Starting phenix.real_space_refine on Fri Aug 22 18:54:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lo8_23464/08_2025/7lo8_23464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lo8_23464/08_2025/7lo8_23464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lo8_23464/08_2025/7lo8_23464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lo8_23464/08_2025/7lo8_23464.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lo8_23464/08_2025/7lo8_23464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lo8_23464/08_2025/7lo8_23464.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 960 atoms to isotropic. 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 30 5.16 5 C 4022 2.51 5 N 999 2.21 5 O 1154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6205 Number of models: 1 Model: "" Number of chains: 3 Chain: "Z" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2835 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 13, 'TRANS': 355} Chain breaks: 1 Chain: "H" Number of atoms: 1734 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1733 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 219} Conformer: "B" Number of residues, atoms: 231, 1733 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 219} bond proxies already assigned to first conformer: 1778 Chain: "L" Number of atoms: 1636 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 215, 1633 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Conformer: "B" Number of residues, atoms: 215, 1633 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} bond proxies already assigned to first conformer: 1661 Time building chain proxies: 2.21, per 1000 atoms: 0.36 Number of scatterers: 6205 At special positions: 0 Unit cell: (62.582, 69.056, 129.48, 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 30 16.00 O 1154 8.00 N 999 7.00 C 4022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 181 " - pdb=" SG CYS H 237 " distance=2.03 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG BCYS H 181 " distance=2.03 Simple disulfide: pdb=" SG CYS H 257 " - pdb=" SG CYS L 238 " distance=2.03 Simple disulfide: pdb=" SG CYS L 47 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " 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: 0.52 Conformation dependent library (CDL) restraints added in 498.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 11 sheets defined 43.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'Z' and resid 3 through 22 removed outlier: 3.524A pdb=" N VAL Z 7 " --> pdb=" O LYS Z 3 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE Z 10 " --> pdb=" O PHE Z 6 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 33 removed outlier: 3.537A pdb=" N LEU Z 30 " --> pdb=" O LEU Z 26 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS Z 31 " --> pdb=" O PRO Z 27 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP Z 32 " --> pdb=" O VAL Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 55 removed outlier: 3.543A pdb=" N GLY Z 41 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA Z 48 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 66 through 86 removed outlier: 3.508A pdb=" N ALA Z 86 " --> pdb=" O GLU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 108 removed outlier: 3.567A pdb=" N VAL Z 99 " --> pdb=" O MET Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 116 Processing helix chain 'Z' and resid 124 through 150 Proline residue: Z 144 - end of helix Processing helix chain 'Z' and resid 156 through 177 removed outlier: 3.696A pdb=" N TYR Z 160 " --> pdb=" O ARG Z 156 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE Z 174 " --> pdb=" O PHE Z 170 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE Z 177 " --> pdb=" O SER Z 173 " (cutoff:3.500A) Processing helix chain 'Z' and resid 200 through 203 removed outlier: 4.170A pdb=" N VAL Z 203 " --> pdb=" O ASN Z 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 200 through 203' Processing helix chain 'Z' and resid 204 through 224 removed outlier: 3.683A pdb=" N VAL Z 208 " --> pdb=" O PHE Z 204 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA Z 220 " --> pdb=" O PHE Z 216 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU