Starting phenix.real_space_refine on Tue Mar 3 16:21:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lo8_23464/03_2026/7lo8_23464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lo8_23464/03_2026/7lo8_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_23464/03_2026/7lo8_23464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lo8_23464/03_2026/7lo8_23464.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lo8_23464/03_2026/7lo8_23464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lo8_23464/03_2026/7lo8_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-dev-5986/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: 1.81, per 1000 atoms: 0.29 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: 0.61 Conformation dependent library (CDL) restraints added in 299.6 milliseconds 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: 0.16 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: 0.79 Time building geometry restraints manager: 0.75 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: 1.430 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.870 ------------------------------------------------------------------------------- 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 are 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 : 0.224 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: 0.0793 time to fit residues: 11.4660 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 : 0.197 ------------------------------------------------------------------------------- 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 are 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 : 0.229 Fit side-chains revert: symmetry clash REVERT: Z 82 GLU cc_start: 0.7845 (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: 0.7889 (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: 0.0731 time to fit residues: 11.0779 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 : 0.180 ------------------------------------------------------------------------------- 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 are 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 : 0.241 Fit side-chains REVERT: Z 118 ASP cc_start: 0.6935 (m-30) cc_final: 0.6735 (m-30) 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: 0.0771 time to fit residues: 11.6991 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 : 0.367 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.154860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119664 restraints weight = 9378.734| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.81 r_work: 0.3371 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 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 = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2256 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= 0.142 Angle : 0.704 9.431 8637 Z= 0.365 Chirality : 0.043 0.208 988 Planarity : 0.007 0.113 1074 Dihedral : 6.251 66.676 869 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.90 % Allowed : 15.01 % Favored : 83.09 % 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 are 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 : -2.62 (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 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6355) covalent geometry : angle 0.70373 ( 8625) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.04237 ( 12) hydrogen bonds : bond 0.03984 ( 303) hydrogen bonds : angle 4.95866 ( 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 128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.236 Fit side-chains REVERT: Z 95 MET cc_start: 0.7771 (tpt) cc_final: 0.7473 (mmm) REVERT: Z 172 MET cc_start: 0.8153 (mtm) cc_final: 0.7568 (mtt) REVERT: Z 290 ASN cc_start: 0.7929 (p0) cc_final: 0.7471 (t0) REVERT: H 102 LYS cc_start: 0.8562 (ptpp) cc_final: 0.7876 (ptpp) REVERT: H 103 ASN cc_start: 0.8143 (t0) cc_final: 0.7593 (t0) REVERT: H 186 TYR cc_start: 0.8494 (p90) cc_final: 0.8198 (p90) REVERT: L 106 ASP cc_start: 0.8320 (m-30) cc_final: 0.7956 (m-30) REVERT: L 225 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8363 (tp) outliers start: 13 outliers final: 6 residues processed: 123 average time/residue: 0.0717 time to fit residues: 11.8707 Evaluate side-chains 114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115725 restraints weight = 12306.737| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 4.39 r_work: 0.3302 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2334 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= 0.164 Angle : 0.721 10.979 8637 Z= 0.376 Chirality : 0.044 0.204 988 Planarity : 0.007 0.114 1074 Dihedral : 6.259 67.043 869 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.04 % Allowed : 16.33 % Favored : 81.63 % 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 are not related in a simple way. whole: -1.43 (0.30), residues: 808 helix: 0.53 (0.30), residues: 321 sheet: -0.97 (0.40), residues: 178 loop : -2.53 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 127 TYR 0.023 0.002 TYR L 210 PHE 0.027 0.002 PHE Z 78 TRP 0.017 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6355) covalent geometry : angle 0.72061 ( 8625) SS BOND : bond 0.00223 ( 6) SS BOND : angle 1.09647 ( 12) hydrogen bonds : bond 0.04076 ( 303) hydrogen bonds : angle 4.96359 ( 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 125 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.201 Fit side-chains REVERT: Z 39 ASP cc_start: 0.7992 (p0) cc_final: 0.7750 (p0) REVERT: Z 82 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7384 (mt-10) REVERT: Z 172 MET cc_start: 0.8141 (mtm) cc_final: 0.7588 (mtt) REVERT: Z 290 ASN cc_start: 0.7938 (p0) cc_final: 0.7488 (t0) REVERT: H 102 LYS cc_start: 0.8530 (ptpp) cc_final: 0.7780 (ptpp) REVERT: H 103 ASN cc_start: 0.8139 (t0) cc_final: 0.7597 (t0) REVERT: H 106 TYR cc_start: 0.7407 (m-80) cc_final: 0.7191 (m-80) REVERT: L 106 ASP cc_start: 0.8264 (m-30) cc_final: 0.7890 (m-30) REVERT: L 225 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8380 (tp) outliers start: 14 outliers final: 10 residues processed: 118 average time/residue: 0.0708 time to fit residues: 11.2413 Evaluate side-chains 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 H residue 134 ARG 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 167 GLU 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: 0.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 378 GLN ** 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 = 0.3848 r_free = 0.3848 target = 0.147026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108618 restraints weight = 14683.021| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.77 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6361 Z= 0.195 Angle : 0.752 10.545 8637 Z= 0.390 Chirality : 0.045 0.205 988 Planarity : 0.007 0.113 1074 Dihedral : 6.370 67.685 869 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 2.19 % Allowed : 16.91 % Favored : 80.90 % 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 are not related in a simple way. whole: -1.49 (0.30), residues: 808 helix: 0.46 (0.30), residues: 321 sheet: -1.01 (0.40), residues: 181 loop : -2.54 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 113 TYR 0.022 0.002 TYR H 120 PHE 0.025 0.002 PHE Z 258 TRP 0.019 0.002 TRP H 133 HIS 0.004 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 6355) covalent geometry : angle 0.75158 ( 8625) SS BOND : bond 0.00213 ( 6) SS BOND : angle 1.13195 ( 12) hydrogen bonds : bond 0.04130 ( 303) hydrogen bonds : angle 5.05994 ( 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 125 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: Z 82 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7299 (mt-10) REVERT: Z 172 MET cc_start: 0.8165 (mtm) cc_final: 0.7796 (mtt) REVERT: Z 290 ASN cc_start: 0.7883 (p0) cc_final: 0.7473 (t0) REVERT: H 102 LYS cc_start: 0.8515 (ptpp) cc_final: 0.7910 (ptpp) REVERT: H 103 ASN cc_start: 0.8128 (t0) cc_final: 0.7597 (t0) REVERT: H 134 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.5714 (mpt180) REVERT: H 186 TYR cc_start: 0.8597 (p90) cc_final: 0.8099 (p90) REVERT: L 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.7792 (m-30) REVERT: L 225 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8501 (tp) outliers start: 15 outliers final: 8 residues processed: 118 average time/residue: 0.0826 time to fit residues: 12.8827 Evaluate side-chains 114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain Z residue 378 GLN Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 167 GLU 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: 0.9980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 378 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 = 0.3878 r_free = 0.3878 target = 0.149773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113881 restraints weight = 9500.360| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.86 r_work: 0.3286 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6361 Z= 0.153 Angle : 0.717 10.202 8637 Z= 0.371 Chirality : 0.044 0.193 988 Planarity : 0.007 0.113 1074 Dihedral : 6.207 67.397 869 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.04 % Allowed : 18.37 % Favored : 79.59 % 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 are not related in a simple way. whole: -1.34 (0.30), residues: 808 helix: 0.62 (0.30), residues: 318 sheet: -0.91 (0.40), residues: 178 loop : -2.49 