Starting phenix.real_space_refine on Sun May 11 01:00:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umc_42375/05_2025/8umc_42375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umc_42375/05_2025/8umc_42375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umc_42375/05_2025/8umc_42375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umc_42375/05_2025/8umc_42375.map" model { file = "/net/cci-nas-00/data/ceres_data/8umc_42375/05_2025/8umc_42375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umc_42375/05_2025/8umc_42375.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians Mn 2 7.51 5 S 54 5.16 5 C 4564 2.51 5 N 1270 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2630 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 307} Chain: "B" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 968 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2630 Classifications: {'peptide': 322} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 307} Chain: "D" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 968 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.76, per 1000 atoms: 0.66 Number of scatterers: 7198 At special positions: 0 Unit cell: (107.06, 80.8, 82.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 2 24.99 S 54 16.00 O 1308 8.00 N 1270 7.00 C 4564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 973.8 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 43.5% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.563A pdb=" N GLU A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.770A pdb=" N ARG A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.860A pdb=" N THR A 180 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.030A pdb=" N LEU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 309 through 325 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 65 through 69 removed outlier: 4.367A pdb=" N ASP B 68 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 25 through 37 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.658A pdb=" N TYR C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 111 removed outlier: 3.659A pdb=" N ASP C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.685A pdb=" N SER C 136 " --> pdb=" O HIS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.996A pdb=" N LEU C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 removed outlier: 3.526A pdb=" N GLU C 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 309 through 325 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.093A pdb=" N ILE A 115 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU A 143 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 117 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 114 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 75 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ARG A 116 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS A 77 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A 41 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS A 77 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER A 43 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 40 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS A 7 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER A 294 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY A 9 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N TYR A 296 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N SER A 11 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 258 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 295 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 260 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48 removed outlier: 4.707A pdb=" N VAL B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 94 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.707A pdb=" N LEU C 140 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 173 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 142 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE C 115 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU C 143 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL C 117 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE C 41 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N HIS C 77 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER C 43 " --> pdb=" O HIS C 77 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 40 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 7 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N