Z 224 " --> pdb=" O ALA Z 220 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 232 removed outlier: 4.035A pdb=" N ALA Z 230 " --> pdb=" O SER Z 226 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP Z 231 " --> pdb=" O LEU Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 257 removed outlier: 4.376A pdb=" N SER Z 241 " --> pdb=" O PRO Z 237 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE Z 242 " --> pdb=" O LYS Z 238 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA Z 243 " --> pdb=" O ASP Z 239 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 265 removed outlier: 3.684A pdb=" N LYS Z 261 " --> pdb=" O TYR Z 257 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE Z 262 " --> pdb=" O PHE Z 258 " (cutoff:3.500A) Processing helix chain 'Z' and resid 267 through 289 removed outlier: 3.647A pdb=" N PHE Z 271 " --> pdb=" O SER Z 267 " (cutoff:3.500A) Processing helix chain 'Z' and resid 292 through 303 removed outlier: 4.255A pdb=" N ILE Z 298 " --> pdb=" O SER Z 294 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL Z 301 " --> pdb=" O LEU Z 297 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE Z 303 " --> pdb=" O SER Z 299 " (cutoff:3.500A) Processing helix chain 'Z' and resid 303 through 308 Processing helix chain 'Z' and resid 308 through 321 removed outlier: 3.811A pdb=" N ALA Z 312 " --> pdb=" O MET Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 324 through 352 Proline residue: Z 344 - end of helix removed outlier: 3.530A pdb=" N ALA Z 349 " --> pdb=" O LEU Z 345 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP Z 352 " --> pdb=" O GLY Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 381 removed outlier: 3.707A pdb=" N TYR Z 360 " --> pdb=" O GLU Z 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 117 removed outlier: 4.089A pdb=" N THR H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 172 Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'H' and resid 228 through 233 removed outlier: 4.529A pdb=" N THR H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 150 removed outlier: 3.618A pdb=" N LYS L 150 " --> pdb=" O ASP L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 212 removed outlier: 3.572A pdb=" N LYS L 212 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 30 through 33 removed outlier: 3.692A pdb=" N LEU H 46 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS H 48 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 59 through 61 Processing sheet with id=AA3, first strand: chain 'H' and resid 71 through 72 removed outlier: 3.988A pdb=" N THR H 149 " --> pdb=" O TYR H 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 130 Processing sheet with id=AA5, first strand: chain 'H' and resid 161 through 165 removed outlier: 3.575A pdb=" N LYS H 184 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY H 180 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER H 221 " --> pdb=" O CYS H 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 191 through 194 removed outlier: 4.043A pdb=" N TYR H 235 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.654A pdb=" N THR L 46 " --> pdb=" O SER L 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 34 through 36 removed outlier: 6.605A pdb=" N LEU L 35 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA L 58 " --> pdb=" O GLN L 113 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 34 through 36 removed outlier: 6.605A pdb=" N LEU L 35 " --> pdb=" O GLU L 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 138 through 142 removed outlier: 3.625A pdb=" N VAL L 157 " --> pdb=" O PHE L 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 169 through 174 removed outlier: 3.913A pdb=" N LYS L 169 " --> pdb=" O THR L 221 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR L 216 " --> pdb=" O PHE L 233 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS L 218 " --> pdb=" O LYS L 231 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS L 231 " --> pdb=" O CYS L 218 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL L 220 " --> pdb=" O VAL L 229 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 229 " --> pdb=" O VAL L 220 