Starting phenix.real_space_refine on Mon Mar 11 05:30:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo8_23464/03_2024/7lo8_23464.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo8_23464/03_2024/7lo8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo8_23464/03_2024/7lo8_23464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo8_23464/03_2024/7lo8_23464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo8_23464/03_2024/7lo8_23464.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo8_23464/03_2024/7lo8_23464.pdb" } 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 Residue "Z PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 82": "OE1" <-> "OE2" Residue "Z PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 194": "OD1" <-> "OD2" Residue "L TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 211": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.05, per 1000 atoms: 0.81 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 - 3.50 Amino acid : False - 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: 2.36 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: 0.77 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: 1.82 Time building geometry restraints manager: 2.58 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: 96.11 - 103.69: 80 103.69 - 111.27: 2585 111.27 - 118.84: 2429 118.84 - 126.42: 3438 126.42 - 134.00: 93 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 2.440 nonbonded pdb=" OE2 GLU Z 222 " pdb=" NH1 ARG H 134 " model vdw 2.153 2.520 nonbonded pdb=" O ALA Z 362 " pdb=" OG SER Z 366 " model vdw 2.214 2.440 nonbonded pdb=" O ILE L 130 " pdb=" OH TYR L 164 " model vdw 2.223 2.440 nonbonded pdb=" OE1 GLU Z 222 " pdb=" OH TYR H 131 " model vdw 2.232 2.440 ... (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 ========== 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: 0.840 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: 0.000 Extract box with map and model: 3.950 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.280 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.672 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: 0.1883 time to fit residues: 26.8547 Evaluate side-chains 94 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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: 1.9990 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6355 Z= 0.275 Angle : 0.763 10.166 8625 Z= 0.398 Chirality : 0.045 0.213 988 Planarity : 0.008 0.114 1074 Dihedral : 6.681 66.925 869 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.54 % Favored : 90.33 % Rotamer: Outliers : 0.44 % Allowed : 9.48 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (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: -2.08 (0.29), residues: 808 helix: -0.19 (0.29), residues: 311 sheet: -1.22 (0.39), residues: 186 loop : -2.68 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 133 HIS 0.004 0.001 HIS Z 354 PHE 0.024 0.002 PHE Z 258 TYR 0.021 0.002 TYR H 120 ARG 0.004 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 108 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.728 Fit side-chains REVERT: Z 172 MET cc_start: 0.8388 (mtm) cc_final: 0.7861 (mtt) REVERT: Z 290 ASN cc_start: 0.7697 (p0) cc_final: 0.7260 (t0) REVERT: H 103 ASN cc_start: 0.8248 (t0) cc_final: 0.7545 (t0) REVERT: H 106 TYR cc_start: 0.7451 (m-80) cc_final: 0.7182 (m-80) REVERT: H 186 TYR cc_start: 0.8492 (p90) cc_final: 0.7898 (p90) REVERT: L 206 SER cc_start: 0.8099 (m) cc_final: 0.7889 (p) outliers start: 3 outliers final: 1 residues processed: 107 average time/residue: 0.1769 time to fit residues: 25.4870 Evaluate side-chains 101 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 49 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN ** Z 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6355 Z= 0.184 Angle : 0.679 9.626 8625 Z= 0.351 Chirality : 0.043 0.199 988 Planarity : 0.007 0.109 1074 Dihedral : 6.231 66.464 869 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.31 % Allowed : 12.39 % Favored : 86.30 % 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: -1.64 (0.30), residues: 808 helix: 0.51 (0.30), residues: 308 sheet: -1.16 (0.39), residues: 185 loop : -2.67 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 139 HIS 0.002 0.001 HIS Z 354 PHE 0.024 0.002 PHE Z 78 TYR 0.019 0.002 TYR L 73 ARG 0.002 0.000 ARG Z 310 *********************** 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 128 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: Z 172 MET cc_start: 0.8308 (mtm) cc_final: 0.7736 (mtt) REVERT: Z 290 ASN cc_start: 0.7694 (p0) cc_final: 0.7417 (t0) REVERT: Z 325 GLN cc_start: 0.6865 (mt0) cc_final: 0.6660 (mm-40) REVERT: H 103 ASN cc_start: 0.8241 (t0) cc_final: 0.7555 (t0) REVERT: H 186 TYR cc_start: 0.8350 (p90) cc_final: 0.7955 (p90) REVERT: L 106 ASP cc_start: 0.8165 (m-30) cc_final: 0.7860 (m-30) REVERT: L 225 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8384 (tp) outliers start: 9 outliers final: 4 residues processed: 122 average time/residue: 0.1725 time to fit residues: 27.8673 Evaluate side-chains 106 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 109 THR 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 54 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 234 ASN ** Z 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2298 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= 0.217 Angle : 0.687 9.076 8625 Z= 0.358 Chirality : 0.043 0.207 988 Planarity : 0.007 0.110 1074 Dihedral : 6.165 66.812 869 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.43 % Favored : 91.45 % Rotamer: Outliers : 2.04 % Allowed : 14.14 % 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: -1.45 (0.30), residues: 808 helix: 0.74 (0.30), residues: 307 sheet: -1.00 (0.39), residues: 184 loop : -2.69 (0.33), residues: 317 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 0.030 0.002 PHE Z 91 TYR 0.023 0.002 TYR L 210 ARG 0.002 0.000 ARG H 134 *********************** 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 125 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.720 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7175 (mt-10) REVERT: Z 172 MET cc_start: 0.8336 (mtm) cc_final: 0.7752 (mtt) REVERT: Z 290 ASN cc_start: 0.7637 (p0) cc_final: 0.7349 (t0) REVERT: H 103 ASN cc_start: 0.8272 (t0) cc_final: 0.7582 (t0) REVERT: H 127 ARG cc_start: 0.7207 (tpp80) cc_final: 0.6903 (ttm110) REVERT: H 186 TYR cc_start: 0.8401 (p90) cc_final: 0.8163 (p90) REVERT: L 106 ASP cc_start: 0.8244 (m-30) cc_final: 0.7922 (m-30) REVERT: L 225 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8390 (tp) outliers start: 14 outliers final: 5 residues processed: 119 average time/residue: 0.1850 time to fit residues: 29.2314 Evaluate side-chains 112 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 109 THR Chi-restraints excluded: chain L residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 234 ASN ** Z 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2343 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= 0.263 Angle : 0.708 8.764 8625 Z= 0.367 Chirality : 0.044 0.206 988 Planarity : 0.007 0.108 1074 Dihedral : 6.235 67.396 869 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.29 % Favored : 90.58 % Rotamer: Outliers : 2.19 % Allowed : 14.72 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (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: -1.37 (0.30), residues: 808 helix: 0.63 (0.31), residues: 315 sheet: -0.86 (0.39), residues: 184 loop : -2.58 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 133 HIS 0.004 0.001 HIS Z 354 PHE 0.024 0.002 PHE Z 78 TYR 0.022 0.002 TYR H 138 ARG 0.002 0.000 ARG H 134 *********************** 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 127 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: Z 82 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7291 (mt-10) REVERT: Z 172 MET cc_start: 0.8321 (mtm) cc_final: 0.7855 (mtt) REVERT: Z 290 ASN cc_start: 0.7609 (p0) cc_final: 0.7305 (t0) REVERT: H 103 ASN cc_start: 0.8329 (t0) cc_final: 0.7620 (t0) REVERT: H 127 ARG cc_start: 0.7235 (tpp80) cc_final: 0.6942 (ttm110) REVERT: H 186 TYR cc_start: 0.8458 (p90) cc_final: 0.8192 (p90) REVERT: L 106 ASP cc_start: 0.8205 (m-30) cc_final: 0.7903 (m-30) REVERT: L 225 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8395 (tp) outliers start: 15 outliers final: 10 residues processed: 117 average time/residue: 0.1794 time to fit residues: 28.0918 Evaluate side-chains 114 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain L residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 0.0000 chunk 45 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 234 ASN ** Z 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6355 Z= 0.215 Angle : 0.677 8.107 8625 Z= 0.352 Chirality : 0.043 0.202 988 Planarity : 0.006 0.107 1074 Dihedral : 6.098 67.261 869 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.30 % Favored : 91.57 % Rotamer: Outliers : 2.48 % Allowed : 15.74 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (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: -1.26 (0.30), residues: 808 helix: 0.78 (0.31), residues: 314 sheet: -0.83 (0.40), residues: 177 loop : -2.53 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 133 HIS 0.003 0.001 HIS Z 354 PHE 0.026 0.002 PHE Z 78 TYR 0.023 0.002 TYR H 138 ARG 0.003 0.000 