026/9ua5_63979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ua5_63979/02_2026/9ua5_63979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ua5_63979/02_2026/9ua5_63979.map" model { file = "/net/cci-nas-00/data/ceres_data/9ua5_63979/02_2026/9ua5_63979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ua5_63979/02_2026/9ua5_63979.cif" } resolution = 3.94 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= 0.043 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 42 5.16 5 C 3847 2.51 5 N 1017 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6054 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 326, 2548 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 20, 'TRANS': 305} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 326, 2548 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 20, 'TRANS': 305} Chain breaks: 3 bond proxies already assigned to first conformer: 2600 Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 906 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Time building chain proxies: 1.69, per 1000 atoms: 0.28 Number of scatterers: 6054 At special positions: 0 Unit cell: (88.81, 94.16, 96.3, 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 42 16.00 O 1148 8.00 N 1017 7.00 C 3847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 113 " distance=2.03 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 363 " - pdb=" SG CYS C 370 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 464.0 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 15 sheets defined 11.2% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 288 through 313 removed outlier: 3.643A pdb=" N VAL C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 293 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.606A pdb=" N HIS C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 400 removed outlier: 4.659A pdb=" N GLN C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.874A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.688A pdb=" N VAL H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 30 removed outlier: 3.687A pdb=" N TYR C 24 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS C 347 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU C 30 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASP C 345 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET C 342 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 335 " --> pdb=" O MET C 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 64 removed outlier: 3.765A pdb=" N THR C 212 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 217 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 229 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 227 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 80 removed outlier: 3.669A pdb=" N CYS C 80 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE C 196 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 242 through 246 Processing sheet with id=AA5, first strand: chain 'C' and resid 314 through 315 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.933A pdb=" N MET G 34 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.364A pdb=" N TYR G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY G 100 " --> pdb=" O PHE G 108 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE G 108 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 19 through 23 removed outlier: 3.932A pdb=" N CYS G 22 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.719A pdb=" N LEU K 47 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR K 49 " --> pdb=" O VAL K 33 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.664A pdb=" N ASP D 75 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 72 " --> pdb=" O ASP D 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.540A pdb=" N VAL D 90 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR D 92 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 41 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU D 38 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR D 54 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.712A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.198A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.198A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 449 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: 0.90 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1926 1.35 - 1.46: 1559 1.46 - 1.58: 2652 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 6200 Sorted by residual: bond pdb=" CA