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 858 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: 0.78 Time building geometry restraints manager: 0.72 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: 1886 1.34 - 1.46: 1315 1.46 - 1.58: 3106 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 6355 Sorted by residual: bond pdb=" C MET Z 157 " pdb=" N PRO Z 158 " ideal model delta sigma weight residual 1.335 1.369 -0.035 1.28e-02 6.10e+03 7.31e+00 bond pdb=" C LEU Z 26 " pdb=" N PRO Z 27 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.41e+00 bond pdb=" CB ILE Z 12 " pdb=" CG2 ILE Z 12 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CG1 ILE Z 23 " pdb=" CD1 ILE Z 23 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.88e+00 bond pdb=" CA PHE L 86 " pdb=" CB PHE L 86 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.65e-02 3.67e+03 1.80e+00 ... (remaining 6350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 8287 2.09 - 4.19: 243 4.19 - 6.28: 71 6.28 - 8.38: 21 8.38 - 10.47: 3 Bond angle restraints: 8625 Sorted by residual: angle pdb=" C SER L 84 " pdb=" N ARG L 85 " pdb=" CA ARG L 85 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.01e+01 angle pdb=" N ILE Z 295 " pdb=" CA ILE Z 295 " pdb=" C ILE Z 295 " ideal model delta sigma weight residual 113.42 107.67 5.75 1.17e+00 7.31e-01 2.42e+01 angle pdb=" C ARG L 85 " pdb=" N PHE L 86 " pdb=" CA PHE L 86 " ideal model delta sigma weight residual 121.76 129.01 -7.25 1.51e+00 4.39e-01 2.30e+01 angle pdb=" C ALA H 132 " pdb=" N TRP H 133 " pdb=" CA TRP H 133 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C LYS H 184 " pdb=" N ASP H 185 " pdb=" CA ASP H 185 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 ... (remaining 8620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3328 17.72 - 35.45: 323 35.45 - 53.17: 68 53.17 - 70.89: 9 70.89 - 88.61: 6 Dihedral angle restraints: 3734 sinusoidal: 1399 harmonic: 2335 Sorted by residual: dihedral pdb=" CA TYR L 164 " pdb=" C TYR L 164 " pdb=" N PRO L 165 " pdb=" CA PRO L 165 " ideal model delta harmonic sigma weight residual -180.00 -114.82 -65.18 0 5.00e+00 4.00e-02 1.70e+02 dihedral pdb=" CA PHE L 163 " pdb=" C PHE L 163 " pdb=" N TYR L 164 " pdb=" CA TYR L 164 " ideal model delta harmonic sigma weight residual 180.00 130.64 49.36 0 5.00e+00 4.00e-02 9.75e+01 dihedral pdb=" CB CYS H 181 " pdb=" SG BCYS H 181 " pdb=" SG CYS H 237 " pdb=" CB CYS H 237 " ideal model delta sinusoidal sigma weight residual 93.00 -178.39 -88.61 1 1.00e+01 1.00e-02 9.37e+01 ... (remaining 3731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 680 0.046 - 0.093: 235 0.093 - 0.139: 60 0.139 - 0.185: 8 0.185 - 0.231: 5 Chirality restraints: 988 Sorted by residual: chirality pdb=" CA THR Z 206 " pdb=" N THR Z 206 " pdb=" C THR Z 206 " pdb=" CB THR Z 206 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO L 83 " pdb=" N PRO L 83 " pdb=" C PRO L 83 " pdb=" CB PRO L 83 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE Z 177 " pdb=" CA ILE Z 177 " pdb=" CG1 ILE Z 177 " pdb=" CG2 ILE Z 177 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 985 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 164 " -0.076 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO L 165 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO L 165 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO L 165 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 63 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO L 64 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 85 " 0.021 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C ARG L 85 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG L 85 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE L 86 " 0.026 2.00e-02 2.50e+03 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 220 2.70 - 3.25: 6400 3.25 - 3.80: 9455 3.80 - 4.35: 12262 4.35 - 4.90: 20858 Nonbonded interactions: 49195 Sorted by model distance: nonbonded pdb=" O SER Z 215 " pdb=" OG SER Z 219 " model vdw 2.152 3.040 nonbonded pdb=" OE2 GLU Z 222 " pdb=" NH1 ARG H 134 " model vdw 2.153 3.120 nonbonded pdb=" O ALA Z 362 " pdb=" OG SER Z 366 " model vdw 2.214 