SER C 294 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY C 9 " --> pdb=" O SER C 294 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N TYR C 296 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER C 11 " --> pdb=" O TYR C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.543A pdb=" N THR D 84 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 32 Processing sheet with id=AA9, first strand: chain 'D' and resid 46 through 47 removed outlier: 3.529A pdb=" N GLU D 46 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 43 " --> pdb=" O GLU D 46 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2438 1.34 - 1.46: 1331 1.46 - 1.57: 3499 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 7368 Sorted by residual: bond pdb=" N VAL A 101 " pdb=" CA VAL A 101 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.01e+00 bond pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.76e+00 bond pdb=" N ASP A 266 " pdb=" CA ASP A 266 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.34e-02 5.57e+03 7.07e+00 bond pdb=" N GLN C 268 " pdb=" CA GLN C 268 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.18e-02 7.18e+03 6.98e+00 bond pdb=" N HIS A 145 " pdb=" CA HIS A 145 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.18e-02 7.18e+03 6.86e+00 ... (remaining 7363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 9339 1.26 - 2.53: 487 2.53 - 3.79: 104 3.79 - 5.05: 21 5.05 - 6.32: 3 Bond angle restraints: 9954 Sorted by residual: angle pdb=" N PRO A 147 " pdb=" CA PRO A 147 " pdb=" CB PRO A 147 " ideal model delta sigma weight residual 103.25 96.93 6.32 1.05e+00 9.07e-01 3.62e+01 angle pdb=" CA ILE A 302 " pdb=" C ILE A 302 " pdb=" O ILE A 302 " ideal model delta sigma weight residual 122.63 118.54 4.09 8.70e-01 1.32e+00 2.21e+01 angle pdb=" N MET C 320 " pdb=" CA MET C 320 " pdb=" C MET C 320 " ideal model delta sigma weight residual 111.14 106.07 5.07 1.08e+00 8.57e-01 2.20e+01 angle pdb=" CA ASP C 266 " pdb=" C ASP C 266 " pdb=" O ASP C 266 " ideal model delta sigma weight residual 122.01 118.23 3.78 1.05e+00 9.07e-01 1.30e+01 angle pdb=" CA ASP A 266 " pdb=" C ASP A 266 " pdb=" O ASP A 266 " ideal model delta sigma weight residual 122.01 118.28 3.73 1.05e+00 9.07e-01 1.26e+01 ... (remaining 9949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.28: 4078 26.28 - 52.56: 288 52.56 - 78.84: 47 78.84 - 105.12: 10 105.12 - 131.40: 1 Dihedral angle restraints: 4424 sinusoidal: 1862 harmonic: 2562 Sorted by residual: dihedral pdb=" CA ALA A 146 " pdb=" C ALA A 146 " pdb=" N PRO A 147 " pdb=" CA PRO A 147 " ideal model delta harmonic sigma weight residual 180.00 48.60 131.40 0 5.00e+00 4.00e-02 6.91e+02 dihedral pdb=" CA ARG C 193 " pdb=" C ARG C 193 " pdb=" N GLN C 194 " pdb=" CA GLN C 194 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ARG C 105 " pdb=" C ARG C 105 " pdb=" N HIS C 106 " pdb=" CA HIS C 106 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 801 0.049 - 0.098: 192 0.098 - 0.147: 55 0.147 - 0.197: 6 0.197 - 0.246: 2 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA MET C 320 " pdb=" N MET C 320 " pdb=" C MET C 320 " pdb=" CB MET C 320 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL B 15 " pdb=" N VAL B 15 " pdb=" C VAL B 15 " pdb=" CB VAL B 15 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 1053 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 210 " 0.313 9.50e-02 1.11e+02 1.40e-01 1.21e+01 pdb=" NE ARG A 210 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 210 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 210 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 210 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 254 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.56e+00 pdb=" NE ARG A 254 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 254 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 254 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 254 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 270 " 0.178 9.50e-02 1.11e+02 7.99e-02 4.29e+00 pdb=" NE ARG A 270 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 270 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 270 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 270 " 0.003 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 113 2.62 - 3.19: 6478 3.19 - 3.76: 11573 3.76 - 4.33: 17203 4.33 - 4.90: 27913 Nonbonded interactions: 63280 Sorted by model distance: nonbonded pdb=" OH TYR B 27 " pdb=" OH TYR B 108 " model vdw 2.045 3.040 nonbonded pdb=" OH TYR D 28 " pdb=" OH TYR D 108 " model vdw 2.048 3.040 nonbonded pdb=" OE1 GLU A 295 " pdb="MN MN A 401 " model vdw 2.101 2.320 nonbonded pdb=" OE1 GLU C 295 " pdb="MN MN C 401 " model vdw 2.115 2.320 nonbonded pdb=" O LYS C 261 " pdb=" OH TYR C 276 " model vdw 2.133 3.040 ... (remaining 63275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.830 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7368 Z= 0.289 Angle : 0.683 6.318 9954 Z= 0.420 Chirality : 0.048 0.246 1056 Planarity : 0.007 0.140 1310 Dihedral : 17.532 131.399 2780 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.16 % Allowed : 19.51 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.28), residues: 882 helix: 0.14 (0.28), residues: 344 sheet: -1.05 (0.42), residues: 154 loop : -0.79 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 242 HIS 0.006 0.001 HIS C 257 PHE 0.012 0.002 PHE C 20 TYR 0.014 0.001 TYR A 13 ARG 0.011 0.001 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.15222 ( 305) hydrogen bonds : angle 6.77669 ( 834) covalent geometry : bond 0.00511 ( 7368) covalent geometry : angle 0.68272 ( 9954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 241 ASN cc_start: 0.8181 (p0) cc_final: 0.7918 (p0) outliers start: 9 outliers final: 5 residues processed: 221 average time/residue: 1.2904 time to fit residues: 298.7238 Evaluate side-chains 214 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 209 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain D residue 62 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.131999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122606 restraints weight = 8877.094| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.28 r_work: 0.3562 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7368 Z= 0.261 Angle : 0.642 6.255 9954 Z= 0.335 Chirality : 0.047 0.170 1056 Planarity : 0.005 0.056 1310 Dihedral : 5.930 68.780 1004 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.01 % Allowed : 19.77 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.28), residues: 882 helix: 0.50 (0.28), residues: 334 sheet: -1.12 (0.43), residues: 150 loop : -0.57 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 242 HIS 0.005 0.001 HIS A 149 PHE 0.016 0.002 PHE C 20 TYR 0.012 0.002 TYR A 13 ARG 0.007 0.001 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 305) hydrogen bonds : angle 5.57912 ( 834) covalent geometry : bond 0.00597 ( 7368) covalent geometry : angle 0.64201 ( 9954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7093 (p0) cc_final: 0.6517 (p0) REVERT: A 61 ASP cc_start: 0.7490 (m-30) cc_final: 0.7224 (m-30) REVERT: A 91 MET cc_start: 0.8111 (mtm) cc_final: 0.7901 (ttm) REVERT: C 278 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: C 284 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8630 (mttp) outliers start: 31 outliers final: 14 residues processed: 232 average time/residue: 1.2227 time to fit residues: 297.9039 Evaluate side-chains 221 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123727 restraints weight = 8978.723| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.30 r_work: 0.3575 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7368 Z= 0.179 Angle : 0.579 5.746 9954 Z= 0.301 Chirality : 0.044 0.164 1056 Planarity : 0.005 0.102 1310 Dihedral : 5.473 59.425 999 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.26 % Allowed : 20.28 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 882 helix: 0.73 (0.28), residues: 334 sheet: -1.01 (0.44), residues: 150 loop : -0.44 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.003 0.001 HIS A 182 PHE 0.013 0.002 PHE C 20 TYR 0.016 0.002 TYR A 13 ARG 0.007 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 305) hydrogen bonds : angle 5.29801 ( 834) covalent geometry : bond 0.00406 ( 7368) covalent geometry : angle 0.57936 ( 9954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7502 (m-30) cc_final: 0.7276 (m-30) REVERT: C 241 ASN cc_start: 0.8132 (p0) cc_final: 0.7864 (p0) REVERT: C 278 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7305 (mm-30) outliers start: 33 outliers final: 17 residues processed: 231 average time/residue: 1.2790 time to fit residues: 309.7191 Evaluate side-chains 229 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 46 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN C 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.133235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.123878 restraints