ILE C 382 " pdb=" CB ILE C 382 " ideal model delta sigma weight residual 1.540 1.556 -0.016 1.36e-02 5.41e+03 1.36e+00 bond pdb=" N ASN C 375 " pdb=" CA ASN C 375 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.33e+00 bond pdb=" C ALA G 40 " pdb=" N PRO G 41 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.36e-01 bond pdb=" CA HIS C 416 " pdb=" CB HIS C 416 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.58e-02 4.01e+03 8.29e-01 bond pdb=" CG1 ILE C 382 " pdb=" CD1 ILE C 382 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.16e-01 ... (remaining 6195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 8150 1.93 - 3.87: 196 3.87 - 5.80: 40 5.80 - 7.74: 7 7.74 - 9.67: 8 Bond angle restraints: 8401 Sorted by residual: angle pdb=" N ILE C 210 " pdb=" CA ILE C 210 " pdb=" C ILE C 210 " ideal model delta sigma weight residual 113.71 105.85 7.86 9.50e-01 1.11e+00 6.85e+01 angle pdb=" N ARG H 101 " pdb=" CA ARG H 101 " pdb=" C ARG H 101 " ideal model delta sigma weight residual 110.91 105.96 4.95 1.17e+00 7.31e-01 1.79e+01 angle pdb=" N GLY G 56 " pdb=" CA GLY G 56 " pdb=" C GLY G 56 " ideal model delta sigma weight residual 115.47 110.55 4.92 1.31e+00 5.83e-01 1.41e+01 angle pdb=" CA GLU C 307 " pdb=" CB GLU C 307 " pdb=" CG GLU C 307 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA ILE C 210 " pdb=" C ILE C 210 " pdb=" N PHE C 211 " ideal model delta sigma weight residual 119.87 115.28 4.59 1.34e+00 5.57e-01 1.17e+01 ... (remaining 8396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 3110 16.14 - 32.27: 432 32.27 - 48.41: 126 48.41 - 64.55: 17 64.55 - 80.68: 8 Dihedral angle restraints: 3693 sinusoidal: 1461 harmonic: 2232 Sorted by residual: dihedral pdb=" CA TYR K 94 " pdb=" C TYR K 94 " pdb=" N PRO K 95 " pdb=" CA PRO K 95 " ideal model delta harmonic sigma weight residual 180.00 142.69 37.31 0 5.00e+00 4.00e-02 5.57e+01 dihedral pdb=" CA HIS C 373 " pdb=" C HIS C 373 " pdb=" N VAL C 374 " pdb=" CA VAL C 374 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA VAL C 390 " pdb=" C VAL C 390 " pdb=" N LEU C 391 " pdb=" CA LEU C 391 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 3690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 886 0.106 - 0.212: 27 0.212 - 0.318: 1 0.318 - 0.424: 0 0.424 - 0.530: 1 Chirality restraints: 915 Sorted by residual: chirality pdb=" CB ILE C 382 " pdb=" CA ILE C 382 " pdb=" CG1 ILE C 382 " pdb=" CG2 ILE C 382 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.03e+00 chirality pdb=" CB ILE D 80 " pdb=" CA ILE D 80 " pdb=" CG1 ILE D 80 " pdb=" CG2 ILE D 80 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL C 296 " pdb=" CA VAL C 296 " pdb=" CG1 VAL C 296 " pdb=" CG2 VAL C 296 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 912 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR K 94 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO K 95 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO K 95 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 95 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " -0.012 2.00e-02 2.50e+03 1.37e-02 3.27e+00 pdb=" CG PHE H 29 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 371 " 0.028 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO C 372 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 372 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 372 " 0.024 5.00e-02 4.00e+02 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 301 2.70 - 3.25: 6303 3.25 - 3.80: 10242 3.80 - 4.35: 12142 4.35 - 4.90: 19101 Nonbonded interactions: 48089 Sorted by model distance: nonbonded pdb=" N GLN C 396 " pdb=" OE1 GLN C 396 " model vdw 2.149 3.120 nonbonded pdb=" O SER C 360 " pdb=" OH TYR G 52 " model vdw 2.179 3.040 nonbonded pdb=" O ASP G 90 " pdb=" OH TYR G 94 " model vdw 2.184 3.040 nonbonded pdb=" NE1 TRP G 47 " pdb=" OD1 ASP G 50 " model vdw 2.196 3.120 nonbonded pdb=" OD2 ASP D 39 " pdb=" OH TYR D 41 " model vdw 2.204 3.040 ... (remaining 48084 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.020 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6210 Z= 0.144 Angle : 0.767 9.671 8421 Z= 0.390 Chirality : 0.047 0.530 915 Planarity : 0.005 0.081 1070 Dihedral : 16.074 80.683 2247 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.69 % Favored : 89.40 % Rotamer: Outliers : 2.99 % Allowed : 27.84 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.03 (0.33), residues: 765 helix: 1.57 (0.77), residues: 44 sheet: -0.08 (0.35), residues: 247 loop : -1.28 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 