Starting phenix.real_space_refine on Wed Mar 12 01:44:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lo8_23464/03_2025/7lo8_23464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lo8_23464/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lo8_23464/03_2025/7lo8_23464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lo8_23464/03_2025/7lo8_23464.map" model { file = "/net/cci-nas-00/data/ceres_data/7lo8_23464/03_2025/7lo8_23464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lo8_23464/03_2025/7lo8_23464.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.54, per 1000 atoms: 1.05 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: 1.36 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.68 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: 1.69 Time building geometry restraints manager: 1.61 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.660 Find NCS groups from input model: 0.060 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- 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 6355 Z= 0.391 Angle : 0.969 10.473 8625 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 : 8.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.002 TRP H 133 HIS 0.006 0.002 HIS Z 379 PHE 0.032 0.003 PHE Z 258 TYR 0.028 0.003 TYR H 138 ARG 0.013 0.001 ARG H 134 *********************** 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 : 0.604 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: 0.1793 time to fit residues: 25.6666 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 : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.156099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117989 restraints weight = 18734.119| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 5.36 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6355 Z= 0.233 Angle : 0.757 10.072 8625 Z= 0.396 Chirality : 0.045 0.206 988 Planarity : 0.008 0.114 1074 Dihedral : 6.582 66.600 869 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.58 % Allowed : 8.89 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.29), residues: 808 helix: -0.15 (0.29), residues: 312 sheet: -1.22 (0.38), residues: 183 loop : -2.59 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.024 0.002 PHE L 163 TYR 0.020 0.002 TYR L 164 ARG 0.005 0.001 ARG H 127 *********************** 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 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: Z 82 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7218 (mt-10) REVERT: Z 172 MET cc_start: 0.8011 (mtm) cc_final: 0.7455 (mtt) REVERT: Z 290 ASN cc_start: 0.7873 (p0) cc_final: 0.7392 (t0) REVERT: Z 360 TYR cc_start: 0.7129 (m-80) cc_final: 0.6688 (m-80) REVERT: H 29 GLN cc_start: 0.6761 (tp-100) cc_final: 0.6475 (tp-100) REVERT: H 103 ASN cc_start: 0.7935 (t0) cc_final: 0.7332 (t0) REVERT: H 186 TYR cc_start: 0.8458 (p90) cc_final: 0.7874 (p90) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 0.1731 time to fit residues: 26.4124 Evaluate side-chains 103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 ** 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 = 0.3943 r_free = 0.3943 target = 0.155180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121441 restraints weight = 7273.790| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.35 r_work: 0.3408 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- 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 = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6355 Z= 0.211 Angle : 0.715 9.686 8625 Z= 0.371 Chirality : 0.044 0.207 988 Planarity : 0.007 0.114 1074 Dihedral : 6.320 66.539 869 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.60 % Allowed : 11.81 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.30), residues: 808 helix: 0.46 (0.30), residues: 307 sheet: -1.18 (0.39), residues: 179 loop : -2.62 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.026 0.002 PHE Z 91 TYR 0.017 0.002 TYR L 164 ARG 0.002 0.000 ARG H 134 *********************** 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 129 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.631 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7464 (mt-10) REVERT: Z 95 MET cc_start: 0.7752 (tpt) cc_final: 0.7401 (mmm) REVERT: Z 172 MET cc_start: 0.8104 (mtm) cc_final: 0.7549 (mtt) REVERT: Z 239 ASP cc_start: 0.7168 (t0) cc_final: 0.6930 (t0) REVERT: Z 290 ASN cc_start: 0.7927 (p0) cc_final: 0.7474 (t0) REVERT: H 102 LYS cc_start: 0.8522 (ptpp) cc_final: 0.7762 (ptpp) REVERT: H 103 ASN cc_start: 0.8182 (t0) cc_final: 0.7592 (t0) REVERT: H 186 TYR cc_start: 0.8438 (p90) cc_final: 0.8037 (p90) REVERT: L 106 ASP cc_start: 0.8229 (m-30) cc_final: 0.7856 (m-30) REVERT: L 225 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8387 (tp) outliers start: 11 outliers final: 5 residues processed: 122 average time/residue: 0.1816 time to fit residues: 29.2198 Evaluate side-chains 109 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 14 LEU 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 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.152922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117673 restraints weight = 9174.663| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.75 r_work: 0.3351 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6355 Z= 0.249 Angle : 0.724 9.471 8625 Z= 0.375 Chirality : 0.044 0.212 988 Planarity : 0.007 0.114 1074 Dihedral : 6.295 66.832 869 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.33 % Allowed : 13.85 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.30), residues: 808 helix: 0.54 (0.30), residues: 313 sheet: -1.02 (0.40), residues: 180 loop : -2.56 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 133 HIS 0.004 0.001 HIS Z 354 PHE 0.023 0.002 PHE Z 258 TYR 0.023 0.002 TYR L 210 ARG 0.004 0.000 ARG H 127 *********************** 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 121 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.711 Fit side-chains REVERT: Z 172 MET cc_start: 0.8097 (mtm) cc_final: 0.7492 (mtt) REVERT: Z 290 ASN cc_start: 0.7943 (p0) cc_final: 0.7458 (t0) REVERT: H 102 LYS cc_start: 0.8516 (ptpp) cc_final: 0.7835 (ptpp) REVERT: H 103 ASN cc_start: 0.8107 (t0) cc_final: 0.7563 (t0) REVERT: H 186 TYR cc_start: 0.8525 (p90) cc_final: 0.8232 (p90) REVERT: L 106 ASP cc_start: 0.8245 (m-30) cc_final: 0.7860 (m-30) REVERT: L 225 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8373 (tp) outliers start: 16 outliers final: 7 residues processed: 115 average time/residue: 0.1786 time to fit residues: 27.2159 Evaluate side-chains 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 14 LEU 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 167 GLU 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 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.154212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118009 restraints weight = 10870.344| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.12 r_work: 0.3342 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6355 Z= 0.225 Angle : 0.704 10.520 8625 Z= 0.366 Chirality : 0.043 0.204 988 Planarity : 0.008 0.125 1074 Dihedral : 6.189 67.023 869 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.46 % Allowed : 16.18 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.30), residues: 808 helix: 0.55 (0.30), residues: 320 sheet: -0.87 (0.40), residues: 178 loop : -2.53 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.022 0.002 PHE Z 78 TYR 0.019 0.002 TYR L 210 ARG 0.004 0.000 ARG H 127 *********************** 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: 10 poor density : 115 time to evaluate : 0.623 Fit side-chains REVERT: Z 39 ASP cc_start: 0.7660 (p0) cc_final: 0.7211 (p0) REVERT: Z 95 MET cc_start: 0.7637 (tpt) cc_final: 0.7410 (mmm) REVERT: Z 290 ASN cc_start: 0.7930 (p0) cc_final: 0.7457 (t0) REVERT: Z 360 TYR cc_start: 0.7359 (m-80) cc_final: 0.7110 (m-80) REVERT: H 102 LYS cc_start: 0.8511 (ptpp) cc_final: 0.7750 (ptpp) REVERT: H 103 ASN cc_start: 0.8127 (t0) cc_final: 0.7569 (t0) REVERT: H 106 TYR cc_start: 0.7312 (m-80) cc_final: 0.7080 (m-80) REVERT: L 106 ASP cc_start: 0.8220 (m-30) cc_final: 0.7856 (m-30) REVERT: L 225 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8374 (tp) outliers start: 10 outliers final: 7 residues processed: 120 average time/residue: 0.1816 time to fit residues: 28.7394 Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 59 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** 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 = 0.3892 r_free = 0.3892 target = 0.151151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112394 restraints weight = 14538.024| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.81 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6355 Z= 0.225 Angle : 0.701 10.078 8625 Z= 0.365 Chirality : 0.043 0.200 988 Planarity : 0.007 0.113 1074 Dihedral : 6.148 67.182 869 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 1.75 % Allowed : 17.49 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.30), residues: 808 helix: 0.68 (0.31), residues: 320 sheet: -0.80 (0.40), residues: 178 loop : -2.52 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.028 0.002 PHE Z 78 TYR 0.021 0.002 TYR H 138 ARG 0.003 0.000 ARG H 134 *********************** 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 : 0.626 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7217 (mt-10) REVERT: Z 95 MET cc_start: 0.7733 (tpt) cc_final: 0.7519 (mmm) REVERT: Z 172 MET cc_start: 0.7755 (mtm) cc_final: 0.7404 (mtt) REVERT: Z 290 ASN cc_start: 0.7846 (p0) cc_final: 0.7427 (t0) REVERT: H 102 LYS cc_start: 0.8512 (ptpp) cc_final: 0.7880 (ptpp) REVERT: H 103 ASN cc_start: 0.8137 (t0) cc_final: 0.7617 (t0) REVERT: H 186 TYR cc_start: 0.8557 (p90) cc_final: 0.8071 (p90) REVERT: L 106 ASP cc_start: 0.8150 (m-30) cc_final: 0.7753 (m-30) REVERT: L 146 ASP cc_start: 0.8511 (t0) cc_final: 0.8190 (p0) REVERT: L 225 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8430 (tp) outliers start: 12 outliers final: 7 residues processed: 113 average time/residue: 0.1744 time to fit residues: 26.1356 Evaluate side-chains 108 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 Z residue 378 GLN 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 48 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 0.0770 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 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 = 0.3925 r_free = 0.3925 target = 0.154279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115291 restraints weight = 14583.318| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.88 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6355 Z= 0.194 Angle : 0.680 9.706 8625 Z= 0.353 Chirality : 0.042 0.188 988 Planarity : 0.007 0.113 1074 Dihedral : 6.005 67.108 869 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.19 % Allowed : 17.49 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.30), residues: 808 helix: 0.88 (0.31), residues: 313 sheet: -0.83 (0.40), residues: 181 loop : -2.54 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 133 HIS 0.006 0.001 HIS Z 379 PHE 0.024 0.001 PHE Z 78 TYR 0.022 0.002 TYR H 138 ARG 0.003 0.000 ARG H 113 *********************** 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 124 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.643 Fit side-chains REVERT: Z 39 ASP cc_start: 0.7559 (p0) cc_final: 0.6952 (p0) REVERT: Z 82 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7160 (mt-10) REVERT: Z 165 LEU cc_start: 0.8178 (mp) cc_final: 0.7926 (mp) REVERT: Z 290 ASN cc_start: 0.7835 (p0) cc_final: 0.7493 (t0) REVERT: H 102 LYS cc_start: 0.8475 (ptpp) cc_final: 0.7820 (ptpp) REVERT: H 103 ASN cc_start: 0.8152 (t0) cc_final: 0.7636 (t0) REVERT: H 186 TYR cc_start: 0.8433 (p90) cc_final: 0.8097 (p90) REVERT: L 106 ASP cc_start: 0.8082 (m-30) cc_final: 0.7716 (m-30) REVERT: L 146 ASP cc_start: 0.8424 (t0) cc_final: 0.8141 (p0) outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.1677 time to fit residues: 26.3595 Evaluate side-chains 107 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 Z residue 378 GLN Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 163 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 0.0060 chunk 60 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 0.0570 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.2114 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.158859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122099 restraints weight = 9458.553| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.92 r_work: 0.3384 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6355 Z= 0.174 Angle : 0.675 9.323 8625 Z= 0.347 Chirality : 0.043 0.195 988 Planarity : 0.007 0.112 1074 Dihedral : 5.864 67.057 869 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.31), residues: 808 helix: 1.02 (0.31), residues: 317 sheet: -0.84 (0.39), residues: 187 loop : -2.46 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 133 HIS 0.001 0.000 HIS Z 379 PHE 0.024 0.001 PHE Z 78 TYR 0.017 0.001 TYR L 210 ARG 0.003 0.000 ARG H 113 *********************** 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 135 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.633 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7365 (mt-10) REVERT: Z 165 LEU cc_start: 0.8140 (mp) cc_final: 0.7920 (mp) REVERT: Z 290 ASN cc_start: 0.7941 (p0) cc_final: 0.7576 (t0) REVERT: Z 310 ARG cc_start: 0.7135 (mtt-85) cc_final: 0.6856 (mtt-85) REVERT: H 102 LYS cc_start: 0.8480 (ptpp) cc_final: 0.7715 (ptpp) REVERT: H 103 ASN cc_start: 0.8158 (t0) cc_final: 0.7655 (t0) REVERT: H 106 TYR cc_start: 0.7353 (m-80) cc_final: 0.7092 (m-80) REVERT: L 106 ASP cc_start: 0.8041 (m-30) cc_final: 0.7674 (m-30) REVERT: L 146 ASP cc_start: 0.8410 (t0) cc_final: 0.8135 (p0) outliers start: 12 outliers final: 7 residues processed: 129 average time/residue: 0.1758 time to fit residues: 30.0662 Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 149 LEU Chi-restraints excluded: chain L residue 174 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 378 GLN Z 379 HIS H 108 GLN ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.155194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115050 