3.040 nonbonded pdb=" O ILE L 130 " pdb=" OH TYR L 164 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLU Z 222 " pdb=" OH TYR H 131 " model vdw 2.232 3.040 ... (remaining 49190 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=0.21 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.006 0.054 6361 Z= 0.252 Angle : 0.969 10.473 8637 Z= 0.517 Chirality : 0.051 0.231 988 Planarity : 0.008 0.117 1074 Dihedral : 14.475 87.622 2230 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.42 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -2.97 (0.27), residues: 808 helix: -1.48 (0.26), residues: 304 sheet: -1.45 (0.39), residues: 181 loop : -2.64 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 134 TYR 0.028 0.003 TYR H 138 PHE 0.032 0.003 PHE Z 258 TRP 0.035 0.002 TRP H 133 HIS 0.006 0.002 HIS Z 379 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 6355) covalent geometry : angle 0.96883 ( 8625) SS BOND : bond 0.00153 ( 6) SS BOND : angle 1.33528 ( 12) hydrogen bonds : bond 0.27520 ( 303) hydrogen bonds : angle 9.88412 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 172 MET cc_start: 0.8446 (mtm) cc_final: 0.8148 (mtt) REVERT: Z 290 ASN cc_start: 0.7712 (p0) cc_final: 0.7255 (t0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0843 time to fit residues: 12.1621 Evaluate side-chains 94 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 137 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 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 = 0.3969 r_free = 0.3969 target = 0.155340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119007 restraints weight = 13757.195| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 4.57 r_work: 0.3362 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6361 Z= 0.167 Angle : 0.771 10.402 8637 Z= 0.403 Chirality : 0.045 0.208 988 Planarity : 0.008 0.115 1074 Dihedral : 6.623 66.688 869 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.58 % Allowed : 9.48 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -2.06 (0.29), residues: 808 helix: -0.18 (0.29), residues: 312 sheet: -1.25 (0.38), residues: 184 loop : -2.61 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 127 TYR 0.019 0.002 TYR L 164 PHE 0.025 0.002 PHE L 163 TRP 0.018 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6355) covalent geometry : angle 0.77055 ( 8625) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.09084 ( 12) hydrogen bonds : bond 0.04959 ( 303) hydrogen bonds : angle 5.68106 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: Z 82 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7460 (mt-10) REVERT: Z 172 MET cc_start: 0.8060 (mtm) cc_final: 0.7531 (mtt) REVERT: Z 290 ASN cc_start: 0.7890 (p0) cc_final: 0.7425 (t0) REVERT: H 29 GLN cc_start: 0.6817 (tp-100) cc_final: 0.6528 (tp-100) REVERT: H 103 ASN cc_start: 0.8057 (t0) cc_final: 0.7446 (t0) REVERT: H 186 TYR cc_start: 0.8517 (p90) cc_final: 0.7884 (p90) outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 0.0786 time to fit residues: 11.8752 Evaluate side-chains 99 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 219 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN Z 137 ASN Z 234 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114321 restraints weight = 14899.338| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.80 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6361 Z= 0.168 Angle : 0.745 10.119 8637 Z= 0.386 Chirality : 0.045 0.211 988 Planarity : 0.007 0.114 1074 Dihedral : 6.470 66.766 869 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 1.60 % Allowed : 12.97 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.75 (0.30), residues: 808 helix: 0.27 (0.30), residues: 312 sheet: -1.20 (0.39), residues: 183 loop : -2.60 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 45 TYR 0.020 0.002 TYR H 120 PHE 0.024 0.002 PHE Z 91 TRP 0.017 0.002 TRP H 133 HIS 0.004 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 6355) covalent geometry : angle 0.74487 ( 8625) SS BOND : bond 0.00265 ( 6) SS BOND : angle 1.07837 ( 12) hydrogen bonds : bond 0.04393 ( 303) hydrogen bonds : angle 5.28073 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.243 