weight = 8999.241| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.31 r_work: 0.3583 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7368 Z= 0.164 Angle : 0.567 5.394 9954 Z= 0.293 Chirality : 0.044 0.159 1056 Planarity : 0.005 0.107 1310 Dihedral : 5.292 54.827 999 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.52 % Allowed : 21.58 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 882 helix: 0.85 (0.28), residues: 334 sheet: -0.92 (0.44), residues: 154 loop : -0.32 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.004 0.001 HIS A 158 PHE 0.012 0.002 PHE C 59 TYR 0.011 0.001 TYR C 13 ARG 0.006 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 305) hydrogen bonds : angle 5.15086 ( 834) covalent geometry : bond 0.00372 ( 7368) covalent geometry : angle 0.56670 ( 9954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8152 (mptt) cc_final: 0.7920 (mttp) REVERT: A 61 ASP cc_start: 0.7510 (m-30) cc_final: 0.7253 (m-30) REVERT: A 187 MET cc_start: 0.7984 (mtt) cc_final: 0.7750 (mtp) REVERT: C 232 ARG cc_start: 0.8269 (ttp80) cc_final: 0.8052 (ttm110) REVERT: C 236 MET cc_start: 0.8822 (mtt) cc_final: 0.8460 (mtt) REVERT: C 241 ASN cc_start: 0.8137 (p0) cc_final: 0.7882 (p0) REVERT: C 278 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7209 (mm-30) outliers start: 35 outliers final: 20 residues processed: 237 average time/residue: 1.2681 time to fit residues: 315.1898 Evaluate side-chains 236 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 145 HIS A 241 ASN C 96 GLN C 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.133309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123915 restraints weight = 8901.635| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.29 r_work: 0.3581 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7368 Z= 0.189 Angle : 0.592 5.899 9954 Z= 0.305 Chirality : 0.045 0.157 1056 Planarity : 0.005 0.106 1310 Dihedral : 5.298 53.618 998 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.75 % Allowed : 22.09 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 882 helix: 0.88 (0.29), residues: 334 sheet: -0.96 (0.44), residues: 152 loop : -0.27 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.004 0.001 HIS A 158 PHE 0.016 0.002 PHE C 20 TYR 0.017 0.002 TYR A 13 ARG 0.006 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 305) hydrogen bonds : angle 5.15259 ( 834) covalent geometry : bond 0.00432 ( 7368) covalent geometry : angle 0.59181 ( 9954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7512 (m-30) cc_final: 0.7263 (m-30) REVERT: C 203 TYR cc_start: 0.8235 (t80) cc_final: 0.7841 (t80) REVERT: C 241 ASN cc_start: 0.8158 (p0) cc_final: 0.7928 (p0) REVERT: C 278 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7212 (mm-30) outliers start: 29 outliers final: 17 residues processed: 231 average time/residue: 1.3427 time to fit residues: 324.2978 Evaluate side-chains 227 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 83 optimal weight: 0.0770 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 145 HIS A 207 GLN A 241 ASN C 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.134874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.125502 restraints weight = 8952.957| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.30 r_work: 0.3601 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7368 Z= 0.140 Angle : 0.568 6.507 9954 Z= 0.293 Chirality : 0.044 0.172 1056 Planarity : 0.005 0.110 1310 Dihedral : 5.097 48.532 998 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.62 % Allowed : 23.26 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.30), residues: 882 helix: 1.01 (0.29), residues: 334 sheet: -1.10 (0.42), residues: 168 loop : -0.14 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.004 0.001 HIS A 158 PHE 0.012 0.001 PHE C 20 TYR 0.011 0.001 TYR C 13 ARG 0.007 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 305) hydrogen bonds : angle 4.99992 ( 834) covalent geometry : bond 0.00319 ( 7368) covalent geometry : angle 0.56762 ( 9954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8154 (mptt) cc_final: 0.7918 (mttp) REVERT: A 61 ASP cc_start: 0.7501 (m-30) cc_final: 0.7244 (m-30) REVERT: A 300 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.7857 (ptp-170) REVERT: C 49 MET cc_start: 0.8382 (mtt) cc_final: 0.7670 (mtt) REVERT: C 203 TYR cc_start: 0.8182 (t80) cc_final: 0.7852 (t80) REVERT: C 241 ASN cc_start: 0.8092 (p0) cc_final: 0.7871 (p0) REVERT: C 278 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7205 (mm-30) outliers start: 28 outliers final: 18 residues processed: 226 average time/residue: 1.3509 time to fit residues: 319.1251 Evaluate side-chains 224 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 145 HIS A 199 HIS A 207 GLN A 241 ASN C 96 GLN C 241 ASN C 244 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123605 restraints weight = 8907.343| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.30 r_work: 0.3575 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7368 Z= 0.220 Angle : 0.624 6.758 9954 Z= 0.322 Chirality : 0.046 0.164 1056 Planarity : 0.006 0.100 1310 Dihedral : 5.292 49.177 998 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.26 % Allowed : 23.26 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 882 helix: 0.94 (0.29), residues: 334 sheet: -1.15 (0.42), residues: 164 loop : -0.21 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 63 HIS 0.005 0.001 HIS A 158 PHE 0.017 0.002 PHE C 20 TYR 0.017 0.002 TYR A 13 ARG 0.007 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 305) hydrogen bonds : angle 5.07483 ( 834) covalent geometry : bond 0.00504 ( 7368) covalent geometry : angle 0.62402 ( 9954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7501 (m-30) cc_final: 0.7244 (m-30) REVERT: B 35 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7100 (mtp) REVERT: C 203 TYR cc_start: 0.8233 (t80) cc_final: 0.7929 (t80) REVERT: C 232 ARG cc_start: 0.8307 (ttp80) cc_final: 0.8083 (ttm110) REVERT: C 241 ASN cc_start: 0.8096 (p0) cc_final: 0.7894 (p0) REVERT: C 261 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8521 (ttmm) REVERT: C 278 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: C 297 GLU cc_start: 0.7445 (tt0) cc_final: 0.7148 (tt0) REVERT: D 35 MET cc_start: 0.7561 (mtp) cc_final: 0.7234 (mtp) outliers start: 33 outliers final: 22 residues processed: 227 average time/residue: 1.3194 time to fit residues: 313.8857 Evaluate side-chains 232 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 145 HIS A 207 GLN A 244 ASN C 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.134767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125422 restraints weight = 9023.930| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.30 r_work: 0.3597 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7368 Z= 0.157 Angle : 0.593 7.500 9954 Z= 0.305 Chirality : 0.044 0.186 1056 Planarity : 0.005 0.096 1310 Dihedral : 5.091 44.443 998 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.26 % Allowed : 23.39 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.30), residues: 882 helix: 1.00 (0.29), residues: 334 sheet: -1.06 (0.42), residues: 168 loop : -0.18 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.005 0.001 HIS A 158 PHE 0.013 0.002 PHE C 20 TYR 0.016 0.001 TYR C 13 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 305) hydrogen bonds : angle 4.98937 ( 834) covalent geometry : bond 0.00357 ( 7368) covalent geometry : angle 0.59337 ( 9954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8153 (mptt) cc_final: 0.7916 (mttp) REVERT: A 61 ASP cc_start: 0.7485 (m-30) cc_final: 0.7221 (m-30) REVERT: A 203 TYR cc_start: 0.8280 (t80) cc_final: 0.8062 (t80) REVERT: A 246 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7808 (mmm160) REVERT: B 35 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6993 (mtp) REVERT: C 161 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7874 (t80) REVERT: C 187 MET cc_start: 0.8139 (mtt) cc_final: 0.7835 (mtp) REVERT: C 203 TYR cc_start: 0.8189 (t80) cc_final: 0.7879 (t80) REVERT: C 261 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8451 (ttmm) REVERT: C 278 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: C 297 GLU cc_start: 0.7331 (tt0) cc_final: 0.7039 (tt0) REVERT: D 35 MET cc_start: 0.7481 (mtp) cc_final: 0.7176 (mtp) outliers start: 33 outliers final: 22 residues processed: 232 average time/residue: 1.3170 time to fit residues: 319.6653 Evaluate side-chains 235 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 145 HIS A 207 GLN A 303 GLN C 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124963 restraints weight = 8965.013| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.30 r_work: 0.3592 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7368 Z= 0.178 Angle : 0.608 7.625 9954 Z= 0.314 Chirality : 0.045 0.187 1056 Planarity : 0.005 0.092 1310 Dihedral : 5.130 44.496 998 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.88 % Allowed : 24.42 