Starting phenix.real_space_refine on Tue Feb 13 18:56:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/02_2024/8faz_28961_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/02_2024/8faz_28961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/02_2024/8faz_28961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/02_2024/8faz_28961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/02_2024/8faz_28961_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/02_2024/8faz_28961_updated.pdb" } resolution = 2.3 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 4619 2.51 5 N 1275 2.21 5 O 1377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2470 Classifications: {'peptide': 314} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 301} Chain breaks: 2 Chain: "D" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2288 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 294} Chain breaks: 2 Chain: "X" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1912 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 229} Chain breaks: 3 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.36, per 1000 atoms: 0.59 Number of scatterers: 7331 At special positions: 0 Unit cell: (68.73, 80.91, 111.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 2 11.99 O 1377 8.00 N 1275 7.00 C 4619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 44.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.121A pdb=" N HIS B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.061A pdb=" N LYS B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 59 removed outlier: 3.532A pdb=" N ALA B 59 " --> pdb=" O MET B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'C' and resid 14 through 16 No H-bonds generated for 'chain 'C' and resid 14 through 16' Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 87 through 96 Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.536A pdb=" N VAL C 140 " --> pdb=" O MET C 136 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 166 through 186 removed outlier: 3.883A pdb=" N GLU C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 removed outlier: 4.103A pdb=" N ALA C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 255 through 276 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'D' and resid 14 through 23 removed outlier: 3.650A pdb=" N HIS D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 36 through 43 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 113 through 126 Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 157 through 166 removed outlier: 3.553A pdb=" N ALA D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 191 Processing helix chain 'D' and resid 208 through 215 Proline residue: D 214 - end of helix Processing helix chain 'D' and resid 222 through 239 Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'X' and resid 24 through 27 No H-bonds generated for 'chain 'X' and resid 24 through 27' Processing helix chain 'X' and resid 54 through 66 Processing helix chain 'X' and resid 89 through 99 Processing helix chain 'X' and resid 105 through 114 removed outlier: 3.683A pdb=" N ARG X 114 " --> pdb=" O TYR X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 139 removed outlier: 3.694A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 161 Processing helix chain 'X' and resid 166 through 169 No H-bonds generated for 'chain 'X' and resid 166 through 169' Processing helix chain 'X' and resid 171 through 187 Processing helix chain 'X' and resid 229 through 234 removed outlier: 3.959A pdb=" N LEU X 234 " --> pdb=" O ALA X 230 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 336 through 338 removed outlier: 6.702A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU C 154 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL C 239 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 156 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL C 241 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 158 " --> pdb=" O VAL C 241 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 340 through 342 Processing sheet with id= C, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.362A pdb=" N ARG D 275 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 274 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL D 245 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE D 105 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 247 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY D 107 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN D 249 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASN D 131 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL D 203 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 133 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL D 205 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 135 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 251 through 253 Processing sheet with id= E, first strand: chain 'X' and resid 276 through 280 removed outlier: 4.168A pdb=" N PHE X 269 " --> pdb=" O CYS X 280 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER X 264 " --> pdb=" O CYS X 259 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS X 237 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY X 48 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU X 148 " --> pdb=" O PHE X 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR X 194 " --> pdb=" O LEU X 148 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLU X 77 " --> pdb=" O CYS X 144 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU X 146 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU X 79 " --> pdb=" O LEU X 146 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU X 148 " --> pdb=" O LEU X 79 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE X 81 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 915 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: 2.26 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2410 1.34 - 1.46: 1539 1.46 - 1.58: 3409 1.58 - 1.69: 13 1.69 - 1.81: 72 Bond restraints: 7443 Sorted by residual: bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP X 301 " pdb=" PB ANP X 301 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O5' ANP D 401 " pdb=" PA ANP D 401 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 7438 not shown) Histogram of bond angle deviations from ideal: 100.05 - 107.22: 217 107.22 - 114.39: 4545 114.39 - 121.57: 3603 121.57 - 128.74: 1645 128.74 - 135.91: 47 Bond angle restraints: 10057 Sorted by residual: angle pdb=" PB ANP X 301 " pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 126.95 109.59 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.85 17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" N ILE C 183 " pdb=" CA ILE C 183 " pdb=" C ILE C 183 " ideal model delta sigma weight residual 112.80 108.50 4.30 1.15e+00 7.56e-01 1.40e+01 angle pdb=" O1B ANP D 401 " pdb=" PB ANP D 401 " pdb=" O2B ANP D 401 " ideal model delta sigma weight residual 120.08 109.22 10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1B ANP X 301 " pdb=" PB ANP X 301 " pdb=" O2B ANP X 301 " ideal model delta sigma weight residual 120.08 109.40 10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 10052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.63: 4424 26.63 - 53.26: 106 53.26 - 79.90: 8 79.90 - 106.53: 3 106.53 - 133.16: 1 Dihedral angle restraints: 4542 sinusoidal: 1879 harmonic: 2663 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 73.16 -133.16 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -147.03 87.03 1 2.00e+01 2.50e-03 2.28e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -0.52 -59.48 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 4539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1038 0.056 - 0.112: 129 0.112 - 0.167: 8 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1177 Sorted by residual: chirality pdb=" C3' ANP X 301 " pdb=" C2' ANP X 301 " pdb=" C4' ANP X 301 " pdb=" O3' ANP X 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ILE C 144 " pdb=" N ILE C 144 " pdb=" C ILE C 144 " pdb=" CB ILE C 144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1174 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY X 48 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO X 49 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO X 49 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO X 49 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 342 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO C 343 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 42 " 0.017 5.00e-02 4.00e+02 2.50e-02 9.98e-01 pdb=" N PRO C 43 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.014 5.00e-02 4.00e+02 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 85 2.57 - 3.15: 6025 3.15 - 3.73: 12124 3.73 - 4.32: 17227 4.32 - 4.90: 27975 Nonbonded interactions: 63436 Sorted by model distance: nonbonded pdb=" OG1 THR X 55 " pdb="MG MG X 302 " model vdw 1.986 2.170 nonbonded pdb=" O3G ANP D 401 " pdb="MG MG D 402 " model vdw 1.992 2.170 nonbonded pdb=" O1G ANP X 301 " pdb="MG MG X 302 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR D 114 " pdb="MG MG D 402 " model vdw 2.013 2.170 nonbonded pdb=" O1B ANP X 301 " pdb="MG MG X 302 " model