Fit side-chains REVERT: Z 137 ASN cc_start: 0.7774 (m-40) cc_final: 0.7574 (m-40) REVERT: Z 172 MET cc_start: 0.8161 (mtm) cc_final: 0.7557 (mtt) REVERT: Z 290 ASN cc_start: 0.7934 (p0) cc_final: 0.7459 (t0) REVERT: H 102 LYS cc_start: 0.8477 (ptpp) cc_final: 0.7764 (ptpp) REVERT: H 103 ASN cc_start: 0.8133 (t0) cc_final: 0.7565 (t0) REVERT: H 186 TYR cc_start: 0.8527 (p90) cc_final: 0.8119 (p90) REVERT: L 225 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8428 (tp) outliers start: 11 outliers final: 5 residues processed: 113 average time/residue: 0.0928 time to fit residues: 13.8152 Evaluate side-chains 105 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain L residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 234 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 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 = 0.3938 r_free = 0.3938 target = 0.154558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119521 restraints weight = 9379.056| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.81 r_work: 0.3371 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6361 Z= 0.143 Angle : 0.707 9.396 8637 Z= 0.366 Chirality : 0.043 0.211 988 Planarity : 0.007 0.113 1074 Dihedral : 6.262 66.682 869 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.90 % Allowed : 15.16 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.52 (0.30), residues: 808 helix: 0.61 (0.30), residues: 311 sheet: -1.08 (0.40), residues: 178 loop : -2.63 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 127 TYR 0.017 0.002 TYR L 164 PHE 0.022 0.002 PHE Z 78 TRP 0.016 0.002 TRP H 133 HIS 0.003 0.000 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6355) covalent geometry : angle 0.70619 ( 8625) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.03640 ( 12) hydrogen bonds : bond 0.03997 ( 303) hydrogen bonds : angle 4.97783 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.240 Fit side-chains REVERT: Z 39 ASP cc_start: 0.7918 (p0) cc_final: 0.7558 (p0) REVERT: Z 95 MET cc_start: 0.7769 (tpt) cc_final: 0.7466 (mmm) REVERT: Z 172 MET cc_start: 0.8144 (mtm) cc_final: 0.7563 (mtt) REVERT: Z 290 ASN cc_start: 0.7944 (p0) cc_final: 0.7477 (t0) REVERT: H 102 LYS cc_start: 0.8549 (ptpp) cc_final: 0.7865 (ptpp) REVERT: H 103 ASN cc_start: 0.8136 (t0) cc_final: 0.7586 (t0) REVERT: H 186 TYR cc_start: 0.8498 (p90) cc_final: 0.8192 (p90) REVERT: L 106 ASP cc_start: 0.8297 (m-30) cc_final: 0.7929 (m-30) REVERT: L 225 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8360 (tp) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.0861 time to fit residues: 14.2467 Evaluate side-chains 108 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 79 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 234 ASN Z 379 HIS ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 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 = 0.3959 r_free = 0.3959 target = 0.156631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119619 restraints weight = 12218.515| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.38 r_work: 0.3360 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6361 Z= 0.134 Angle : 0.690 10.549 8637 Z= 0.360 Chirality : 0.043 0.199 988 Planarity : 0.007 0.113 1074 Dihedral : 6.104 66.732 869 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.60 % Allowed : 16.62 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.39 (0.30), residues: 808 helix: 0.72 (0.30), residues: 312 sheet: -0.97 (0.40), residues: 180 loop : -2.61 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 127 TYR 0.025 0.002 TYR L 210 PHE 0.028 0.002 PHE Z 78 TRP 0.016 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 379 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6355) covalent geometry : angle 0.68927 ( 8625) SS BOND : bond 0.00246 ( 6) SS BOND : angle 0.98243 ( 12) hydrogen bonds : bond 0.03963 ( 303) hydrogen bonds : angle 4.82693 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.307 Fit side-chains REVERT: Z 31 LYS cc_start: 0.7059 (ptpt) cc_final: 0.6799 (tptt) REVERT: Z 82 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7297 (mt-10) REVERT: Z 95 MET cc_start: 0.7734 (tpt) cc_final: 