369 TYR 0.012 0.001 TYR G 27 PHE 0.032 0.002 PHE H 29 TRP 0.008 0.001 TRP C 259 HIS 0.005 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6200) covalent geometry : angle 0.76620 ( 8401) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.95350 ( 20) hydrogen bonds : bond 0.26444 ( 180) hydrogen bonds : angle 9.73642 ( 449) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 63 MET cc_start: 0.7029 (tmm) cc_final: 0.6504 (tmm) REVERT: C 76 ASN cc_start: 0.8710 (t0) cc_final: 0.7992 (p0) REVERT: C 255 MET cc_start: 0.8861 (mmm) cc_final: 0.8567 (mmp) REVERT: C 283 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7697 (ttt180) REVERT: C 287 ILE cc_start: 0.9054 (pt) cc_final: 0.8808 (pt) REVERT: C 289 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7377 (p-80) REVERT: G 31 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.7497 (p0) REVERT: G 67 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7789 (ptmt) REVERT: G 81 MET cc_start: 0.8415 (tpp) cc_final: 0.7783 (tpp) REVERT: G 102 ASP cc_start: 0.8330 (p0) cc_final: 0.7766 (t0) REVERT: K 4 MET cc_start: 0.8880 (mmm) cc_final: 0.7361 (mtp) REVERT: K 94 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7128 (t80) REVERT: H 36 TRP cc_start: 0.9065 (m100) cc_final: 0.8771 (m100) REVERT: H 65 MET cc_start: 0.7988 (tpp) cc_final: 0.7432 (tpp) REVERT: H 102 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7400 (mtt180) REVERT: H 105 TYR cc_start: 0.7180 (m-80) cc_final: 0.6666 (m-10) outliers start: 20 outliers final: 15 residues processed: 87 average time/residue: 0.0659 time to fit residues: 7.9434 Evaluate side-chains 92 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain H residue 104 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 401 GLN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043881 restraints weight = 76303.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045948 restraints weight = 36057.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.047395 restraints weight = 22057.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.048369 restraints weight = 15465.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.049056 restraints weight = 11870.338| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6210 Z= 0.203 Angle : 0.739 8.748 8421 Z= 0.375 Chirality : 0.046 0.414 915 Planarity : 0.005 0.083 1070 Dihedral : 7.836 50.241 887 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.34 % Favored : 88.74 % Rotamer: Outliers : 5.99 % Allowed : 23.20 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.14 % 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: -1.24 (0.32), residues: 765 helix: 1.25 (0.76), residues: 45 sheet: -0.19 (0.36), residues: 236 loop : -1.42 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 319 TYR 0.016 0.002 TYR G 54 PHE 0.011 0.002 PHE C 378 TRP 0.012 0.002 TRP G 111 HIS 0.004 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6200) covalent geometry : angle 0.73763 ( 8401) SS BOND : bond 0.00381 ( 10) SS BOND : angle 1.05268 ( 20) hydrogen bonds : bond 0.04589 ( 180) hydrogen bonds : angle 6.83624 ( 449) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 MET cc_start: 0.7037 (tmm) cc_final: 0.6669 (tmm) REVERT: C 76 ASN cc_start: 0.8808 (t0) cc_final: 0.7911 (p0) REVERT: C 255 MET cc_start: 0.9046 (mmm) cc_final: 0.8687 (mmp) REVERT: C 283 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7800 (ttt180) REVERT: C 287 ILE cc_start: 0.9074 (pt) cc_final: 0.8789 (pt) REVERT: C 289 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7582 (p-80) REVERT: C 415 MET cc_start: 0.6761 (ptt) cc_final: 0.6508 (ptp) REVERT: G 31 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.7521 (p0) REVERT: G 83 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7195 (mm) REVERT: G 102 ASP cc_start: 0.8410 (p0) cc_final: 0.7811 (t0) REVERT: K 4 MET cc_start: 0.8886 (mmm) cc_final: 0.7253 (mtp) REVERT: K 55 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7422 (p90) REVERT: D 95 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8750 (pp30) REVERT: H 105 TYR cc_start: 0.7347 (m-80) cc_final: 0.6791 (m-10) outliers start: 40 outliers final: 26 residues processed: 106 average time/residue: 0.0631 time to fit residues: 9.0705 Evaluate side-chains 97 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 371 HIS ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.064859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.055211 restraints weight = 100543.