Starting phenix.real_space_refine on Fri Jun 6 02:11:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lo8_23464/06_2025/7lo8_23464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lo8_23464/06_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_23464/06_2025/7lo8_23464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lo8_23464/06_2025/7lo8_23464.map" model { file = "/net/cci-nas-00/data/ceres_data/7lo8_23464/06_2025/7lo8_23464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lo8_23464/06_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-5710/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: 5.48, per 1000 atoms: 0.88 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: 1.40 Conformation dependent library (CDL) restraints added in 1.1 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: 0.77 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: 1.87 Time building geometry restraints manager: 1.67 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- 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 : 8.93 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 Details of bonding type rmsd hydrogen bonds : bond 0.27520 ( 303) hydrogen bonds : angle 9.88412 ( 858) SS BOND : bond 0.00153 ( 6) SS BOND : angle 1.33528 ( 12) covalent geometry : bond 0.00614 ( 6355) covalent geometry : angle 0.96883 ( 8625) *********************** 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 : 0.704 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: 0.1918 time to fit residues: 27.6037 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 : 0.720 ------------------------------------------------------------------------------- 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: 0.9990 chunk 60 optimal weight: 0.5980 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: 0.6980 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: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.156082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118195 restraints weight = 18723.624| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 5.30 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 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 = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1653 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= 0.161 Angle : 0.761 10.207 8637 Z= 0.398 Chirality : 0.045 0.206 988 Planarity : 0.008 0.115 1074 Dihedral : 6.593 66.624 869 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.58 % Allowed : 9.04 % Favored : 90.38 % 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: -2.02 (0.29), residues: 808 helix: -0.14 (0.29), residues: 311 sheet: -1.22 (0.39), residues: 183 loop : -2.61 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.025 0.002 PHE L 163 TYR 0.019 0.002 TYR L 164 ARG 0.005 0.001 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 303) hydrogen bonds : angle 5.59839 ( 858) SS BOND : bond 0.00327 ( 6) SS BOND : angle 1.05844 ( 12) covalent geometry : bond 0.00380 ( 6355) covalent geometry : angle 0.76005 ( 8625) *********************** 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 117 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: Z 82 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7255 (mt-10) REVERT: Z 172 MET cc_start: 0.8086 (mtm) cc_final: 0.7552 (mtt) REVERT: Z 290 ASN cc_start: 0.7879 (p0) cc_final: 0.7409 (t0) REVERT: Z 360 TYR cc_start: 0.7198 (m-80) cc_final: 0.6748 (m-80) REVERT: H 29 GLN cc_start: 0.6800 (tp-100) cc_final: 0.6507 (tp-100) REVERT: H 103 ASN cc_start: 0.8002 (t0) cc_final: 0.7424 (t0) REVERT: H 106 TYR cc_start: 0.7413 (m-80) cc_final: 0.6993 (m-80) REVERT: H 186 TYR cc_start: 0.8517 (p90) cc_final: 0.7935 (p90) outliers start: 4 outliers final: 1 residues processed: 116 average time/residue: 0.1604 time to fit residues: 25.3759 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 : 0.659 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.153029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119440 restraints weight = 7302.713| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.33 r_work: 0.3379 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6361 Z= 0.159 Angle : 0.736 9.993 8637 Z= 0.381 Chirality : 0.044 0.209 988 Planarity : 0.007 0.114 1074 Dihedral : 6.417 66.715 869 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.46 % Allowed : 12.39 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (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: -1.69 (0.30), residues: 808 helix: 0.34 (0.30), residues: 312 sheet: -1.20 (0.39), residues: 183 loop : -2.57 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.025 0.002 PHE Z 91 TYR 0.019 0.002 TYR H 120 ARG 0.002 0.000 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 303) hydrogen bonds : angle 5.21850 ( 858) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.05172 ( 12) covalent geometry : bond 0.00379 ( 6355) covalent geometry : angle 0.73509 ( 8625) *********************** 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 122 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.656 Fit side-chains REVERT: Z 172 MET cc_start: 0.8249 (mtm) cc_final: 0.7679 (mtt) REVERT: Z 290 ASN cc_start: 0.7916 (p0) cc_final: 0.7478 (t0) REVERT: H 102 LYS cc_start: 0.8576 (ptpp) cc_final: 0.7819 (ptpp) REVERT: H 103 ASN cc_start: 0.8252 (t0) cc_final: 0.7646 (t0) REVERT: H 186 TYR cc_start: 0.8563 (p90) cc_final: 0.8228 (p90) REVERT: L 225 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8382 (tp) outliers start: 10 outliers final: 4 residues processed: 116 average time/residue: 0.1830 time to fit residues: 27.9972 Evaluate side-chains 103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 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 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 = 0.3929 r_free = 0.3929 target = 0.153840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118628 restraints weight = 9152.760| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.78 r_work: 0.3363 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6361 Z= 0.148 Angle : 0.710 9.534 8637 Z= 0.368 Chirality : 0.044 0.207 988 Planarity : 0.007 0.113 1074 Dihedral : 6.270 66.797 869 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.90 % Allowed : 15.45 % Favored : 82.65 % 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: -1.51 (0.30), residues: 808 helix: 0.52 (0.30), residues: 318 sheet: -1.09 (0.39), residues: 180 loop : -2.56 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.022 0.002 PHE Z 78 TYR 0.017 0.002 TYR H 120 ARG 0.004 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 303) hydrogen bonds : angle 4.98604 ( 858) SS BOND : bond 0.00265 ( 6) SS BOND : angle 1.04147 ( 12) covalent geometry : bond 0.00353 ( 6355) covalent geometry : angle 0.70975 ( 8625) *********************** 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 123 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.623 Fit side-chains REVERT: Z 39 ASP cc_start: 0.7659 (p0) cc_final: 0.7267 (p0) REVERT: Z 95 MET cc_start: 0.7735 (tpt) cc_final: 0.7494 (mmm) REVERT: Z 172 MET cc_start: 0.8104 (mtm) cc_final: 0.7560 (mtt) REVERT: Z 290 ASN cc_start: 0.7944 (p0) cc_final: 0.7490 (t0) REVERT: H 102 LYS cc_start: 0.8541 (ptpp) cc_final: 0.7853 (ptpp) REVERT: H 103 ASN cc_start: 0.8138 (t0) cc_final: 0.7575 (t0) REVERT: H 186 TYR cc_start: 0.8520 (p90) cc_final: 0.8260 (p90) REVERT: L 106 ASP cc_start: 0.8304 (m-30) cc_final: 0.7937 (m-30) REVERT: L 225 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8363 (tp) outliers start: 13 outliers final: 5 residues processed: 119 average time/residue: 0.1822 time to fit residues: 28.7131 Evaluate side-chains 103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 234 ASN Z 379 HIS ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.154027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117736 restraints weight = 10894.034| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.15 r_work: 0.3341 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6361 Z= 0.146 Angle : 0.701 10.679 8637 Z= 0.365 Chirality : 0.043 0.206 988 Planarity : 0.007 0.114 1074 Dihedral : 6.175 66.910 869 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.75 % Allowed : 16.03 % Favored : 82.22 % 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: -0.95 (0.40), residues: 180 loop : -2.48 (0.33), residues: 308 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 0.025 0.002 TYR L 210 ARG 0.004 0.000 ARG H 127 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 303) hydrogen bonds : angle 4.85978 ( 858) SS BOND : bond 0.00247 ( 6) SS BOND : angle 1.03301 ( 12) covalent geometry : bond 0.00346 ( 6355) covalent geometry : angle 0.70089 ( 8625) *********************** 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 116 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.709 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7310 (mt-10) REVERT: Z 95 MET cc_start: 0.7705 (tpt) cc_final: 0.7473 (mmm) REVERT: Z 290 ASN cc_start: 0.7925 (p0) cc_final: 0.7493 (t0) REVERT: H 102 LYS cc_start: 0.8509 (ptpp) cc_final: 0.7737 (ptpp) REVERT: H 103 ASN cc_start: 0.8119 (t0) cc_final: 0.7572 (t0) REVERT: H 106 TYR cc_start: 0.7334 (m-80) cc_final: 0.7086 (m-80) REVERT: L 106 ASP cc_start: 0.8244 (m-30) cc_final: 0.7884 (m-30) REVERT: L 225 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8375 (tp) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 0.2018 time to fit residues: 28.9926 Evaluate side-chains 107 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 0.0370 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.149024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110521 restraints weight = 14616.083| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 4.77 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6361 Z= 0.172 Angle : 0.722 10.374 8637 Z= 0.374 Chirality : 0.044 0.204 988 Planarity : 0.008 0.146 1074 Dihedral : 6.241 67.408 869 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.04 % Allowed : 17.64 % 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: -1.36 (0.30), residues: 808 helix: 0.62 (0.30), residues: 320 sheet: -0.91 (0.40), residues: 180 loop : -2.56 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 133 HIS 0.004 0.001 HIS Z 354 PHE 0.024 0.002 PHE Z 78 TYR 0.019 0.002 TYR H 120 ARG 0.003 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 303) hydrogen bonds : angle 4.90405 ( 858) SS BOND : bond 0.00222 ( 6) SS BOND : angle 1.08913 ( 12) covalent geometry : bond 0.00418 ( 6355) covalent geometry : angle 0.72112 ( 8625) *********************** 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 120 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.664 Fit side-chains REVERT: Z 39 ASP cc_start: 0.7598 (p0) cc_final: 0.7175 (p0) REVERT: Z 82 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7259 (mt-10) REVERT: Z 95 MET cc_start: 0.7819 (tpt) cc_final: 0.7521 (mmm) REVERT: Z 290 ASN cc_start: 0.7855 (p0) cc_final: 0.7465 (t0) REVERT: H 102 LYS cc_start: 0.8514 (ptpp) cc_final: 0.7894 (ptpp) REVERT: H 103 ASN cc_start: 0.8150 (t0) cc_final: 0.7642 (t0) REVERT: H 186 TYR cc_start: 0.8561 (p90) cc_final: 0.8111 (p90) REVERT: L 106 ASP cc_start: 0.8187 (m-30) cc_final: 0.7786 (m-30) REVERT: L 225 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8499 (tp) outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.1821 time to fit residues: 27.2638 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 : 0.655 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.0020 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.152184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113103 restraints weight = 14633.424| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.87 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6361 Z= 0.138 Angle : 0.691 9.954 8637 Z= 0.358 Chirality : 0.043 0.190 988 Planarity : 0.007 0.118 1074 Dihedral : 6.095 67.289 869 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.60 % Allowed : 18.80 % 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 (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: 0.79 (0.30), residues: 321 sheet: -0.80 (0.41), residues: 178 loop : -2.53 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 133 HIS 0.003 0.000 HIS Z 354 PHE 0.024 0.001 PHE Z 78 TYR 0.019 0.002 TYR L 210 ARG 0.003 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 303) hydrogen bonds : angle 4.77350 ( 858) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.97092 ( 12) covalent geometry : bond 0.00326 ( 6355) covalent geometry : angle 0.69082 ( 8625) *********************** 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 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.695 Fit side-chains REVERT: Z 39 ASP cc_start: 0.7556 (p0) cc_final: 0.7140 (p0) REVERT: Z 82 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7173 (mt-10) REVERT: Z 95 MET cc_start: 0.7726 (tpt) cc_final: 0.7478 (mmm) REVERT: Z 165 LEU cc_start: 0.8187 (mp) cc_final: 0.7964 (mp) REVERT: Z 290 ASN cc_start: 0.7892 (p0) cc_final: 0.7532 (t0) REVERT: H 102 LYS cc_start: 0.8501 (ptpp) cc_final: 0.7857 (ptpp) REVERT: H 103 ASN cc_start: 0.8123 (t0) cc_final: 0.7604 (t0) REVERT: H 186 TYR cc_start: 0.8497 (p90) cc_final: 0.8122 (p90) REVERT: L 106 ASP cc_start: 0.8123 (m-30) cc_final: 0.7754 (m-30) REVERT: L 146 ASP cc_start: 0.8521 (t0) cc_final: 0.8193 (p0) REVERT: L 225 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8474 (tp) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.1794 time to fit residues: 26.2503 Evaluate side-chains 110 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 Z residue 378 GLN Chi-restraints excluded: chain L residue 45 ILE 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 59 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.156257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119256 restraints weight = 9571.405| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.95 r_work: 0.3373 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6361 Z= 0.125 Angle : 0.672 9.572 8637 Z= 0.347 Chirality : 0.043 0.180 988 Planarity : 0.007 0.112 1074 Dihedral : 5.929 67.178 869 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.46 % Allowed : 19.83 % 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 (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: -1.12 (0.31), residues: 808 helix: 1.03 (0.31), residues: 311 sheet: -0.95 (0.40), residues: 187 loop : -2.49 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 133 HIS 0.008 0.001 HIS Z 379 PHE 0.021 0.001 PHE Z 78 TYR 0.018 0.001 TYR L 210 ARG 0.002 0.000 ARG H 113 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 303) hydrogen bonds : angle 4.67365 ( 858) SS BOND : bond 0.00258 ( 6) SS BOND : angle 0.88037 ( 12) covalent geometry : bond 0.00286 ( 6355) covalent geometry : angle 0.67123 ( 8625) *********************** 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 128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.722 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7278 (mt-10) REVERT: Z 165 LEU cc_start: 0.8159 (mp) cc_final: 0.7925 (mp) REVERT: Z 172 MET cc_start: 0.7557 (mtm) cc_final: 0.7272 (mtt) REVERT: Z 290 ASN cc_start: 0.7930 (p0) cc_final: 0.7662 (t0) REVERT: H 102 LYS cc_start: 0.8477 (ptpp) cc_final: 0.7691 (ptpp) REVERT: H 103 ASN cc_start: 0.8152 (t0) cc_final: 0.7609 (t0) REVERT: H 106 TYR cc_start: 0.7436 (m-80) cc_final: 0.7181 (m-80) REVERT: H 130 TYR cc_start: 0.7848 (t80) cc_final: 0.6343 (t80) REVERT: H 186 TYR cc_start: 0.8449 (p90) cc_final: 0.8216 (p90) REVERT: L 106 ASP cc_start: 0.8117 (m-30) cc_final: 0.7722 (m-30) REVERT: L 146 ASP cc_start: 0.8420 (t0) cc_final: 0.8130 (p0) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.1728 time to fit residues: 28.8149 Evaluate side-chains 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 PHE 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: 0.5980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 ** 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 = 0.3935 r_free = 0.3935 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114839 restraints weight = 16052.738| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 5.08 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6361 Z= 0.135 Angle : 0.697 11.694 8637 Z= 0.357 Chirality : 0.043 0.187 988 Planarity : 0.007 0.112 1074 Dihedral : 5.919 67.538 869 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.75 % Allowed : 19.97 % Favored : 78.28 % 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: -1.09 (0.31), residues: 808 helix: 0.92 (0.31), residues: 319 sheet: -0.92 (0.39), residues: 189 loop : -2.40 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 133 HIS 0.002 0.000 HIS H 241 PHE 0.023 0.002 PHE Z 258 TYR 0.019 0.002 TYR H 138 ARG 0.005 0.000 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 303) hydrogen bonds : angle 4.68390 ( 858) SS BOND : bond 0.00240 ( 6) SS BOND : angle 0.95094 ( 12) covalent geometry : bond 0.00318 ( 6355) covalent geometry : angle 0.69681 ( 8625) *********************** 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 124 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.712 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7098 (mt-10) REVERT: Z 165 LEU cc_start: 0.8229 (mp) cc_final: 0.7997 (mp) REVERT: Z 290 ASN cc_start: 0.7806 (p0) cc_final: 0.7602 (t0) REVERT: H 