0.7501 (mmm) REVERT: Z 165 LEU cc_start: 0.8152 (mp) cc_final: 0.7893 (mp) REVERT: Z 290 ASN cc_start: 0.7943 (p0) cc_final: 0.7506 (t0) REVERT: H 102 LYS cc_start: 0.8508 (ptpp) cc_final: 0.7734 (ptpp) REVERT: H 103 ASN cc_start: 0.8117 (t0) cc_final: 0.7575 (t0) REVERT: H 106 TYR cc_start: 0.7397 (m-80) cc_final: 0.7107 (m-80) REVERT: L 106 ASP cc_start: 0.8203 (m-30) cc_final: 0.7873 (m-30) REVERT: L 225 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8354 (tp) outliers start: 11 outliers final: 7 residues processed: 118 average time/residue: 0.1002 time to fit residues: 15.2998 Evaluate side-chains 111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN Z 379 HIS ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 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 = 0.3887 r_free = 0.3887 target = 0.150542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111042 restraints weight = 14763.375| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.83 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6361 Z= 0.166 Angle : 0.723 10.149 8637 Z= 0.375 Chirality : 0.045 0.200 988 Planarity : 0.008 0.134 1074 Dihedral : 6.199 67.313 869 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 1.75 % Allowed : 18.22 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.29 (0.30), residues: 808 helix: 0.69 (0.30), residues: 320 sheet: -0.79 (0.40), residues: 178 loop : -2.59 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 134 TYR 0.019 0.002 TYR L 210 PHE 0.025 0.002 PHE Z 258 TRP 0.015 0.002 TRP H 133 HIS 0.004 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6355) covalent geometry : angle 0.72208 ( 8625) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.05588 ( 12) hydrogen bonds : bond 0.03928 ( 303) hydrogen bonds : angle 4.90387 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.249 Fit side-chains REVERT: Z 39 ASP cc_start: 0.7978 (p0) cc_final: 0.7576 (p0) REVERT: Z 82 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7216 (mt-10) REVERT: Z 172 MET cc_start: 0.7742 (mtm) cc_final: 0.7391 (mtt) REVERT: Z 290 ASN cc_start: 0.7875 (p0) cc_final: 0.7487 (t0) REVERT: H 102 LYS cc_start: 0.8471 (ptpp) cc_final: 0.7867 (ptpp) REVERT: H 103 ASN cc_start: 0.8104 (t0) cc_final: 0.7612 (t0) REVERT: L 106 ASP cc_start: 0.8167 (m-30) cc_final: 0.7774 (m-30) REVERT: L 225 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8432 (tp) outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.0926 time to fit residues: 13.9965 Evaluate side-chains 108 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 86 PHE Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 30 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 = 0.3880 r_free = 0.3880 target = 0.149718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113897 restraints weight = 9445.740| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.84 r_work: 0.3286 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6361 Z= 0.168 Angle : 0.724 10.061 8637 Z= 0.375 Chirality : 0.044 0.196 988 Planarity : 0.007 0.113 1074 Dihedral : 6.211 67.558 869 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.19 % Allowed : 18.66 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.26 (0.30), residues: 808 helix: 0.67 (0.30), residues: 322 sheet: -0.87 (0.40), residues: 184 loop : -2.49 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 45 TYR 0.018 0.002 TYR L 210 PHE 0.023 0.002 PHE Z 258 TRP 0.017 0.002 TRP H 133 HIS 0.004 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6355) covalent geometry : angle 0.72348 ( 8625) SS BOND : bond 0.00226 ( 6) SS BOND : angle 1.07602 ( 12) hydrogen bonds : bond 0.03890 ( 303) hydrogen bonds : angle 4.91139 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.241 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7452 (mt-10) REVERT: Z 95 MET cc_start: 0.7873 (tpt) cc_final: 0.7569 (mmm) REVERT: Z 290 ASN cc_start: 0.7976 (p0) cc_final: 0.7600 (t0) REVERT: H 102 LYS cc_start: 0.8541 (ptpp) cc_final: 0.7910 (ptpp) REVERT: H 103 ASN cc_start: 0.8174 (t0) cc_final: 0.7659 (t0) REVERT: H 186 TYR cc_start: 0.8570 (p90) cc_final: 0.8163 (p90) REVERT: L 106 ASP cc_start: 0.8238 (m-30) cc_final: 0.7881 (m-30) REVERT: L 146 ASP cc_start: 0.8539 (t0) cc_final: 0.8191 (p0) REVERT: L 225 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8458 (tp) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 0.0856 time to fit residues: 12.8211 Evaluate side-chains 110 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 86 PHE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 225 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 30 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 = 0.3875 r_free = 0.3875 target = 0.149161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111046 restraints weight = 13568.751| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.62 r_work: 0.3227 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6361 Z= 0.170 Angle : 0.733 10.097 8637 Z= 0.379 Chirality : 0.045 0.192 988 Planarity : 0.007 0.113 1074 Dihedral : 6.210 67.693 869 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.60 % Allowed : 19.24 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.32 (0.30), residues: 808 helix: 0.62 (0.30), residues: 321 sheet: -1.00 (0.39), residues: 189 loop : -2.44 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 45 TYR 0.021 0.002 TYR H 138 PHE 0.024 0.002 PHE Z 78 TRP 0.020 0.002 TRP H 133 HIS 0.004 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6355) covalent geometry : angle 0.73272 ( 8625) SS BOND : bond 0.00212 ( 6) SS BOND : angle 1.08125 ( 12) hydrogen bonds : bond 0.03872 ( 303) hydrogen bonds : angle 4.94688 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.253 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7488 (mt-10) REVERT: Z 290 ASN cc_start: 0.8024 (p0) cc_final: 0.7638 (t0) REVERT: H 102 LYS cc_start: 0.8511 (ptpp) cc_final: 0.7842 (ptpp) REVERT: H 103 ASN cc_start: 0.8240 (t0) cc_final: 0.7670 (t0) REVERT: H 186 TYR cc_start: 0.8623 (p90) cc_final: 0.8208 (p90) REVERT: L 106 ASP cc_start: 0.8295 (m-30) cc_final: 0.7862 (m-30) REVERT: L 146 ASP cc_start: 0.8539 (t0) cc_final: 0.8210 (p0) REVERT: L 225 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8412 (tp) outliers start: 11 outliers final: 9 residues processed: 107 average time/residue: 0.0792 time to fit residues: 11.4747 Evaluate side-chains 107 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 86 PHE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN Z 378 GLN ** L 30 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 = 0.3938 r_free = 0.3938 target = 0.155249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115481 restraints weight = 14983.477| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.95 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6361 Z= 0.129 Angle : 0.689 9.750 8637 Z= 0.356 Chirality : 0.043 0.179 988 Planarity : 0.007 0.112 1074 Dihedral : 5.964 67.256 869 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.90 % Allowed : 19.10 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.10 (0.31), residues: 808 helix: 0.87 (0.30), residues: 322 sheet: -0.89 (0.39), residues: 187 loop : -2.42 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 45 TYR 0.020 0.002 TYR H 138 PHE 0.024 0.001 PHE Z 78 TRP 0.020 0.001 TRP H 133 HIS 0.001 0.000 HIS L 222 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6355) covalent geometry : angle 0.68815 ( 8625) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.91431 ( 12) hydrogen bonds : bond 0.03655 ( 303) hydrogen bonds : angle 4.71826 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.235 Fit side-chains REVERT: Z 39 ASP cc_start: 0.8050 (p0) cc_final: 0.7576 (p0) REVERT: Z 82 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7180 (mt-10) REVERT: Z 95 MET cc_start: 0.7762 (tpt) cc_final: 0.7555 (mmm) REVERT: Z 165 LEU cc_start: 0.8177 (mp) cc_final: 0.7939 (mp) REVERT: Z 172 MET cc_start: 0.7526 (mtm) cc_final: 0.7224 (mtt) REVERT: Z 290 ASN cc_start: 0.7854 (p0) cc_final: 0.7500 (t0) REVERT: H 102 LYS cc_start: 0.8402 (ptpp) cc_final: 0.7667 (ptpp) REVERT: H 103 ASN cc_start: 0.8115 (t0) cc_final: 0.7565 (t0) REVERT: H 106 TYR cc_start: 0.7250 (m-80) cc_final: 0.6966 (m-80) REVERT: H 186 TYR cc_start: 0.8435 (p90) cc_final: 0.8133 (p90) REVERT: L 106 ASP