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.30), residues: 882 helix: 1.03 (0.29), residues: 334 sheet: -1.05 (0.43), residues: 168 loop : -0.18 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.006 0.001 HIS A 158 PHE 0.015 0.002 PHE C 20 TYR 0.019 0.002 TYR D 108 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 305) hydrogen bonds : angle 4.98335 ( 834) covalent geometry : bond 0.00407 ( 7368) covalent geometry : angle 0.60777 ( 9954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7510 (m-30) cc_final: 0.7241 (m-30) REVERT: A 246 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7814 (mmm160) REVERT: B 35 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7169 (mtp) REVERT: C 48 MET cc_start: 0.8572 (mtt) cc_final: 0.8262 (mtt) REVERT: C 161 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7895 (t80) REVERT: C 187 MET cc_start: 0.8146 (mtt) cc_final: 0.7855 (mtp) REVERT: C 203 TYR cc_start: 0.8196 (t80) cc_final: 0.7923 (t80) REVERT: C 232 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8271 (ttp80) REVERT: C 261 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8448 (ttmm) REVERT: C 278 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: C 297 GLU cc_start: 0.7337 (tt0) cc_final: 0.7064 (tt0) outliers start: 30 outliers final: 20 residues processed: 230 average time/residue: 1.3069 time to fit residues: 314.7941 Evaluate side-chains 232 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 145 HIS ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN C 96 GLN C 145 HIS C 241 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.134089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124493 restraints weight = 9218.492| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.36 r_work: 0.3601 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7368 Z= 0.156 Angle : 0.607 7.935 9954 Z= 0.312 Chirality : 0.045 0.176 1056 Planarity : 0.005 0.091 1310 Dihedral : 5.076 44.078 998 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.49 % Allowed : 25.45 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.30), residues: 882 helix: 1.08 (0.29), residues: 334 sheet: -1.03 (0.43), residues: 168 loop : -0.14 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 63 HIS 0.006 0.001 HIS A 158 PHE 0.013 0.002 PHE C 20 TYR 0.019 0.001 TYR C 13 ARG 0.015 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 305) hydrogen bonds : angle 4.94870 ( 834) covalent geometry : bond 0.00354 ( 7368) covalent geometry : angle 0.60672 ( 9954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8135 (mptt) cc_final: 0.7895 (mttp) REVERT: A 61 ASP cc_start: 0.7520 (m-30) cc_final: 0.7283 (m-30) REVERT: A 246 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7837 (mmm160) REVERT: C 48 MET cc_start: 0.8527 (mtt) cc_final: 0.8223 (mtt) REVERT: C 161 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7865 (t80) REVERT: C 187 MET cc_start: 0.8125 (mtt) cc_final: 0.7874 (mtp) REVERT: C 203 TYR cc_start: 0.8219 (t80) cc_final: 0.7913 (t80) REVERT: C 232 ARG cc_start: 0.8477 (ttm110) cc_final: 0.8252 (ttp80) REVERT: C 261 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8452 (ttmm) REVERT: C 297 GLU cc_start: 0.7384 (tt0) cc_final: 0.7097 (tt0) outliers start: 27 outliers final: 21 residues processed: 221 average time/residue: 1.3415 time to fit residues: 310.9926 Evaluate side-chains 233 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 145 HIS A 207 GLN A 244 ASN C 96 GLN C 313 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.123483 restraints weight = 9093.074| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.35 r_work: 0.3589 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7368 Z= 0.194 Angle : 0.640 8.155 9954 Z= 0.329 Chirality : 0.045 0.174 1056 Planarity : 0.005 0.088 1310 Dihedral : 5.186 44.306 998 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.62 % Allowed : 25.84 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.30), residues: 882 helix: 1.05 (0.29), residues: 334 sheet: -1.00 (0.43), residues: 168 loop : -0.17 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 63 HIS 0.007 0.001 HIS A 158 PHE 0.016 0.002 PHE C 20 TYR 0.019 0.002 TYR D 108 ARG 0.014 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 305) hydrogen bonds : angle 4.99489 ( 834) covalent geometry : bond 0.00444 ( 7368) covalent geometry : angle 0.63975 ( 9954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6813.07 seconds wall clock time: 118 minutes 12.37 seconds (7092.37 seconds total)