vdw 2.027 2.170 ... (remaining 63431 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=1.00 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.004 0.145 7443 Z= 0.284 Angle : 0.616 17.364 10057 Z= 0.269 Chirality : 0.039 0.279 1177 Planarity : 0.003 0.028 1258 Dihedral : 11.246 133.159 2814 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.50 % Allowed : 2.74 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.35 (0.28), residues: 904 helix: 0.68 (0.25), residues: 417 sheet: 0.30 (0.45), residues: 151 loop : -0.19 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 231 HIS 0.002 0.001 HIS X 40 PHE 0.007 0.001 PHE D 173 TYR 0.011 0.001 TYR C 210 ARG 0.002 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6856 (mm-40) REVERT: B 46 TYR cc_start: 0.7941 (t80) cc_final: 0.7361 (t80) REVERT: C 181 GLN cc_start: 0.7027 (tt0) cc_final: 0.6563 (tm-30) REVERT: D 36 LEU cc_start: 0.7396 (mt) cc_final: 0.7161 (mm) REVERT: D 174 ASP cc_start: 0.7860 (m-30) cc_final: 0.7649 (m-30) REVERT: D 292 MET cc_start: 0.8468 (mmm) cc_final: 0.8043 (mmp) REVERT: X 26 GLU cc_start: 0.7634 (tt0) cc_final: 0.6915 (tp30) REVERT: X 64 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7911 (mmm160) REVERT: X 224 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.8192 (ttt-90) outliers start: 4 outliers final: 2 residues processed: 193 average time/residue: 1.1199 time to fit residues: 228.6371 Evaluate side-chains 149 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN C 263 ASN C 267 GLN D 60 GLN D 301 GLN X 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7443 Z= 0.201 Angle : 0.553 6.547 10057 Z= 0.268 Chirality : 0.041 0.143 1177 Planarity : 0.003 0.042 1258 Dihedral : 7.558 95.485 1067 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.24 % Allowed : 11.69 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.44 (0.28), residues: 904 helix: 0.90 (0.25), residues: 435 sheet: -0.11 (0.46), residues: 136 loop : -0.16 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 231 HIS 0.004 0.001 HIS X 60 PHE 0.011 0.001 PHE X 80 TYR 0.015 0.001 TYR X 131 ARG 0.008 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6827 (mm-40) REVERT: C 181 GLN cc_start: 0.7146 (tt0) cc_final: 0.6604 (tm-30) REVERT: C 205 LEU cc_start: 0.7908 (mt) cc_final: 0.7661 (mp) REVERT: D 36 LEU cc_start: 0.7580 (mt) cc_final: 0.7358 (mm) REVERT: D 259 ARG cc_start: 0.7338 (pmm-80) cc_final: 0.7066 (pmm-80) REVERT: X 26 GLU cc_start: 0.7653 (tt0) cc_final: 0.6924 (tp30) REVERT: X 64 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7894 (mmm160) REVERT: X 173 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8491 (tm) outliers start: 18 outliers final: 7 residues processed: 172 average time/residue: 1.1754 time to fit residues: 213.3895 Evaluate side-chains 156 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 171 SER Chi-restraints excluded: chain X residue 173 LEU Chi-restraints excluded: chain X residue 182 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 196 GLN X 252 GLN X 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7443 Z= 0.207 Angle : 0.544 7.149 10057 Z= 0.263 Chirality : 0.041 0.238 1177 Planarity : 0.003 0.048 1258 Dihedral : 6.799 75.049 1065 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.24 % Allowed : 14.68 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.59 (0.28), residues: 904 helix: 1.08 (0.25), residues: 433 sheet: -0.08 (0.44), residues: 150 loop : -0.15 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 231 HIS 0.003 0.001 HIS X 60 PHE 0.010 0.001 PHE C 346 TYR 0.013 0.001 TYR X 131 ARG 0.010 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7055 (mm-40) cc_final: 0.6816 (mm-40) REVERT: C 181 GLN cc_start: 0.7147 (tt0) cc_final: 0.6590 (tm-30) REVERT: C 205 LEU cc_start: 0.7873 (mt) cc_final: 0.7641 (mp) REVERT: D 36 LEU cc_start: 0.7596 (mt) cc_final: 0.7390 (mm) REVERT: D 259 ARG cc_start: 0.7386 (pmm-80) cc_final: 0.7139 (pmm-80) REVERT: X 26 GLU cc_start: 0.7660 (tt0) cc_final: 0.7048 (tp30) REVERT: X 236 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8306 (mmmm) outliers start: 18 outliers final: 11 residues processed: 160 average time/residue: 1.1097 time to fit residues: 188.1649 Evaluate side-chains 155 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 236 LYS Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7443 Z= 0.217 Angle : 0.548 6.957 10057 Z= 0.264 Chirality : 0.041 0.185 1177 Planarity : 0.004 0.053 1258 Dihedral : 6.435 71.563 1065 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.86 % Allowed : 14.80 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.57 (0.29), residues: 904 helix: 1.06 (0.25), residues: 436 sheet: -0.21 (0.43), residues: 154 loop : -0.10 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 314 HIS 0.003 0.001 HIS X 40 PHE 0.009 0.001 PHE C 346 TYR 0.013 0.001 TYR X 131 ARG 0.012 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6818 (mm-40) REVERT: C 181 GLN cc_start: 0.7154 (tt0) cc_final: 0.6604 (tm-30) REVERT: C 205 LEU cc_start: 0.7851 (mt) cc_final: 0.7650 (mp) REVERT: D 36 LEU cc_start: 0.7602 (mt) cc_final: 0.7398 (mm) REVERT: D 259 ARG cc_start: 0.7406 (pmm-80) cc_final: 0.7148 (pmm-80) REVERT: X 26 GLU cc_start: 0.7669 (tt0) cc_final: 0.7062 (tp30) outliers start: 23 outliers final: 11 residues processed: 163 average time/residue: 1.0520 time to fit residues: 181.8294 Evaluate side-chains 155 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 252 GLN X 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7443 Z= 0.171 Angle : 0.557 7.941 10057 Z= 0.263 Chirality : 0.041 0.182 1177 Planarity : 0.004 0.057 1258 Dihedral : 6.175 66.126 1065 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.36 % Allowed : 15.92 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.63 (0.29), residues: 904 helix: 1.22 (0.25), residues: 432 sheet: -0.14 (0.43), residues: 153 loop : -0.26 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 314 HIS 0.003 0.001 HIS X 40 PHE 0.009 0.001 PHE C 346 TYR 0.013 0.001 TYR X 131 ARG 0.015 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7083 (mm-40) cc_final: 0.6871 (mm-40) REVERT: C 103 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7230 (t80) REVERT: C 181 GLN cc_start: 0.7132 (tt0) cc_final: 0.6583 (tm-30) REVERT: D 259 ARG cc_start: 0.7414 (pmm-80) cc_final: 0.7071 (pmm-80) REVERT: X 26 GLU cc_start: 0.7649 (tt0) cc_final: 0.7003 (tp30) outliers start: 19 outliers final: 10 residues processed: 169 average time/residue: 1.0992 time to fit residues: 196.8097 Evaluate side-chains 152 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 0.0070 chunk 29 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7443 Z= 0.170 Angle : 0.560 7.925 10057 Z= 0.268 Chirality : 0.042 0.257 1177 Planarity : 0.003 0.045 1258 Dihedral : 6.031 62.330 1065 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.24 % Allowed : 17.79 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.69 (0.29), residues: 904 helix: 1.28 (0.25), residues: 434 sheet: -0.16 (0.43), residues: 154 loop : -0.24 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 314 HIS 0.003 0.001 HIS X 60 PHE 0.010 0.001 PHE X 80 TYR 0.013 0.001 TYR X 131 ARG 0.010 0.001 ARG X 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7138 (t80) REVERT: C 181 GLN cc_start: 0.7060 (tt0) cc_final: 0.6549 (tm-30) REVERT: C 260 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7336 (ptt90) REVERT: D 259 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7095 (pmm-80) REVERT: X 26 GLU cc_start: 0.7582 (tt0) cc_final: 0.6937 (tp30) outliers start: 18 outliers final: 12 residues processed: 153 average time/residue: 1.2856 time to fit residues: 207.7662 Evaluate side-chains 150 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 40 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN C 133 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7443 Z= 0.182 Angle : 0.574 9.401 10057 Z= 0.273 Chirality : 0.041 0.267 1177 Planarity : 0.003 0.045 1258 Dihedral : 6.022 60.436 1065 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.11 % Allowed : 18.03 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.72 (0.29), residues: 904 helix: 1.29 (0.25), residues: 434 sheet: -0.08 (0.42), residues: 161 loop : -0.24 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 314 HIS 0.004 0.001 HIS C 276 PHE 0.010 0.001 PHE X 80 TYR 0.014 0.001 TYR X 131 ARG 0.010 0.001 ARG X 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 MET cc_start: 0.7244 (ptt) cc_final: 0.6903 (ptt) REVERT: C 103 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7170 (t80) REVERT: C 181 GLN cc_start: 0.7034 (tt0) cc_final: 0.6522 (tm-30) REVERT: C 205 LEU cc_start: 0.7767 (mt) cc_final: 0.7564 (mp) REVERT: C 260 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7294 (ptt90) REVERT: D 259 ARG cc_start: 0.7396 (pmm-80) cc_final: 0.7070 (pmm-80) REVERT: D 290 ARG cc_start: 0.7395 (mtp85) cc_final: 0.7112 (mtp85) REVERT: X 26 GLU cc_start: 0.7583 (tt0) cc_final: 0.6941 (tp30) outliers start: 17 outliers final: 13 residues processed: 149 average time/residue: 1.1926 time to fit residues: 187.8092 Evaluate side-chains 150 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7443 Z= 0.206 Angle : 0.582 10.270 