102 LYS cc_start: 0.8404 (ptpp) cc_final: 0.7680 (ptpp) REVERT: H 103 ASN cc_start: 0.8101 (t0) cc_final: 0.7628 (t0) REVERT: H 106 TYR cc_start: 0.7353 (m-80) cc_final: 0.6993 (m-80) REVERT: H 108 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6958 (tp40) REVERT: H 186 TYR cc_start: 0.8384 (p90) cc_final: 0.8178 (p90) REVERT: L 106 ASP cc_start: 0.8036 (m-30) cc_final: 0.7581 (m-30) REVERT: L 146 ASP cc_start: 0.8389 (t0) cc_final: 0.8134 (p0) outliers start: 12 outliers final: 10 residues processed: 118 average time/residue: 0.1830 time to fit residues: 28.8099 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 : 0.691 ------------------------------------------------------------------------------- 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 H residue 108 GLN Chi-restraints excluded: chain L residue 45 ILE 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: 1.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.153594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117050 restraints weight = 9202.024| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.82 r_work: 0.3340 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3019 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= 0.151 Angle : 0.712 11.877 8637 Z= 0.366 Chirality : 0.044 0.182 988 Planarity : 0.007 0.112 1074 Dihedral : 5.958 67.694 869 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.46 % Allowed : 20.70 % Favored : 77.84 % 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: -1.11 (0.31), residues: 808 helix: 0.87 (0.31), residues: 319 sheet: -0.97 (0.39), residues: 191 loop : -2.36 (0.34), residues: 298 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 0.031 0.002 PHE Z 91 TYR 0.022 0.002 TYR H 138 ARG 0.006 0.001 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 303) hydrogen bonds : angle 4.71505 ( 858) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.99450 ( 12) covalent geometry : bond 0.00361 ( 6355) covalent geometry : angle 0.71143 ( 8625) ********************** 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 121 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.692 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7329 (mt-10) REVERT: Z 165 LEU cc_start: 0.8279 (mp) cc_final: 0.8053 (mp) REVERT: H 102 LYS cc_start: 0.8526 (ptpp) cc_final: 0.7740 (ptpp) REVERT: H 103 ASN cc_start: 0.8167 (t0) cc_final: 0.7672 (t0) REVERT: H 106 TYR cc_start: 0.7460 (m-80) cc_final: 0.7120 (m-80) REVERT: H 108 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7340 (tp40) REVERT: H 186 TYR cc_start: 0.8470 (p90) cc_final: 0.8253 (p90) REVERT: L 106 ASP cc_start: 0.8153 (m-30) cc_final: 0.7742 (m-30) REVERT: L 146 ASP cc_start: 0.8437 (t0) cc_final: 0.8160 (p0) outliers start: 10 outliers final: 8 residues processed: 116 average time/residue: 0.1804 time to fit residues: 28.0364 Evaluate side-chains 116 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 H residue 108 GLN Chi-restraints excluded: chain L residue 45 ILE 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: 4.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 77 optimal weight: 0.0370 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3940 r_free = 0.3940 target = 0.155122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117309 restraints weight = 11198.500| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.26 r_work: 0.3335 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6361 Z= 0.139 Angle : 0.711 11.705 8637 Z= 0.371 Chirality : 0.043 0.178 988 Planarity : 0.007 0.112 1074 Dihedral : 5.947 67.681 869 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.31 % Allowed : 20.99 % Favored : 77.70 % 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: -1.07 (0.31), residues: 808 helix: 0.91 (0.31), residues: 319 sheet: -0.90 (0.39), residues: 189 loop : -2.37 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 133 HIS 0.002 0.000 HIS Z 354 PHE 0.025 0.002 PHE Z 91 TYR 0.023 0.002 TYR H 138 ARG 0.006 0.001 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 303) hydrogen bonds : angle 4.70278 ( 858) SS BOND : bond 0.00241 ( 6) SS BOND : angle 0.95112 ( 12) covalent geometry : bond 0.00323 ( 6355) covalent geometry : angle 0.71029 ( 8625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4125.18 seconds wall clock time: 71 minutes 16.24 seconds (4276.24 seconds total)