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.057094 restraints weight = 41245.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.058292 restraints weight = 22296.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.059069 restraints weight = 14148.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.059591 restraints weight = 10065.839| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6210 Z= 0.163 Angle : 0.718 9.040 8421 Z= 0.357 Chirality : 0.044 0.360 915 Planarity : 0.005 0.081 1070 Dihedral : 7.347 58.960 868 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.47 % Favored : 88.61 % Rotamer: Outliers : 5.99 % Allowed : 23.50 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.14 % 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: -1.32 (0.32), residues: 765 helix: 1.22 (0.72), residues: 45 sheet: -0.33 (0.34), residues: 244 loop : -1.44 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 319 TYR 0.014 0.001 TYR G 54 PHE 0.012 0.001 PHE K 71 TRP 0.010 0.001 TRP G 111 HIS 0.003 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6200) covalent geometry : angle 0.71738 ( 8401) SS BOND : bond 0.00362 ( 10) SS BOND : angle 0.93575 ( 20) hydrogen bonds : bond 0.03707 ( 180) hydrogen bonds : angle 6.16081 ( 449) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 MET cc_start: 0.7156 (tmm) cc_final: 0.6788 (tmm) REVERT: C 76 ASN cc_start: 0.8450 (t0) cc_final: 0.7547 (p0) REVERT: C 255 MET cc_start: 0.8865 (mmm) cc_final: 0.8545 (mmp) REVERT: C 283 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7685 (ttt180) REVERT: C 287 ILE cc_start: 0.9077 (pt) cc_final: 0.8786 (pt) REVERT: C 289 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7426 (p-80) REVERT: G 31 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.7549 (p0) REVERT: G 102 ASP cc_start: 0.8197 (p0) cc_final: 0.7782 (t0) REVERT: D 87 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.6891 (t0) REVERT: H 81 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8831 (mt) REVERT: H 105 TYR cc_start: 0.7207 (m-80) cc_final: 0.6666 (m-80) outliers start: 40 outliers final: 28 residues processed: 109 average time/residue: 0.0607 time to fit residues: 9.1922 Evaluate side-chains 101 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 104 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 39 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.0000 chunk 10 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 371 HIS ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.066661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.056953 restraints weight = 98643.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.058847 restraints weight = 40419.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.060067 restraints weight = 21757.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.060846 restraints weight = 13711.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.061380 restraints weight = 9697.752| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6210 Z= 0.124 Angle : 0.724 10.284 8421 Z= 0.352 Chirality : 0.045 0.316 915 Planarity : 0.005 0.081 1070 Dihedral : 7.066 59.173 867 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.21 % Favored : 88.87 % Rotamer: Outliers : 6.14 % Allowed : 23.20 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.22 (0.32), residues: 765 helix: 1.37 (0.74), residues: 45 sheet: -0.35 (0.33), residues: 254 loop : -1.33 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.011 0.001 TYR G 54 PHE 0.011 0.001 PHE C 378 TRP 0.011 0.001 TRP H 36 HIS 0.012 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6200) covalent geometry : angle 0.72155 ( 8401) SS BOND : bond 0.00401 ( 10) SS BOND : angle 1.43312 ( 20) hydrogen bonds : bond 0.03303 ( 180) hydrogen bonds : angle 5.63060 ( 449) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 MET cc_start: 0.7272 (tmm) cc_final: 0.6947 (tmm) REVERT: C 76 ASN cc_start: 0.8376 (t0) cc_final: 0.7464 (p0) REVERT: C 121 MET cc_start: 0.8594 (mmm) cc_final: 0.7752 (ppp) REVERT: C 255 MET cc_start: 0.8815 (mmm) cc_final: 0.8615 (mmm) REVERT: C 283 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7574 (ttt180) REVERT: C 287 ILE cc_start: 0.9082 (pt) cc_final: 0.8784 (pt) REVERT: C 289 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7196 (p-80) REVERT: C 395 MET cc_start: 0.8819 (mpp) cc_final: 0.8300 (mpp) REVERT: G 31 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.7429 (p0) REVERT: G 44 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8809 (mtp180) REVERT: G 67 LYS cc_start: 