10057 Z= 0.280 Chirality : 0.041 0.207 1177 Planarity : 0.004 0.047 1258 Dihedral : 6.027 60.540 1065 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.61 % Allowed : 18.28 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.67 (0.28), residues: 904 helix: 1.27 (0.25), residues: 434 sheet: -0.09 (0.42), residues: 161 loop : -0.29 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 314 HIS 0.003 0.001 HIS X 40 PHE 0.011 0.001 PHE X 80 TYR 0.016 0.001 TYR X 131 ARG 0.011 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7219 (t80) REVERT: C 144 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8114 (mp) REVERT: C 181 GLN cc_start: 0.7020 (tt0) cc_final: 0.6518 (tm-30) REVERT: C 260 ARG cc_start: 0.7516 (mtm110) cc_final: 0.7297 (ptt90) REVERT: D 259 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7059 (pmm-80) REVERT: D 290 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7111 (mtp85) REVERT: X 26 GLU cc_start: 0.7630 (tt0) cc_final: 0.7018 (tp30) REVERT: X 185 ASN cc_start: 0.8291 (m110) cc_final: 0.8080 (m110) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 1.1864 time to fit residues: 193.0166 Evaluate side-chains 153 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.0570 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 0.0040 chunk 52 optimal weight: 0.5980 overall best weight: 0.5110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7443 Z= 0.178 Angle : 0.579 8.409 10057 Z= 0.277 Chirality : 0.041 0.198 1177 Planarity : 0.004 0.049 1258 Dihedral : 5.930 62.622 1065 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.99 % Allowed : 18.16 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.73 (0.29), residues: 904 helix: 1.31 (0.25), residues: 434 sheet: -0.09 (0.42), residues: 161 loop : -0.24 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 314 HIS 0.003 0.001 HIS X 40 PHE 0.010 0.001 PHE X 80 TYR 0.017 0.001 TYR X 131 ARG 0.011 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7169 (t80) REVERT: C 181 GLN cc_start: 0.7035 (tt0) cc_final: 0.6506 (tm-30) REVERT: D 259 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7064 (pmm-80) REVERT: D 290 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7072 (mtp85) REVERT: X 26 GLU cc_start: 0.7625 (tt0) cc_final: 0.6994 (tp30) REVERT: X 185 ASN cc_start: 0.8282 (m110) cc_final: 0.8063 (m110) outliers start: 24 outliers final: 17 residues processed: 153 average time/residue: 1.1874 time to fit residues: 191.9048 Evaluate side-chains 152 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7443 Z= 0.211 Angle : 0.600 10.330 10057 Z= 0.289 Chirality : 0.042 0.272 1177 Planarity : 0.004 0.055 1258 Dihedral : 5.986 64.691 1065 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.36 % Allowed : 18.91 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.70 (0.29), residues: 904 helix: 1.30 (0.26), residues: 434 sheet: -0.12 (0.42), residues: 161 loop : -0.27 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 314 HIS 0.003 0.001 HIS B 50 PHE 0.009 0.001 PHE X 80 TYR 0.020 0.001 TYR X 131 ARG 0.013 0.001 ARG B 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7221 (t80) REVERT: C 181 GLN cc_start: 0.7028 (tt0) cc_final: 0.6501 (tm-30) REVERT: C 260 ARG cc_start: 0.7545 (mtm110) cc_final: 0.7337 (ptt90) REVERT: D 259 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7083 (pmm-80) REVERT: X 26 GLU cc_start: 0.7647 (tt0) cc_final: 0.7025 (tp30) REVERT: X 185 ASN cc_start: 0.8278 (m110) cc_final: 0.8073 (m110) outliers start: 19 outliers final: 15 residues processed: 143 average time/residue: 1.1549 time to fit residues: 174.9389 Evaluate side-chains 153 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.0010 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.133503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.121873 restraints weight = 11798.580| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.12 r_work: 0.3921 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7443 Z= 0.175 Angle : 0.612 10.925 10057 Z= 0.293 Chirality : 0.041 0.178 1177 Planarity : 0.004 0.053 1258 Dihedral : 5.856 66.995 1065 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.24 % Allowed : 19.40 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.74 (0.29), residues: 904 helix: 1.34 (0.26), residues: 434 sheet: -0.08 (0.43), residues: 160 loop : -0.28 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 314 HIS 0.003 0.001 HIS B 22 PHE 0.012 0.001 PHE X 80 TYR 0.019 0.001 TYR X 131 ARG 0.013 0.001 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3588.68 seconds wall clock time: 64 minutes 34.85 seconds (3874.85 seconds total)