cc_start: 0.8035 (m-30) cc_final: 0.7614 (m-30) REVERT: L 146 ASP cc_start: 0.8431 (t0) cc_final: 0.8173 (p0) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 0.0788 time to fit residues: 13.5082 Evaluate side-chains 119 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain Z residue 378 GLN Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 86 PHE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 163 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 59 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN Z 379 HIS ** L 30 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 = 0.3911 r_free = 0.3911 target = 0.152549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111868 restraints weight = 18036.527| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 5.33 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6361 Z= 0.154 Angle : 0.720 10.413 8637 Z= 0.373 Chirality : 0.044 0.180 988 Planarity : 0.007 0.113 1074 Dihedral : 6.028 67.561 869 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.60 % Allowed : 19.53 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.14 (0.30), residues: 808 helix: 0.82 (0.30), residues: 319 sheet: -0.92 (0.39), residues: 190 loop : -2.38 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 45 TYR 0.025 0.002 TYR H 138 PHE 0.024 0.002 PHE Z 258 TRP 0.019 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6355) covalent geometry : angle 0.71980 ( 8625) SS BOND : bond 0.00206 ( 6) SS BOND : angle 1.02374 ( 12) hydrogen bonds : bond 0.03754 ( 303) hydrogen bonds : angle 4.81798 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.246 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7228 (mt-10) REVERT: Z 95 MET cc_start: 0.7808 (tpt) cc_final: 0.7568 (mmm) REVERT: Z 165 LEU cc_start: 0.8225 (mp) cc_final: 0.7983 (mp) REVERT: Z 263 MET cc_start: 0.6348 (mmt) cc_final: 0.6106 (tpp) REVERT: Z 290 ASN cc_start: 0.7843 (p0) cc_final: 0.7535 (t0) REVERT: H 102 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7654 (ptpp) REVERT: H 103 ASN cc_start: 0.8088 (t0) cc_final: 0.7589 (t0) REVERT: H 106 TYR cc_start: 0.7353 (m-80) cc_final: 0.7070 (m-80) REVERT: H 186 TYR cc_start: 0.8475 (p90) cc_final: 0.8268 (p90) REVERT: L 73 TYR cc_start: 0.8442 (m-10) cc_final: 0.8109 (m-10) REVERT: L 106 ASP cc_start: 0.8070 (m-30) cc_final: 0.7650 (m-30) REVERT: L 146 ASP cc_start: 0.8454 (t0) cc_final: 0.8194 (p0) outliers start: 11 outliers final: 11 residues processed: 118 average time/residue: 0.0809 time to fit residues: 12.9301 Evaluate side-chains 121 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 135 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 86 PHE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 174 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 0.0070 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.0170 chunk 67 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 68 optimal weight: 0.0470 chunk 55 optimal weight: 0.6980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN Z 378 GLN L 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.157031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117974 restraints weight = 12884.477| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.61 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6361 Z= 0.126 Angle : 0.689 10.639 8637 Z= 0.356 Chirality : 0.043 0.174 988 Planarity : 0.007 0.111 1074 Dihedral : 5.875 67.388 869 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.46 % Allowed : 19.97 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -0.92 (0.31), residues: 808 helix: 1.02 (0.31), residues: 319 sheet: -0.80 (0.39), residues: 187 loop : -2.27 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 45 TYR 0.024 0.002 TYR H 138 PHE 0.024 0.001 PHE Z 78 TRP 0.019 0.001 TRP H 133 HIS 0.002 0.000 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6355) covalent geometry : angle 0.68842 ( 8625) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.89462 ( 12) hydrogen bonds : bond 0.03595 ( 303) hydrogen bonds : angle 4.67593 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.87 seconds wall clock time: 34 minutes 9.69 seconds (2049.69 seconds total)