0.7971 (pttm) cc_final: 0.7575 (tttp) REVERT: G 102 ASP cc_start: 0.8314 (p0) cc_final: 0.7693 (t0) REVERT: K 4 MET cc_start: 0.8710 (mmm) cc_final: 0.7025 (mtp) REVERT: K 37 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6631 (tp40) REVERT: K 55 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7405 (p90) REVERT: D 42 LEU cc_start: 0.7723 (tp) cc_final: 0.7379 (tp) REVERT: D 87 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6876 (t0) REVERT: H 102 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7713 (ptm160) REVERT: H 105 TYR cc_start: 0.6916 (m-80) cc_final: 0.6384 (m-80) outliers start: 41 outliers final: 25 residues processed: 107 average time/residue: 0.0578 time to fit residues: 8.5629 Evaluate side-chains 105 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 102 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 371 HIS ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.062547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.053817 restraints weight = 64808.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.055306 restraints weight = 31582.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.056282 restraints weight = 18831.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.056929 restraints weight = 12822.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.057361 restraints weight = 9578.115| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6210 Z= 0.250 Angle : 0.779 8.822 8421 Z= 0.392 Chirality : 0.046 0.443 915 Planarity : 0.005 0.084 1070 Dihedral : 7.579 54.038 867 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.92 % Allowed : 11.39 % Favored : 87.70 % Rotamer: Outliers : 7.04 % Allowed : 23.80 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.14 % 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: -1.57 (0.31), residues: 765 helix: 1.54 (0.77), residues: 45 sheet: -0.67 (0.33), residues: 242 loop : -1.56 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 324 TYR 0.015 0.002 TYR H 59 PHE 0.015 0.002 PHE K 71 TRP 0.013 0.002 TRP H 36 HIS 0.014 0.002 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 6200) covalent geometry : angle 0.77655 ( 8401) SS BOND : bond 0.00611 ( 10) SS BOND : angle 1.43532 ( 20) hydrogen bonds : bond 0.03798 ( 180) hydrogen bonds : angle 6.01682 ( 449) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 68 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.9468 (mp) cc_final: 0.9003 (tp) REVERT: C 76 ASN cc_start: 0.8664 (t0) cc_final: 0.7577 (p0) REVERT: C 283 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7592 (ttt180) REVERT: C 289 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7465 (p-80) REVERT: G 31 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.7540 (p0) REVERT: G 102 ASP cc_start: 0.8591 (p0) cc_final: 0.8034 (t0) REVERT: K 55 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7631 (p90) REVERT: D 87 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7086 (t0) REVERT: H 36 TRP cc_start: 0.8585 (m100) cc_final: 0.8318 (m100) REVERT: H 105 TYR cc_start: 0.7261 (m-80) cc_final: 0.6563 (m-80) outliers start: 47 outliers final: 31 residues processed: 106 average time/residue: 0.0498 time to fit residues: 7.4957 Evaluate side-chains 102 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 111 TRP Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 104 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.065406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.055837 restraints weight = 98408.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.057713 restraints weight = 40348.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.058920 restraints weight = 21913.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.059671 restraints weight = 13918.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.060216 restraints weight = 10009.686| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6210 Z= 0.131 Angle : 0.740 11.442 8421 Z= 0.357 Chirality : 0.045 0.408 915 Planarity : 0.005 0.079 1070 Dihedral : 7.027 51.941 866 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.82 % Favored : 89.27 % Rotamer: Outliers : 5.54 % Allowed : 25.00 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.14 % 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: -1.44 (0.31), residues: 765 helix: 1.46 (0.75), residues: 45 sheet: -0.58 (0.32), residues: 254 loop : -1.46 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.019 0.001 TYR G 27 PHE 0.012 0.001 PHE C 378 TRP 0.015 0.001 TRP H 36 HIS 0.003 