ARG H 113 *********************** 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 132 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.854 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7338 (mt-10) REVERT: Z 95 MET cc_start: 0.7511 (tpt) cc_final: 0.7263 (mmm) REVERT: Z 172 MET cc_start: 0.8302 (mtm) cc_final: 0.7818 (mtt) REVERT: Z 290 ASN cc_start: 0.7600 (p0) cc_final: 0.7363 (t0) REVERT: H 103 ASN cc_start: 0.8324 (t0) cc_final: 0.7595 (t0) REVERT: H 127 ARG cc_start: 0.7270 (tpp80) cc_final: 0.7019 (ttm110) REVERT: L 106 ASP cc_start: 0.8210 (m-30) cc_final: 0.7914 (m-30) REVERT: L 146 ASP cc_start: 0.8518 (t70) cc_final: 0.8235 (p0) REVERT: L 225 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8460 (tp) outliers start: 17 outliers final: 13 residues processed: 121 average time/residue: 0.1993 time to fit residues: 31.6988 Evaluate side-chains 113 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 H residue 28 VAL Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 109 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6355 Z= 0.224 Angle : 0.697 11.091 8625 Z= 0.358 Chirality : 0.043 0.193 988 Planarity : 0.006 0.107 1074 Dihedral : 6.104 67.394 869 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.55 % Favored : 91.33 % Rotamer: Outliers : 2.48 % Allowed : 17.20 % 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: -1.24 (0.30), residues: 808 helix: 0.79 (0.31), residues: 313 sheet: -0.78 (0.40), residues: 177 loop : -2.53 (0.33), residues: 318 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 Z 78 TYR 0.021 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 122 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.726 Fit side-chains REVERT: Z 82 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7309 (mt-10) REVERT: Z 95 MET cc_start: 0.7529 (tpt) cc_final: 0.7246 (mmm) REVERT: Z 165 LEU cc_start: 0.8277 (mp) cc_final: 0.8026 (mp) REVERT: Z 172 MET cc_start: 0.8304 (mtm) cc_final: 0.7990 (mtt) REVERT: H 103 ASN cc_start: 0.8320 (t0) cc_final: 0.7592 (t0) REVERT: H 127 ARG cc_start: 0.7261 (tpp80) cc_final: 0.7010 (ttm110) REVERT: H 186 TYR cc_start: 0.8390 (p90) cc_final: 0.7948 (p90) REVERT: L 106 ASP cc_start: 0.8192 (m-30) cc_final: 0.7893 (m-30) REVERT: L 146 ASP cc_start: 0.8509 (t70) cc_final: 0.8237 (p0) REVERT: L 225 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8463 (tp) outliers start: 17 outliers final: 13 residues processed: 112 average time/residue: 0.1907 time to fit residues: 28.3195 Evaluate side-chains 113 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 29 TYR Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 233 VAL Chi-restraints excluded: chain Z residue 378 GLN Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 109 THR 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 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN ** Z 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 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 : 0.005 0.060 6355 Z= 0.294 Angle : 0.737 11.013 8625 Z= 0.382 Chirality : 0.044 0.194 988 Planarity : 0.007 0.107 1074 Dihedral : 6.264 67.904 869 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.42 % Favored : 90.46 % Rotamer: Outliers : 3.06 % Allowed : 17.06 % Favored : 79.88 % 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: 0.63 (0.30), residues: 316 sheet: -0.79 (0.40), residues: 178 loop : -2.60 (0.32), residues: 314 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 0.025 0.002 PHE Z 258 TYR 0.023 0.002 TYR L 164 ARG 0.005 0.001 ARG H 45 *********************** 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 120 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.734 Fit side-chains REVERT: Z 172 MET cc_start: 0.8311 (mtm) cc_final: 0.8031 (mtt) REVERT: H 103 ASN cc_start: 0.8334 (t0) cc_final: 0.7607 (t0) REVERT: H 108 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7183 (tp40) REVERT: L 106 ASP cc_start: 0.8227 (m-30) cc_final: 0.7914 (m-30) REVERT: L 146 ASP cc_start: 0.8503 (t70) cc_final: 0.8237 (p0) REVERT: L 225 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8491 (tp) outliers start: 21 outliers final: 16 residues processed: 108 average time/residue: 0.1759 time to fit residues: 25.3778 Evaluate side-chains 116 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 63 ASP 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 H residue 108 GLN Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 149 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 67 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.0470 chunk 46 optimal weight: 0.5980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 GLN ** Z 