restraints weight = 15891.609| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 5.06 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6355 Z= 0.209 Angle : 0.700 11.679 8625 Z= 0.361 Chirality : 0.044 0.190 988 Planarity : 0.007 0.113 1074 Dihedral : 5.880 67.570 869 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.31), residues: 808 helix: 0.86 (0.30), residues: 324 sheet: -0.86 (0.39), residues: 190 loop : -2.34 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 133 HIS 0.007 0.001 HIS Z 379 PHE 0.024 0.002 PHE Z 78 TYR 0.022 0.002 TYR H 138 ARG 0.004 0.000 ARG H 45 *********************** 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 117 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.664 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7230 (mt-10) REVERT: Z 107 MET cc_start: 0.7481 (ptp) cc_final: 0.7043 (ptp) REVERT: Z 165 LEU cc_start: 0.8168 (mp) cc_final: 0.7925 (mp) REVERT: Z 290 ASN cc_start: 0.7804 (p0) cc_final: 0.7502 (t0) REVERT: Z 324 ARG cc_start: 0.7498 (mtp85) cc_final: 0.7167 (mtp85) REVERT: H 102 LYS cc_start: 0.8417 (ptpp) cc_final: 0.7821 (ptpp) REVERT: H 103 ASN cc_start: 0.8051 (t0) cc_final: 0.7632 (t0) REVERT: H 108 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6920 (tp40) REVERT: L 73 TYR cc_start: 0.8437 (m-10) cc_final: 0.8051 (m-10) REVERT: L 106 ASP cc_start: 0.7915 (m-30) cc_final: 0.7483 (m-30) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 0.1772 time to fit residues: 26.0258 Evaluate side-chains 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 H residue 108 GLN Chi-restraints excluded: chain L residue 70 LEU 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 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 11 ASN Z 234 ASN Z 379 HIS H 108 GLN ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.152283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116071 restraints weight = 9153.784| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.83 r_work: 0.3320 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6355 Z= 0.260 Angle : 0.724 11.897 8625 Z= 0.374 Chirality : 0.045 0.184 988 Planarity : 0.007 0.113 1074 Dihedral : 5.981 67.814 869 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.90 % Allowed : 19.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.30), residues: 808 helix: 0.70 (0.30), residues: 325 sheet: -0.87 (0.39), residues: 190 loop : -2.33 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 133 HIS 0.005 0.001 HIS Z 379 PHE 0.024 0.002 PHE Z 78 TYR 0.016 0.002 TYR H 120 ARG 0.007 0.001 ARG H 45 ********************** 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 118 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.711 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7396 (mt-10) REVERT: Z 107 MET cc_start: 0.7685 (ptp) cc_final: 0.7235 (ptp) REVERT: Z 290 ASN cc_start: 0.7885 (p0) cc_final: 0.7593 (t0) REVERT: Z 324 ARG cc_start: 0.7528 (mtp85) cc_final: 0.7166 (mtp85) REVERT: H 29 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6684 (tp-100) REVERT: H 102 LYS cc_start: 0.8503 (ptpp) cc_final: 0.7859 (ptpp) REVERT: H 103 ASN cc_start: 0.8174 (t0) cc_final: 0.7703 (t0) REVERT: H 108 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7192 (tp40) REVERT: L 106 ASP cc_start: 0.8090 (m-30) cc_final: 0.7658 (m-30) REVERT: L 109 THR cc_start: 0.7987 (p) cc_final: 0.7563 (p) REVERT: L 146 ASP cc_start: 0.8395 (t0) cc_final: 0.8124 (p0) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 0.1840 time to fit residues: 27.4888 Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 H residue 108 GLN Chi-restraints excluded: chain L residue 70 LEU 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 16 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ** 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 = 0.3922 r_free = 0.3922 target = 0.153718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115989 restraints weight = 11092.958| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.25 r_work: 0.3317 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6355 Z= 0.214 Angle : 0.712 11.665 8625 Z= 0.367 Chirality : 0.044 0.180 988 Planarity : 0.007 0.113 1074 Dihedral : 5.963 67.744 869 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.46 % Allowed : 19.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.30), residues: 808 helix: 0.76 (0.30), residues: 324 sheet: -0.85 (0.39), residues: 190 loop : -2.32 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.046 0.002 PHE Z 161 TYR 0.016 0.002 TYR L 210 ARG 0.006 0.001 ARG H 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3764.37 seconds wall clock time: 65 minutes 27.18 seconds (3927.18 seconds total)