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6200) covalent geometry : angle 0.73853 ( 8401) SS BOND : bond 0.00493 ( 10) SS BOND : angle 1.17851 ( 20) hydrogen bonds : bond 0.03207 ( 180) hydrogen bonds : angle 5.48115 ( 449) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 ASN cc_start: 0.8346 (t0) cc_final: 0.7362 (p0) REVERT: C 121 MET cc_start: 0.8548 (mmm) cc_final: 0.7830 (ppp) REVERT: C 283 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7647 (ttt180) REVERT: C 287 ILE cc_start: 0.9168 (pt) cc_final: 0.8887 (pt) REVERT: C 289 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7172 (p-80) REVERT: G 31 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.7366 (p0) REVERT: G 44 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8804 (mtp180) REVERT: G 102 ASP cc_start: 0.8299 (p0) cc_final: 0.7774 (t0) REVERT: K 4 MET cc_start: 0.8760 (mmm) cc_final: 0.6986 (mtp) REVERT: K 55 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7612 (p90) REVERT: H 36 TRP cc_start: 0.8439 (m100) cc_final: 0.7816 (m100) REVERT: H 65 MET cc_start: 0.8040 (tpp) cc_final: 0.7476 (tpp) REVERT: H 102 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7739 (ptm160) REVERT: H 105 TYR cc_start: 0.6973 (m-80) cc_final: 0.6405 (m-80) outliers start: 37 outliers final: 27 residues processed: 106 average time/residue: 0.0637 time to fit residues: 9.4536 Evaluate side-chains 105 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 102 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 371 HIS ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.067915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.059560 restraints weight = 47975.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.060910 restraints weight = 24747.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.061783 restraints weight = 15188.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.062374 restraints weight = 10548.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.062780 restraints weight = 8010.841| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6210 Z= 0.119 Angle : 0.785 11.209 8421 Z= 0.369 Chirality : 0.046 0.386 915 Planarity : 0.005 0.080 1070 Dihedral : 6.814 57.609 866 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.08 % Favored : 89.01 % Rotamer: Outliers : 4.49 % Allowed : 26.65 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.31 (0.32), residues: 765 helix: 1.36 (0.73), residues: 45 sheet: -0.49 (0.32), residues: 273 loop : -1.37 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.017 0.001 TYR D 91 PHE 0.013 0.001 PHE C 378 TRP 0.012 0.001 TRP C 259 HIS 0.002 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6200) covalent geometry : angle 0.78377 ( 8401) SS BOND : bond 0.00406 ( 10) SS BOND : angle 1.09670 ( 20) hydrogen bonds : bond 0.03059 ( 180) hydrogen bonds : angle 5.19192 ( 449) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 ASN cc_start: 0.8040 (t0) cc_final: 0.7312 (p0) REVERT: C 121 MET cc_start: 0.8548 (mmm) cc_final: 0.7863 (ppp) REVERT: C 283 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7428 (ttt180) REVERT: C 287 ILE cc_start: 0.9087 (pt) cc_final: 0.8794 (pt) REVERT: C 289 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.6970 (p-80) REVERT: C 307 GLU cc_start: 0.9317 (pp20) cc_final: 0.8912 (tp30) REVERT: G 31 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.7554 (p0) REVERT: G 44 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8797 (mtp180) REVERT: G 67 LYS cc_start: 0.7997 (pttm) cc_final: 0.7766 (tttm) REVERT: G 81 MET cc_start: 0.8233 (tpp) cc_final: 0.7824 (tpp) REVERT: G 102 ASP cc_start: 0.8181 (p0) cc_final: 0.7678 (t0) REVERT: K 4 MET cc_start: 0.8677 (mmm) cc_final: 0.7090 (mtp) REVERT: D 42 LEU cc_start: 0.7919 (tp) cc_final: 0.7664 (mt) REVERT: D 91 TYR cc_start: 0.9317 (m-80) cc_final: 0.8771 (m-80) REVERT: H 36 TRP cc_start: 0.8371 (m100) cc_final: 0.7767 (m100) REVERT: H 102 ARG cc_start: 0.8388 (ptt180) cc_final: 0.7777 (ptm160) REVERT: H 105 TYR cc_start: 0.6735 (m-80) cc_final: 0.6267 (m-80) outliers start: 29 outliers final: 21 residues processed: 111 average time/residue: 0.0552 time to fit residues: 8.5752 Evaluate side-chains 103 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 371 HIS ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.067708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.057914 restraints weight = 90976.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.059768 restraints weight = 38739.