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 378 GLN H 108 GLN ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6355 Z= 0.182 Angle : 0.690 10.901 8625 Z= 0.355 Chirality : 0.042 0.180 988 Planarity : 0.006 0.107 1074 Dihedral : 5.965 67.280 869 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.18 % Favored : 91.70 % Rotamer: Outliers : 2.62 % Allowed : 17.78 % 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: -1.16 (0.30), residues: 808 helix: 0.80 (0.31), residues: 321 sheet: -0.75 (0.41), residues: 179 loop : -2.50 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 133 HIS 0.002 0.000 HIS Z 354 PHE 0.033 0.001 PHE Z 78 TYR 0.021 0.002 TYR H 138 ARG 0.005 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 123 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.707 Fit side-chains REVERT: Z 95 MET cc_start: 0.7483 (tpt) cc_final: 0.7209 (mmm) REVERT: Z 165 LEU cc_start: 0.8251 (mp) cc_final: 0.7976 (mp) REVERT: H 103 ASN cc_start: 0.8310 (t0) cc_final: 0.7558 (t0) REVERT: H 108 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7152 (tp40) REVERT: H 127 ARG cc_start: 0.7218 (tpp80) cc_final: 0.6991 (ttm110) REVERT: H 186 TYR cc_start: 0.8318 (p90) cc_final: 0.8035 (p90) REVERT: L 106 ASP cc_start: 0.8180 (m-30) cc_final: 0.7913 (m-30) REVERT: L 146 ASP cc_start: 0.8454 (t70) cc_final: 0.8207 (p0) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 0.1813 time to fit residues: 27.7199 Evaluate side-chains 115 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 H residue 108 GLN Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.0030 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 0.0040 chunk 73 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 0.0000 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.0040 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 overall best weight: 0.0096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 340 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3049 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= 0.169 Angle : 0.687 10.857 8625 Z= 0.354 Chirality : 0.042 0.171 988 Planarity : 0.006 0.107 1074 Dihedral : 5.840 67.037 869 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 2.04 % Allowed : 19.24 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.13 % Rama-Z (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: -1.00 (0.31), residues: 808 helix: 1.02 (0.31), residues: 319 sheet: -0.72 (0.40), residues: 180 loop : -2.46 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 133 HIS 0.002 0.000 HIS Z 379 PHE 0.022 0.001 PHE Z 258 TYR 0.023 0.002 TYR H 138 ARG 0.005 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 130 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.705 Fit side-chains REVERT: Z 73 ILE cc_start: 0.7524 (mt) cc_final: 0.7314 (mp) REVERT: Z 165 LEU cc_start: 0.8174 (mp) cc_final: 0.7949 (mp) REVERT: Z 172 MET cc_start: 0.8152 (mtm) cc_final: 0.7823 (mtt) REVERT: H 103 ASN cc_start: 0.8265 (t0) cc_final: 0.7584 (t0) REVERT: H 127 ARG cc_start: 0.7179 (tpp80) cc_final: 0.6966 (ttm110) REVERT: H 186 TYR cc_start: 0.8239 (p90) cc_final: 0.8031 (p90) REVERT: L 106 ASP cc_start: 0.8153 (m-30) cc_final: 0.7901 (m-30) REVERT: L 146 ASP cc_start: 0.8474 (t70) cc_final: 0.8271 (p0) REVERT: L 233 PHE cc_start: 0.7171 (p90) cc_final: 0.6819 (p90) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.1814 time to fit residues: 29.4659 Evaluate side-chains 122 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 135 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 29 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 163 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN L 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117630 restraints weight = 14893.184| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.94 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 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 = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3154 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= 0.183 Angle : 0.695 11.253 8625 Z= 0.355 Chirality : 0.043 0.198 988 Planarity : 0.006 0.107 1074 Dihedral : 5.796 67.311 869 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.19 % Allowed : 19.83 % Favored : 77.99 % 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: -0.94 (0.31), residues: 808 helix: 1.14 (0.31), residues: 313 sheet: -0.68 (0.40), residues: 182 loop : -2.47 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 133 HIS 0.002 0.000 HIS Z 354 PHE 0.016 0.002 PHE Z 78 TYR 0.023 0.002 TYR H 138 ARG 0.005 0.000 ARG H 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1769.17 seconds wall clock time: 32 minutes 37.18 seconds (1957.18 seconds total)