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 113 TYR 0.019 0.002 TYR L 210 PHE 0.025 0.002 PHE Z 258 TRP 0.017 0.002 TRP H 133 HIS 0.006 0.001 HIS Z 379 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6355) covalent geometry : angle 0.71624 ( 8625) SS BOND : bond 0.00242 ( 6) SS BOND : angle 1.05462 ( 12) hydrogen bonds : bond 0.03986 ( 303) hydrogen bonds : angle 4.92587 ( 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 120 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.222 Fit side-chains REVERT: Z 39 ASP cc_start: 0.8061 (p0) cc_final: 0.7670 (p0) REVERT: Z 82 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7453 (mt-10) REVERT: Z 172 MET cc_start: 0.8204 (mtm) cc_final: 0.7788 (mtt) REVERT: Z 290 ASN cc_start: 0.7958 (p0) cc_final: 0.7572 (t0) REVERT: H 102 LYS cc_start: 0.8562 (ptpp) cc_final: 0.7902 (ptpp) REVERT: H 103 ASN cc_start: 0.8189 (t0) cc_final: 0.7626 (t0) REVERT: H 186 TYR cc_start: 0.8569 (p90) cc_final: 0.8159 (p90) REVERT: L 106 ASP cc_start: 0.8253 (m-30) cc_final: 0.7891 (m-30) REVERT: L 146 ASP cc_start: 0.8548 (t0) cc_final: 0.8191 (p0) REVERT: L 225 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8364 (tp) outliers start: 14 outliers final: 9 residues processed: 113 average time/residue: 0.0843 time to fit residues: 12.4634 Evaluate side-chains 104 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain Z residue 378 GLN 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: 0.5980 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 378 GLN ** 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 = 0.3915 r_free = 0.3915 target = 0.153024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114268 restraints weight = 13689.585| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.68 r_work: 0.3276 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6361 Z= 0.141 Angle : 0.707 9.379 8637 Z= 0.366 Chirality : 0.043 0.183 988 Planarity : 0.008 0.131 1074 Dihedral : 6.109 67.302 869 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.75 % Allowed : 19.68 % 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 are not related in a simple way. whole: -1.32 (0.30), residues: 808 helix: 0.65 (0.31), residues: 319 sheet: -0.95 (0.40), residues: 184 loop : -2.48 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 113 TYR 0.018 0.002 TYR L 210 PHE 0.023 0.002 PHE Z 78 TRP 0.012 0.002 TRP H 133 HIS 0.002 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6355) covalent geometry : angle 0.70675 ( 8625) SS BOND : bond 0.00239 ( 6) SS BOND : angle 0.99295 ( 12) hydrogen bonds : bond 0.03914 ( 303) hydrogen bonds : angle 4.82454 ( 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 114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.223 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7452 (mt-10) REVERT: Z 95 MET cc_start: 0.7817 (tpt) cc_final: 0.7613 (mmm) REVERT: Z 165 LEU cc_start: 0.8243 (mp) cc_final: 0.7976 (mp) REVERT: Z 172 MET cc_start: 0.8132 (mtm) cc_final: 0.7682 (mtt) REVERT: Z 290 ASN cc_start: 0.8004 (p0) cc_final: 0.7635 (t0) REVERT: H 102 LYS cc_start: 0.8525 (ptpp) cc_final: 0.7754 (ptpp) REVERT: H 103 ASN cc_start: 0.8176 (t0) cc_final: 0.7626 (t0) REVERT: H 186 TYR cc_start: 0.8583 (p90) cc_final: 0.8164 (p90) REVERT: L 106 ASP cc_start: 0.8223 (m-30) cc_final: 0.7822 (m-30) REVERT: L 146 ASP cc_start: 0.8509 (t0) cc_final: 0.8195 (p0) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.0772 time to fit residues: 11.1395 Evaluate side-chains 105 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain Z residue 378 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 379 HIS H 108 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 = 0.3901 r_free = 0.3901 target = 0.151397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111937 restraints weight = 15075.223| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.87 r_work (final): 0.3435 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2782 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= 0.154 Angle : 0.715 9.514 8637 Z= 0.370 Chirality : 0.044 0.187 988 Planarity : 0.008 0.129 1074 Dihedral : 6.131 67.584 869 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.04 % Allowed : 19.24 % Favored : 78.72 % 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 are not related in a simple way. whole: -1.27 (0.30), residues: 808 helix: 0.70 (0.30), residues: 319 sheet: -0.96 (0.40), residues: 187 loop : -2.45 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 45 TYR 0.017 0.002 TYR L 210 PHE 0.023 0.002 PHE Z 258 TRP 0.015 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 379 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6355) covalent geometry : angle 0.71466 ( 8625) SS BOND : bond 0.00234 ( 6) SS BOND : angle 1.03665 ( 12) hydrogen bonds : bond 0.03871 ( 303) hydrogen bonds : angle 4.86441 ( 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 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.219 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7208 (mt-10) REVERT: Z 95 MET cc_start: 0.7811 (tpt) cc_final: 0.7531 (mmm) REVERT: Z 165 LEU cc_start: 0.8234 (mp) cc_final: 0.7988 (mp) REVERT: Z 172 MET cc_start: 0.8103 (mtm) cc_final: 0.7696 (mtt) REVERT: Z 290 ASN cc_start: 0.7881 (p0) cc_final: 0.7551 (t0) REVERT: H 102 LYS cc_start: 0.8494 (ptpp) cc_final: 0.7832 (ptpp) REVERT: H 103 ASN cc_start: 0.8134 (t0) cc_final: 0.7624 (t0) REVERT: H 108 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7101 (tp40) REVERT: H 186 TYR cc_start: 0.8573 (p90) cc_final: 0.8190 (p90) REVERT: L 106 ASP cc_start: 0.8108 (m-30) cc_final: 0.7651 (m-30) REVERT: L 146 ASP cc_start: 0.8473 (t0) cc_final: 0.8200 (p0) outliers start: 14 outliers final: 9 residues processed: 108 average time/residue: 0.0706 time to fit residues: 10.4153 Evaluate side-chains 111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain H residue 108 GLN 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: 0.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.149744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110147 restraints weight = 17819.811| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 5.26 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2763 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= 0.168 Angle : 0.726 9.676 8637 Z= 0.376 Chirality : 0.044 0.184 988 Planarity : 0.008 0.129 1074 Dihedral : 6.164 67.737 869 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.75 % Allowed : 19.24 % 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 are not related in a simple way. whole: -1.26 (0.30), residues: 808 helix: 0.69 (0.30), residues: 319 sheet: -0.90 (0.40), residues: 187 loop : -2.46 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 45 TYR 0.017 0.002 TYR L 210 PHE 0.023 0.002 PHE Z 258 TRP 0.015 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6355) covalent geometry : angle 0.72587 ( 8625) SS BOND : bond 0.00209 ( 6) SS BOND : angle 1.07146 ( 12) hydrogen bonds : bond 0.03915 ( 303) hydrogen bonds : angle 4.88191 ( 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 119 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.178 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7200 (mt-10) REVERT: Z 95 MET cc_start: 0.7809 (tpt) cc_final: 0.7498 (mmm) REVERT: Z 165 LEU cc_start: 0.8185 (mp) cc_final: 0.7947 (mp) REVERT: Z 172 MET cc_start: 0.7906 (mtm) cc_final: 0.7506 (mtt) REVERT: Z 290 ASN cc_start: 0.7879 (p0) cc_final: 0.7537 (t0) REVERT: H 102 LYS cc_start: 0.8501 (ptpp) cc_final: 0.7832 (ptpp) REVERT: H 103 ASN cc_start: 0.8162 (t0) cc_final: 0.7615 (t0) REVERT: H 108 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6968 (tp40) REVERT: H 186 TYR cc_start: 0.8597 (p90) cc_final: 0.8247 (p90) REVERT: L 106 ASP cc_start: 0.8111 (m-30) cc_final: 0.7623 (m-30) REVERT: L 146 ASP cc_start: 0.8475 (t0) cc_final: 0.8199 (p0) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.0689 time to fit residues: 10.6300 Evaluate side-chains 118 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 61 LEU 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 H residue 108 GLN 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 37 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 54 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.150546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111972 restraints weight = 12971.190| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 4.55 r_work: 0.3251 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 6361 Z= 0.200 Angle : 1.122 59.198 8637 Z= 0.639 Chirality : 0.052 0.901 988 Planarity : 0.008 0.124 1074 Dihedral : 6.172 67.738 869 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 1.60 % Allowed : 19.10 % Favored : 79.30 % Cbeta Deviations : 0.13 % 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 are not related in a simple way. whole: -1.26 (0.30), residues: 808 helix: 0.70 (0.30), residues: 319 sheet: -0.90 (0.40), residues: 187 loop : -2.46 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 45 TYR 0.016 0.002 TYR L 210 PHE 0.024 0.002 PHE Z 258 TRP 0.016 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 6355) covalent geometry : angle 1.12227 ( 8625) SS BOND : bond 0.00202 ( 6) SS BOND : angle 1.06309 ( 12) hydrogen bonds : bond 0.03904 ( 303) hydrogen bonds : angle 4.90721 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1800.37 seconds wall clock time: 31 minutes 29.68 seconds (1889.68 seconds total)