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.060960 restraints weight = 21350.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.061734 restraints weight = 13740.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.062268 restraints weight = 9873.914| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6210 Z= 0.120 Angle : 0.764 10.575 8421 Z= 0.363 Chirality : 0.044 0.178 915 Planarity : 0.005 0.079 1070 Dihedral : 6.740 59.028 866 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.08 % Favored : 89.27 % Rotamer: Outliers : 4.19 % Allowed : 27.25 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.26 (0.32), residues: 765 helix: 1.38 (0.74), residues: 45 sheet: -0.43 (0.32), residues: 269 loop : -1.36 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.015 0.001 TYR G 27 PHE 0.021 0.001 PHE C 378 TRP 0.010 0.001 TRP C 259 HIS 0.008 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6200) covalent geometry : angle 0.76318 ( 8401) SS BOND : bond 0.00473 ( 10) SS BOND : angle 1.10274 ( 20) hydrogen bonds : bond 0.03035 ( 180) hydrogen bonds : angle 5.12814 ( 449) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 ASN cc_start: 0.8568 (t0) cc_final: 0.7588 (p0) REVERT: C 121 MET cc_start: 0.8446 (mmm) cc_final: 0.7831 (ppp) REVERT: C 206 MET cc_start: 0.7675 (pmm) cc_final: 0.7451 (tpt) REVERT: C 231 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7940 (pm20) REVERT: C 283 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7449 (ttt180) REVERT: C 287 ILE cc_start: 0.9114 (pt) cc_final: 0.8822 (pt) REVERT: C 289 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6948 (p-80) REVERT: G 31 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.7631 (p0) REVERT: G 67 LYS cc_start: 0.8098 (pttm) cc_final: 0.7852 (tttm) REVERT: G 81 MET cc_start: 0.8218 (tpp) cc_final: 0.7853 (tpp) REVERT: G 102 ASP cc_start: 0.8141 (p0) cc_final: 0.7533 (t0) REVERT: K 4 MET cc_start: 0.8725 (mmm) cc_final: 0.7164 (mtp) REVERT: H 36 TRP cc_start: 0.8305 (m100) cc_final: 0.7697 (m100) REVERT: H 65 MET cc_start: 0.7801 (tpp) cc_final: 0.7297 (tpp) REVERT: H 102 ARG cc_start: 0.8386 (ptt180) cc_final: 0.7750 (ptm160) REVERT: H 105 TYR cc_start: 0.6790 (m-80) cc_final: 0.6278 (m-80) outliers start: 27 outliers final: 21 residues processed: 101 average time/residue: 0.0680 time to fit residues: 9.4817 Evaluate side-chains 100 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.063807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.054368 restraints weight = 89601.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.056082 restraints weight = 38677.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.057200 restraints weight = 21843.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.057951 restraints weight = 14360.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.058458 restraints weight = 10481.603| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6210 Z= 0.202 Angle : 0.808 10.165 8421 Z= 0.394 Chirality : 0.044 0.333 915 Planarity : 0.005 0.083 1070 Dihedral : 7.282 55.077 866 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.60 % Favored : 88.48 % Rotamer: Outliers : 4.79 % Allowed : 27.54 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.14 % 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: -1.44 (0.32), residues: 765 helix: 1.66 (0.77), residues: 45 sheet: -0.61 (0.31), residues: 273 loop : -1.48 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 319 TYR 0.022 0.002 TYR D 91 PHE 0.015 0.002 PHE K 71 TRP 0.014 0.002 TRP G 111 HIS 0.005 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 6200) covalent geometry : angle 0.80694 ( 8401) SS BOND : bond 0.00424 ( 10) SS BOND : angle 1.19608 ( 20) hydrogen bonds : bond 0.03474 ( 180) hydrogen bonds : angle 5.54324 ( 449) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.8503 (mmm) cc_final: 0.7842 (ppp) REVERT: C 209 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7842 (p0) REVERT: C 231 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7876 (pm20) REVERT: C 283 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7556 (ttt180) REVERT: C 287 ILE cc_start: 0.9234 (pt) cc_final: 0.8991 (pt) REVERT: C 289 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7069 (p-80) REVERT: C 306 LEU cc_start: 0.9632 (tt) cc_final: 0.9331 (pp) REVERT: G 31 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.7677 (p0) REVERT: G 43 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8792 (pm20) REVERT: G 102 ASP cc_start: 0.8230 (p0) cc_final: 0.7739 (t0) REVERT: K 37 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6623 (tp40) REVERT: H 36 TRP cc_start: 0.8478 (m100) cc_final: 0.7676 (m100) REVERT: H 65 MET cc_start: 0.7949 (tpp) cc_final: 0.7422 (tpp) REVERT: H 105 TYR cc_start: 0.7032 (m-80) cc_final: 0.6352 (m-80) outliers start: 31 outliers final: 25 residues processed: 96 average time/residue: 0.0617 time to fit residues: 8.3505 Evaluate side-chains 99 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.066627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.057663 restraints weight = 60943.