Starting phenix.real_space_refine on Sun Dec 10 13:50:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/12_2023/8ouy_17205_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/12_2023/8ouy_17205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/12_2023/8ouy_17205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/12_2023/8ouy_17205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/12_2023/8ouy_17205_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/12_2023/8ouy_17205_trim_updated.pdb" } resolution = 3.4 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= 0.002 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 50 5.16 5 C 4608 2.51 5 N 1268 2.21 5 O 1378 1.98 5 H 7380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14695 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1131 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "B" Number of atoms: 4977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4977 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4722 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 7, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3773 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.97, per 1000 atoms: 0.47 Number of scatterers: 14695 At special positions: 0 Unit cell: (98.28, 104.76, 95.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 3 11.99 O 1378 8.00 N 1268 7.00 C 4608 6.00 H 7380 1.00 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: 11.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 4 sheets defined 43.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.969A pdb=" N HIS A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.866A pdb=" N ALA A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.992A pdb=" N LYS B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 65 removed outlier: 3.627A pdb=" N ARG B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.825A pdb=" N ILE B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 removed outlier: 4.289A pdb=" N LEU B 196 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 3.754A pdb=" N HIS B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 232 Proline residue: B 227 - end of helix removed outlier: 3.763A pdb=" N SER B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 264 through 275 removed outlier: 5.281A pdb=" N MET B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.683A pdb=" N GLY B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 22 removed outlier: 4.297A pdb=" N LEU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 68 through 78 removed outlier: 3.602A pdb=" N GLU C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 157 through 166 removed outlier: 3.681A pdb=" N ARG C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 191 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 222 through 241 removed outlier: 3.591A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'D' and resid 24 through 27 No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 89 through 99 removed outlier: 3.611A pdb=" N ILE D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 removed outlier: 4.384A pdb=" N TYR D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 137 removed outlier: 3.639A pdb=" N GLU D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.570A pdb=" N VAL D 160 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 169 No H-bonds generated for 'chain 'D' and resid 166 through 169' Processing helix chain 'D' and resid 171 through 186 removed outlier: 3.590A pdb=" N LYS D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 232 No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing sheet with id= A, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.820A pdb=" N CYS B 335 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 337 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 316 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG B 312 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 280 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE B 123 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 282 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N GLY B 125 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU B 154 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL B 239 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 156 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL B 241 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 158 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 340 through 342 Processing sheet with id= C, first strand: chain 'C' and resid 307 through 309 removed outlier: 6.138A pdb=" N ARG C 275 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 274 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 245 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE C 105 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 247 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 203 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 248 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 133 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP C 206 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 135 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 276 through 279 removed outlier: 3.592A pdb=" N SER D 257 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS D 237 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU D 191 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE D 46 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA D 193 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU D 146 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR D 194 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 148 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU D 79 " --> pdb=" O ILE D 147 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 741 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: 5.14 Time building geometry restraints manager: 11.