Starting phenix.real_space_refine on Thu Nov 16 07:19:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2023/8ouy_17205_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_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_17205/11_2023/8ouy_17205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2023/8ouy_17205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_2023/8ouy_17205_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/11_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 6.71, per 1000 atoms: 0.46 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: 12.57 Conformation dependent library (CDL) restraints added in 1.8 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: 2.43 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: 5.34 Time building geometry restraints manager: 12.93 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: 5660 31.12 - 62.23: 179 62.23 - 93.35: 27 93.35 - 124.46: 1 124.46 - 155.58: 2 Dihedral angle restraints: 5869 sinusoidal: 2833 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 5866 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: 0.830 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: 0.230 Extract box with map and model: 4.240 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 53.020 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.030 ------------------------------------------------------------------------------- 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 : 16.927 155.580 2747 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 *********************** 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 : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4461 time to fit residues: 60.3882 Evaluate side-chains 100 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5898 ------------------------------------------------------------------------------- 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: 0.0470 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: 0.7980 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7428 Z= 0.211 Angle : 0.509 6.338 10043 Z= 0.262 Chirality : 0.038 0.137 1177 Planarity : 0.003 0.027 1257 Dihedral : 8.128 167.009 1007 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.87 % Allowed : 14.20 % Favored : 84.93 % 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: -0.65 (0.28), residues: 907 helix: 0.29 (0.26), residues: 423 sheet: -1.12 (0.42), residues: 146 loop : -0.85 (0.34), residues: 338 *********************** 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 106 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 104 average time/residue: 0.4455 time to fit residues: 62.1171 Evaluate side-chains 102 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1826 time to fit residues: 2.8590 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 0.7980 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: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7746 moved from start: 0.1146 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= 0.274 Angle : 0.540 6.017 10043 Z= 0.277 Chirality : 0.039 0.141 1177 Planarity : 0.004 0.028 1257 Dihedral : 6.792 127.918 1007 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.25 % Allowed : 14.94 % Favored : 83.81 % 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: -0.75 (0.28), residues: 907 helix: 0.21 (0.26), residues: 419 sheet: -1.29 (0.42), residues: 137 loop : -0.86 (0.33), residues: 351 *********************** 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 107 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.353 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 107 average time/residue: 0.3951 time to fit residues: 58.4719 Evaluate side-chains 100 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1679 time to fit residues: 2.9034 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1277 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= 0.185 Angle : 0.485 6.078 10043 Z= 0.246 Chirality : 0.038 0.138 1177 Planarity : 0.003 0.028 1257 Dihedral : 6.098 110.273 1007 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.75 % Allowed : 15.69 % Favored : 83.56 % 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: -0.54 (0.28), residues: 907 helix: 0.49 (0.26), residues: 417 sheet: -1.37 (0.41), residues: 139 loop : -0.80 (0.33), residues: 351 *********************** 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 112 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.3975 time to fit residues: 61.5548 Evaluate side-chains 102 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1620 time to fit residues: 2.3841 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 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: 3.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.8604 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.1409 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= 0.186 Angle : 0.481 6.159 10043 Z= 0.243 Chirality : 0.038 0.138 1177 Planarity : 0.003 0.027 1257 Dihedral : 5.802 91.941 1007 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.62 % Allowed : 16.06 % Favored : 83.31 % 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: -0.48 (0.28), residues: 907 helix: 0.67 (0.27), residues: 409 sheet: -1.58 (0.39), residues: 151 loop : -0.76 (0.34), residues: 347 *********************** 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 108 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 107 average time/residue: 0.3987 time to fit residues: 59.1568 Evaluate side-chains 102 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1605 time to fit residues: 2.3802 ------------------------------------------------------------------------------- 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: 0.9980 chunk 88 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7428 Z= 0.204 Angle : 0.492 6.327 10043 Z= 0.248 Chirality : 0.038 0.140 1177 Planarity : 0.003 0.027 1257 Dihedral : 5.652 71.305 1007 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.62 % Allowed : 16.06 % Favored : 83.31 % 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: -0.60 (0.28), residues: 907 helix: 0.62 (0.27), residues: 411 sheet: -1.69 (0.39), residues: 151 loop : -0.88 (0.33), residues: 345 *********************** 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 103 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 102 average time/residue: 0.4233 time to fit residues: 59.4077 Evaluate side-chains 100 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1673 time to fit residues: 2.8902 ------------------------------------------------------------------------------- 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: 2.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7428 Z= 0.244 Angle : 0.508 6.335 10043 Z= 0.259 Chirality : 0.039 0.142 1177 Planarity : 0.003 0.027 1257 Dihedral : 5.295 78.709 1007 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.75 % Allowed : 16.06 % Favored : 83.19 % 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: -0.72 (0.28), residues: 907 helix: 0.55 (0.27), residues: 409 sheet: -1.79 (0.39), residues: 150 loop : -0.95 (0.33), residues: 348 *********************** 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 106 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.292 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 106 average time/residue: 0.4298 time to fit residues: 62.6098 Evaluate side-chains 99 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1762 time to fit residues: 2.0195 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1630 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= 0.180 Angle : 0.476 6.168 10043 Z= 0.241 Chirality : 0.038 0.139 1177 Planarity : 0.003 0.027 1257 Dihedral : 5.028 72.902 1007 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.75 % Allowed : 16.44 % Favored : 82.81 % 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: -0.44 (0.28), residues: 907 helix: 0.76 (0.27), residues: 402 sheet: -1.50 (0.41), residues: 138 loop : -0.87 (0.33), residues: 367 *********************** 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 107 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.261 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.3891 time to fit residues: 57.9720 Evaluate side-chains 102 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1543 time to fit residues: 2.5193 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.0050 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1698 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= 0.161 Angle : 0.473 6.049 10043 Z= 0.237 Chirality : 0.037 0.137 1177 Planarity : 0.003 0.028 1257 Dihedral : 4.840 67.683 1007 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.62 % Allowed : 16.44 % 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: -0.36 (0.29), residues: 907 helix: 0.90 (0.27), residues: 401 sheet: -1.67 (0.39), residues: 150 loop : -0.77 (0.33), residues: 356 *********************** 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 107 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.335 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 106 average time/residue: 0.4229 time to fit residues: 61.4952 Evaluate side-chains 102 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2286 time to fit residues: 1.9908 ------------------------------------------------------------------------------- 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: 0.7980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7708 moved from start: 0.1745 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= 0.143 Angle : 0.466 5.952 10043 Z= 0.233 Chirality : 0.037 0.136 1177 Planarity : 0.003 0.027 1257 Dihedral : 4.671 63.773 1007 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 16.56 % Favored : 83.44 % 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: -0.23 (0.29), residues: 907 helix: 1.01 (0.27), residues: 402 sheet: -1.57 (0.40), residues: 150 loop : -0.72 (0.34), residues: 355 ********************** 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 101 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4111 time to fit residues: 57.7688 Evaluate side-chains 100 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5092 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113342 restraints weight = 29070.492| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.87 r_work: 0.3236 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7428 Z= 0.224 Angle : 0.502 6.183 10043 Z= 0.255 Chirality : 0.038 0.140 1177 Planarity : 0.003 0.027 1257 Dihedral : 4.981 64.402 1007 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.12 % Allowed : 16.81 % 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: -0.47 (0.28), residues: 907 helix: 0.83 (0.27), residues: 399 sheet: -1.72 (0.39), residues: 150 loop : -0.87 (0.33), residues: 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3582.92 seconds wall clock time: 64 minutes 5.97 seconds (3845.97 seconds total)