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.059165 restraints weight = 29550.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.060146 restraints weight = 17606.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.060794 restraints weight = 11935.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.061243 restraints weight = 8898.263| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6210 Z= 0.127 Angle : 0.800 10.989 8421 Z= 0.380 Chirality : 0.045 0.304 915 Planarity : 0.005 0.079 1070 Dihedral : 7.049 56.623 866 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.55 % Favored : 89.53 % Rotamer: Outliers : 4.04 % Allowed : 28.44 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.14 % 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: -1.34 (0.32), residues: 765 helix: 1.50 (0.76), residues: 45 sheet: -0.55 (0.32), residues: 274 loop : -1.39 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.019 0.001 TYR D 91 PHE 0.013 0.001 PHE C 378 TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6200) covalent geometry : angle 0.79924 ( 8401) SS BOND : bond 0.00358 ( 10) SS BOND : angle 1.09322 ( 20) hydrogen bonds : bond 0.03099 ( 180) hydrogen bonds : angle 5.28288 ( 449) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8519 (pmm) cc_final: 0.7930 (pmm) REVERT: C 76 ASN cc_start: 0.8723 (t0) cc_final: 0.8438 (t0) REVERT: C 121 MET cc_start: 0.8587 (mmm) cc_final: 0.7946 (ppp) REVERT: C 231 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7944 (pm20) REVERT: C 283 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7617 (ttt180) REVERT: C 287 ILE cc_start: 0.9199 (pt) cc_final: 0.8920 (pt) REVERT: C 289 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7012 (p-80) REVERT: C 306 LEU cc_start: 0.9647 (tt) cc_final: 0.9327 (pp) REVERT: G 31 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.7635 (p0) REVERT: G 43 GLN cc_start: 0.9184 (tm-30) cc_final: 0.8872 (pm20) REVERT: G 67 LYS cc_start: 0.8357 (pttm) cc_final: 0.7985 (tttm) REVERT: G 102 ASP cc_start: 0.8482 (p0) cc_final: 0.7860 (t0) REVERT: K 4 MET cc_start: 0.8673 (mmm) cc_final: 0.7016 (mtp) REVERT: H 65 MET cc_start: 0.7931 (tpp) cc_final: 0.7371 (tpp) REVERT: H 105 TYR cc_start: 0.6911 (m-80) cc_final: 0.6274 (m-80) outliers start: 26 outliers final: 22 residues processed: 95 average time/residue: 0.0674 time to fit residues: 9.0206 Evaluate side-chains 98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 94 TYR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.065482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.055298 restraints weight = 121000.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.057276 restraints weight = 46035.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.058549 restraints weight = 24537.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.059376 restraints weight = 15498.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.059943 restraints weight = 10999.565| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6210 Z= 0.148 Angle : 0.800 11.357 8421 Z= 0.383 Chirality : 0.044 0.308 915 Planarity : 0.005 0.082 1070 Dihedral : 7.086 56.472 866 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.34 % Favored : 88.87 % Rotamer: Outliers : 4.49 % Allowed : 28.29 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.14 % 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: -1.36 (0.32), residues: 765 helix: 1.60 (0.77), residues: 45 sheet: -0.58 (0.32), residues: 274 loop : -1.40 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.013 0.001 TYR G 27 PHE 0.012 0.001 PHE K 71 TRP 0.017 0.002 TRP H 36 HIS 0.003 0.001 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6200) covalent geometry : angle 0.79942 ( 8401) SS BOND : bond 0.00378 ( 10) SS BOND : angle 1.13983 ( 20) hydrogen bonds : bond 0.03136 ( 180) hydrogen bonds : angle 5.26358 ( 449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1160.55 seconds wall clock time: 20 minutes 43.23 seconds (1243.23 seconds total)