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7352 1.03 - 1.23: 34 1.23 - 1.42: 2983 1.42 - 1.62: 4367 1.62 - 1.81: 72 Bond restraints: 14808 Sorted by residual: bond pdb=" N GLY C 2 " pdb=" CA GLY C 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.40e+00 bond pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.08e+00 bond pdb=" N LYS A 4 " pdb=" CA LYS A 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N GLY D 20 " pdb=" H GLY D 20 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N GLY C 2 " pdb=" H GLY C 2 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 ... (remaining 14803 not shown) Histogram of bond angle deviations from ideal: 65.08 - 80.05: 1 80.05 - 95.01: 0 95.01 - 109.97: 13088 109.97 - 124.93: 13157 124.93 - 139.89: 535 Bond angle restraints: 26781 Sorted by residual: angle pdb=" C MET B 10 " pdb=" N GLN B 11 " pdb=" H GLN B 11 " ideal model delta sigma weight residual 123.68 65.08 58.60 3.00e+00 1.11e-01 3.82e+02 angle pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" O4' ATP C 401 " ideal model delta sigma weight residual 105.22 101.39 3.83 1.30e+00 5.94e-01 8.72e+00 angle pdb=" C2' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O3' ATP C 401 " ideal model delta sigma weight residual 111.83 105.17 6.66 2.67e+00 1.40e-01 6.23e+00 angle pdb=" C3' ATP C 401 " pdb=" C2' ATP C 401 " pdb=" O2' ATP C 401 " ideal model delta sigma weight residual 111.83 105.41 6.42 2.67e+00 1.40e-01 5.78e+00 angle pdb=" C1' ATP D 302 " pdb=" C2' ATP D 302 " pdb=" O2' ATP D 302 " ideal model delta sigma weight residual 110.58 103.86 6.72 2.79e+00 1.28e-01 5.78e+00 ... (remaining 26776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 6474 31.12 - 62.23: 220 62.23 - 93.35: 33 93.35 - 124.46: 1 124.46 - 155.58: 2 Dihedral angle restraints: 6730 sinusoidal: 3694 harmonic: 3036 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 95.58 -155.58 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 88.76 -148.76 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.52 116.52 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 6727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1057 0.060 - 0.120: 102 0.120 - 0.179: 12 0.179 - 0.239: 1 0.239 - 0.299: 5 Chirality restraints: 1177 Sorted by residual: chirality pdb=" C2' ATP D 302 " pdb=" C1' ATP D 302 " pdb=" C3' ATP D 302 " pdb=" O2' ATP D 302 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP C 401 " pdb=" C2' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" O3' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1174 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 10 " 0.092 2.00e-02 2.50e+03 2.32e-01 5.39e+02 pdb=" N GLN B 11 " -0.399 2.00e-02 2.50e+03 pdb=" CA GLN B 11 " 0.135 2.00e-02 2.50e+03 pdb=" H GLN B 11 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 247 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 37 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO D 38 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 38 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 38 " -0.016 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 356 2.13 - 2.75: 26758 2.75 - 3.37: 39814 3.37 - 3.98: 50290 3.98 - 4.60: 80071 Nonbonded interactions: 197289 Sorted by model distance: nonbonded pdb=" OE1 GLU D 164 " pdb=" H GLU D 164 " model vdw 1.513 1.850 nonbonded pdb=" HG1 THR C 209 " pdb=" OD1 ASN C 249 " model vdw 1.625 1.850 nonbonded pdb=" OD1 ASP C 279 " pdb=" H THR C 280 " model vdw 1.631 1.850 nonbonded pdb=" O LEU D 58 " pdb=" HG1 THR D 62 " model vdw 1.636 1.850 nonbonded pdb=" OE1 GLU D 28 " pdb=" H ASN D 30 " model vdw 1.636 1.850 ... (remaining 197284 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 4.170 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 48.320 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.002 0.040 7428 Z= 0.166 Angle : 0.523 6.715 10043 Z= 0.264 Chirality : 0.042 0.299 1177 Planarity : 0.003 0.031 1257 Dihedral : 17.648 155.580 2809 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.78 (0.28), residues: 907 helix: 0.06 (0.27), residues: 407 sheet: -1.02 (0.41), residues: 153 loop : -0.79 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.007 0.001 PHE B 199 TYR 0.010 0.001 TYR C 72 ARG 0.002 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4459 time to fit residues: 60.3106 Evaluate side-chains 100 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7428 Z= 0.260 Angle : 0.531 6.271 10043 Z= 0.276 Chirality : 0.039 0.139 1177 Planarity : 0.004 0.030 1257 Dihedral : 10.635 168.321 1069 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.25 % Allowed : 14.20 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.84 (0.28), residues: 907 helix: 0.15 (0.25), residues: 423 sheet: -1.29 (0.41), residues: 148 loop : -0.94 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.005 0.001 HIS D 47 PHE 0.012 0.001 PHE B 346 TYR 0.014 0.001 TYR C 72 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 105 average time/residue: 0.4206 time to fit residues: 60.6515 Evaluate side-chains 103 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1755 time to fit residues: 4.0626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7428 Z= 0.316 Angle : 0.559 6.089 10043 Z= 0.290 Chirality : 0.040 0.142 1177 Planarity : 0.004 0.033 1257 Dihedral : 9.703 131.744 1069 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.25 % Allowed : 15.07 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.03 (0.28), residues: 907 helix: 0.01 (0.25), residues: 425 sheet: -1.44 (0.41), residues: 137 loop : -1.05 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 317 HIS 0.006 0.001 HIS D 60 PHE 0.013 0.002 PHE B 346 TYR 0.017 0.002 TYR C 72 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 109 average time/residue: 0.4035 time to fit residues: 60.4390 Evaluate side-chains 102 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1761 time to fit residues: 2.3616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7428 Z= 0.201 Angle : 0.497 6.082 10043 Z= 0.255 Chirality : 0.038 0.139 1177 Planarity : 0.003 0.032 1257 Dihedral : 9.045 115.765 1069 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.00 % Allowed : 15.94 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.64 (0.28), residues: 907 helix: 0.43 (0.26), residues: 411 sheet: -1.39 (0.41), residues: 137 loop : -0.88 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 317 HIS 0.004 0.001 HIS D 47 PHE 0.010 0.001 PHE B 346 TYR 0.013 0.001 TYR C 72 ARG 0.002 0.000 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 110 average time/residue: 0.3969 time to fit residues: 60.5493 Evaluate side-chains 105 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1622 time to fit residues: 2.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7428 Z= 0.285 Angle : 0.536 6.538 10043 Z= 0.277 Chirality : 0.039 0.144 1177 Planarity : 0.004 0.034 1257 Dihedral : 9.172 101.857 1069 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.75 % Allowed : 16.31 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.94 (0.28), residues: 907 helix: 0.30 (0.26), residues: 404 sheet: -1.69 (0.40), residues: 139 loop : -1.10 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.005 0.001 HIS D 60 PHE 0.012 0.001 PHE B 346 TYR 0.016 0.001 TYR C 72 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.078 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.4001 time to fit residues: 61.7567 Evaluate side-chains 104 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1682 time to fit residues: 2.4877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7428 Z= 0.155 Angle : 0.474 6.116 10043 Z= 0.240 Chirality : 0.037 0.137 1177 Planarity : 0.003 0.033 1257 Dihedral : 8.465 78.331 1069 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.87 % Allowed : 16.19 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.62 (0.28), residues: 907 helix: 0.68 (0.27), residues: 409 sheet: -1.69 (0.39), residues: 149 loop : -1.00 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.003 0.001 HIS B 307 PHE 0.009 0.001 PHE B 346 TYR 0.010 0.001 TYR C 72 ARG 0.002 0.000 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 110 average time/residue: 0.4143 time to fit residues: 63.9986 Evaluate side-chains 104 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1777 time to fit residues: 2.5506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7428 Z= 0.312 Angle : 0.549 6.711 10043 Z= 0.284 Chirality : 0.040 0.145 1177 Planarity : 0.004 0.033 1257 Dihedral : 8.796 87.645 1069 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.75 % Allowed : 17.19 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.03 (0.28), residues: 907 helix: 0.36 (0.26), residues: 404 sheet: -1.97 (0.38), residues: 151 loop : -1.17 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 268 HIS 0.005 0.001 HIS D 60 PHE 0.012 0.002 PHE B 346 TYR 0.017 0.002 TYR C 72 ARG 0.002 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.180 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 0.4014 time to fit residues: 58.6218 Evaluate side-chains 102 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.258 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2106 time to fit residues: 2.9696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7428 Z= 0.170 Angle : 0.479 6.088 10043 Z= 0.245 Chirality : 0.038 0.139 1177 Planarity : 0.003 0.033 1257 Dihedral : 8.135 75.261 1069 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.75 % Allowed : 17.43 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 907 helix: 0.75 (0.27), residues: 398 sheet: -1.62 (0.41), residues: 139 loop : -1.05 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 317 HIS 0.004 0.001 HIS B 250 PHE 0.009 0.001 PHE B 346 TYR 0.011 0.001 TYR C 72 ARG 0.002 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.281 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.4871 time to fit residues: 71.2329 Evaluate side-chains 101 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.382 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2384 time to fit residues: 3.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 0.0060 chunk 86 optimal weight: 0.0000 chunk 52 optimal weight: 0.5980 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7428 Z= 0.135 Angle : 0.465 5.958 10043 Z= 0.234 Chirality : 0.037 0.135 1177 Planarity : 0.003 0.033 1257 Dihedral : 7.750 69.641 1069 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.50 % Allowed : 17.06 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.41 (0.29), residues: 907 helix: 0.92 (0.27), residues: 406 sheet: -1.75 (0.38), residues: 157 loop : -0.85 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS B 250 PHE 0.009 0.001 PHE B 346 TYR 0.008 0.001 TYR C 72 ARG 0.002 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.231 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 105 average time/residue: 0.3948 time to fit residues: 57.7961 Evaluate side-chains 103 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.127 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1771 time to fit residues: 2.3668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 0.0470 chunk 72 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7428 Z= 0.125 Angle : 0.455 5.853 10043 Z= 0.229 Chirality : 0.037 0.135 1177 Planarity : 0.003 0.034 1257 Dihedral : 7.550 65.729 1069 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.25 % Allowed : 17.06 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.18 (0.29), residues: 907 helix: 1.03 (0.27), residues: 410 sheet: -1.50 (0.39), residues: 154 loop : -0.73 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 317 HIS 0.004 0.001 HIS B 250 PHE 0.009 0.001 PHE B 346 TYR 0.007 0.001 TYR C 72 ARG 0.001 0.000 ARG C 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.4246 time to fit residues: 59.6801 Evaluate side-chains 100 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.240 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2162 time to fit residues: 1.7655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115153 restraints weight = 29312.825| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.90 r_work: 0.3246 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7428 Z= 0.176 Angle : 0.476 5.998 10043 Z= 0.241 Chirality : 0.038 0.137 1177 Planarity : 0.004 0.061 1257 Dihedral : 7.819 75.311 1069 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.25 % Allowed : 17.43 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.32 (0.29), residues: 907 helix: 0.97 (0.27), residues: 408 sheet: -1.62 (0.39), residues: 156 loop : -0.84 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 317 HIS 0.005 0.001 HIS B 250 PHE 0.007 0.001 PHE D 80 TYR 0.010 0.001 TYR C 72 ARG 0.011 0.000 ARG D 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3559.78 seconds wall clock time: 63 minutes 43.50 seconds (3823.50 seconds total)